CCG CCG SVL Exchange

SVL Exchange is a collection of recipes, algorithms and program samples created by users and developers of MOE™. Search below for specialized applications, utilities, SVL examples or MOE customizations. All users are encouraged to make submissions.
Download Instructions
How to Submit

To download an item:

  1. Click on a link below to download the package of interest.
  2. Open the downloaded .svlx file in MOE (through browser download dialog or drag-and-drop on MOE 3D window).
  3. A folder will be unpacked on the Desktop, that contains the item you requested.

Note:

To submit a new item, email to svlexch@chemcomp.com.

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SVL syntax highlighting for KDE texteditors
Date 2019-03-11
Author Richard Bartelt
Category SVL Utilities
Downloads 18
Details
This script enables SVL highlighting in a katepart texteditor such as KWrite/Kate/KDevelop (part of KDE).
SVL files are recognized using their file extension .svl.

Kate is available in your repos (Linux) or here: https://kate-editor.org/ (Linux, Windows, Mac).


Installation (version numbers might need to be adapted to your KDE/katepart version):

Linux:
Copy the extracted xml file to

/usr/share/kde4/apps/katepart/syntax (all users installation; needs root privileges)

or

$HOME/.kde4/share/apps/katepart/syntax (single user installation)


Windows:
$HOME\AppData\Local\katepart5\syntax (single user installation)


*** Update ***
function list: MOE2019.01
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Workflow showing the usage of the MedChemTransformer and Scaffold Replacement Node
Date 2019-03-06
Author Guido Kirsten
Category KNIME
Downloads 81
Details
Workflow for Exercise 2 "Fragment Based Design" as described in the documentation of the MOE Extensions for KNIME version 2.4.0
See documentation for further details.
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A collection of QuaSAR descriptors calculated on amino acid sequence.
Date 2019-02-21
Author Richard Bartelt
Category Molecular Descriptors and QSAR
Downloads 2
Details
These proteins descriptors are calculated on sequence only. I.e. there is no need for atomic data.

INSTRUCTIONS:
- copy this file to $HOME/moefiles/svl/
($HOME is your home folder)
- restart MOE
- the new descriptors will be available from:
DBV | Compute | Descriptors | Calculate...

List of descriptors:
seq_nChains: Number of chains, regardless of type.
seq_nChainsAA: Number of chains that contain at least one amino acid residue. (protein or peptidic ligand)
seq_nRes: Total number of residues.
seq_nResAA: Total number of amino acid residues.
seq_n***: Overall number of amino acid residues of type ***. *** = amino acid 3-letter code.
seq_MW: Sequence based protein mass in kilodalton. I.e. sum of internal amino acids masses + free termini. The masses correspond to the mass of the most abundant protomeric and isomeric species at pH = 7.0. I.e. Glu,Asp are deprotonated, Lys,Arg are protonated, His and all other amino acids are neutral. One pair of free termini is added per amino acid chain.
seq_n+: Number of positively charged amino acids. I.e. seq_n+ = seq_nLys + seq_nArg
seq_n-: Number of negatively charged amino acids. I.e. seq_n- = seq_nAsp + seq_nGlu
seq_PI: Sequence based isoelectric point as calculated in MOE release code ($MOE/svl/biopolymer/proprop.svl).
seq_aliphIdx: Aliphatic index. Ref: A. Ikai (1980) J Biochem 88: 1895-8
seq_GRAVY: Grand Average of Hydrophathy score. Ref: J. Kyte, R.F. Doolittle (1982) J Mol Biol 157: 105-32
seq_polariz: Sum of residue polarizabilities based on M. Swart (2004) J Comp Meth Sci Eng 4: 419-25. Please note that polarizabity varies with conformation!
seq_InstabIdx: Instability Index. Ref: K. Guruprasad, B.V.B. Reddy, M.W. Pandit (1990) Prot Eng 4: 155-61
seq_PI_Bellqvist: Sequence based isoelectric point as published by B. Bjellqvist et al. (1993) Electrophoresis 14: 1023-31
seq_ExtCoeff_280: Extinction Coefficient at 280 nm assuming that half of the cysteins form cystines.
seq_Absorb_280: Absorbance at 280 nm (0.1%).
Computes the PBSA solvation energy
Date 2019-02-19
Author Chris Williams
Category Basic Molecular Tools
Downloads 7
Details
--------------------------------------------------------------------
Description:
--------------------------------------------------------------------
Code to compute the PBSA estimate of the solvation free energy
of selected atoms in the MOE window (or on a database of molecules)

--------------------------------------------------------------------
Usage:
--------------------------------------------------------------------
MOE:
(1) Load the structure of interest
(2) Run this code. A GUI will appear.
(3) Set the 'Source:' option to MOE (atoms in the MOE window)
(4) Use the option pull-down to specify the atoms whose solvation
energy you wish to measure
(5) Press 'Compute'. The PBSA solvation energy will be written the
text field in the panel. e.g,

PB Solvation Energy: -8.00656 (kcal/mol)

MDB:
(1) Run this code. A GUI will appear
(2) Set the 'Source:' to MDB
(3) Use the 'VBrowse..' button to select the database
(3) Press 'Compute'. The panel will disappear and the PBSA solvation
energy will be computed for all entries in the database and
written to the field 'PBSA_sol'


TITRATE (i.e.., loop over salts and conditions)
(1) Load this function
(2) Enter

svl>PBSA_Solvation_Energy_MDB_titrate opts

at the SVL command line. Here opts is a tagged vector of options:

opts= [
dbfile: 'database filename',
mfield:'molecule field'
(defaults to first mol field in database)
salts: vector of salt tokens
(default: SALTS_TO_USE = ['NaCl','KCl','MgCl2'];
concs: vector of concentrations
(default: [0.1, 0.05, 0.01];)
temps: vector of temps
(default: 300)
]
(3) The code will loop over all combinations of salts, conc.
and temperature and output the PBSA solvation energies to
the database. The conditions are recorded in the database field
names
--------------------------------------------------------------------

Read and Write Excel xlsx file into MOE databases.
Date 2019-02-12
Author Guido Kirsten
Category Informatics and File I/O
Downloads 2
Details
The Excel interface is based on the Apache POI library which has to be downloaded and installed separately. We also recommend having Oracle Java installed.

Installation:
1) Download the Apache POI Library from https://poi.apache.org
2) Extract the downloaded archive file to your hard drive.
3) Add the poi library to your CLASSPATH environment variable.
for example if you extracted the library in c:/javalibs/poi-4.0.1
you would have to add:
C:/javalibs/poi-4.0.1/*;c:/javalibs/poi-4.0.1/ooxml-lib/*;c:/javalibs/poi-4.0.1/lib/*
to CLASSPATH.

4) Extract the archive file you downloaded from the SVL Exchange website.

5) Copy io_excel.svl into $MOE/custom/svl or $HOME/moefiles/svl

6) Copy SVL_Excel.class into $MOE/java

7) In MOE|File|Open you should get the option to Import the XLS file when selecting an excel file.

8) To export an excel file use:
db_ExportXLS[
'$MOE/sample/mol/gmp_inhibitors.mdb',
'$HOME/gmp_inhibitors.xlsx',
'Sheetname',
0,
0
];
where the first number after the sheetname is a flag indicating that only selected entries should be exported.
The second number is for selected fields only.
A command line tool to generate small molecule conformations from one or MOE SD files.
Date 2019-02-05
Author Andrew Henry
Category Simulations
Downloads 1
Details
sdconf and sdconf.bat are tools that can generate small molecule conformations from the operating system command line. They can be combined with other SD files, as explained in the document "SD Pipelining Tools - How to Create a Fragment Database" that can be accessed from (MOE | Help | Tutorials)
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A panel that creates difference, intersection and union maps from a a set of aligned protein pockets. Used maps to highlight differeneces between pockets of similar proteins.
Date 2019-01-30
Author Chris Williams
Category Graphics and Rendering
Downloads 82
Details
Download and unpack the zip file. This contains the SVL script, a PDF document and example files.

(1) Select the protein_pocket_volumes.svl file from a MOE| File | Open panel.

(2) A GUI will appear.

(3) Use the 'Pocket Set A' and 'Pocket Set B' options to select the 'A set' and the 'B set' for the operation. The pocket will be defined around the ligand atoms. To compare proteins with no ligands, first use the Site Finder to create dummy atoms in the binding site. These will then be used to identify the pockets.

(4) Press Create. The pocket volume comparison will proceed and a new graphics object rendering the volume difference will be create and listed in the panel. The volume enclosed by each surface is shown in name of the graphic object.
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Interface to the compound collection API from molport.com
Date 2018-12-19
Author Guido Kirsten
Category Utilities
Downloads 10
Details
To install extract the zip file into your MOE installation folder. After restarting MOE you will find a new entry in the configuration (gear wheel) menu (MolPort). Enter the username and password you got from MolPort there. Click OK. Now you can enter a MolPort ID in the text widget of the builder (e.g. MolPort-000-219-650) to get the structure or use the Interface MOE|Extra|MolPort to search or import structures from MolPort. Databases for imported structures contain links to the MolPort website which can be opened from the database browser by clicking (Open in Browser).
If you have questions, please let us know.
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Expert system for QSAR study.
You can directly get good QSAR model either from sd or mdb file with only molecule and activity data by single click.
Date 2018-12-17
Author junichi goto
Category Molecular Descriptors and QSAR
Downloads 543
Details
To get good QSAR model in MOE, you have to run several commands under the 'Compute' pull-down menu of database viewer, such as Partial Charge, Descriptors, QuaSAR-Contingency, QuaSAR-Model and so on. After you get one model, you have to delete less important descriptors step by step to get better model.

AutoQuaSAR was designed to make this process as easy as possible. By single click, you can get good QSAR model directly either from sd or mdb file with molecule and activity data only. AutoQuaSAR automatically makes working file, calculate descriptors and generate QSAR model by removing less important descriptors step by step to find out the model with best XR2 (XA1, in case of binary model).

Default setting works fine for most cases but AutoQuaSAR also provides lots of options to refine model.

Usage:
load autoqsar.svl
type AutoQSAR [] in the commad line
or just double click autoqsar.svl in 'Open' panel.
Click triangle in 'Oritginal File:' column and select mdb or sd file name in the list of files. If you want to use a file in other directory, select 'Others...' to open File Selection Panel.
For example, select $MOE/sample/mol/blood_brain.mdb for 'Original File' and click 'Fit'.
You will get the result just like this screenshot.

New in ver.2015.12.15
- general bugfixes

New Features in ver.2006.08.02
- Support QuaSAR-Evolution(ver.2006.06.12)
- Added structure display area
- keep all models to allow users to browse/select models

ver.2008.05.14
revised code with manual
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Grid based analysis of molecular potentials similar to Comfa or ComSia
Date 2018-11-12
Author Guido Kirsten
Category Molecular Descriptors and QSAR
Downloads 18
Details
Based on a given alignment of a set of small molecules with activities, a grid potential analysis is applied using the principles of CoMFA. Hereby, steric and electrostatic interaction energies of a positively charged carbon probe atom placed on grid points around the aligned molecules are determined and grid potentials are calculated. Then a partial least square model is created by fitting the activities to the grid point potential values. This process starts with a principal component analysis of the descriptors to reduce the number of components in the model to a value set by the user. The model coefficients for the principal components are then mapped back to the descriptors. These contributions can be visualized to identify areas with positive or negative contribution to the model spatially (pre-condition: numerically higher activity values mean higher biological activities).
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An implementation of the Torsion Analyzer published by Schaerfer et al.
Date 2018-11-07
Author Richard Bartelt
Category Basic Molecular Tools
Downloads 24
Details
In 2013 the group of Prof. Rarey (Uni Hamburg) in cooperation with the CADD group of Roche AG published the Torsion Analyzer.
This program accesses the quality (i.e. the strain) of individual bonds of the conformation of a molecule.
The bonds are colored in green/yellow/red based on their individual quality.


INSTALL INSTRUCTIONS:
In the following instructions:
- $HOME needs to be replaced with your home folder (e.g. C:\users\myaccount\)
- folders that do not already exist need to be created.

0) Make sure to use MOE 2018.0101 or newer. Check the Window Title of the MOE window.

1) Get a copy of the XML file which contains the relevant data from the website of the Rarey workgroup:
https://www.zbh.uni-hamburg.de/forschung/amd/datasets/torsion-analyzer-datasets.html
Rename the XML file to rochetor.xml and copy it to $HOME/moefiles/lib/

2) Extract the attached rochetor.zip and copy
rochetor.svl to $HOME/moefiles/svl/
rochetor.menu to $HOME/moefiles/menu/

3) Restart MOE. There will be a red button button "TorAnalyzer" in the RHS. This button will allow to toggle the Torsion Analyzer.


REFERENCES:
Torsion Angle Preferences in Druglike Chemical Space: A Comprehensive Guide
Schaerfer,C., Schulz-Gasch,T., Ehrlich,H.C., Guba,W., Rarey,M., Stahl,M.
J. Med. Chem. 56 (2013) 2016-2028 http://dx.doi.org/10.1021/jm3016816

Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules
for Assessing Conformations of Small Molecules.
Guba, W., Meyder, A., Rarey, M., and Hert, J.
J. Chem. Info. Model. (2015) DOI: acs.jcim.5b00522

The authors of the of the original Torsion Analyzer are not affiliated with the authors of this implementation! Please report all bugs to
support@chemcomp.com!

*** update ***
QuaSAR descriptor has been added - thanks to Okada Akitoshi!
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Benchmark Tests for MOE
Date 2018-10-22
Author Hooman Shadnia
Category Utilities
Downloads 5
Details
This script provides a few basic tests to measure the performance of hardware/software running MOE.

Extract the archive to $HOME/moefiles (for current user) or $MOE/custom (for all users).
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A collection of basic small molecule descriptors.
Date 2018-10-16
Author CCG Support Team
Category Molecular Descriptors and QSAR
Downloads 11
Details
DESCRIPTION:
This package contains more than 100 small molecule descriptors.
Most of these molecular descriptors are suitable for statistical modelling of molecular properties or activities (e.g. machine learning).

All descriptors use the descriptor plug-in system in MOE. The are divided 3 classes:
2D - conformation-independent
i3D - conformation-dependent
x3D - dependent on conformation and the structure currently in your MOE window

Note: each of the descriptor files contains a number of related descriptors. There are redundant descriptors in case they make sense in more than one file.



INSTALLATION:
1) unzip attached folder
2) Copy the desired descriptor file(s) to $HOME/moefiles/svl, where $HOME is your home directory
(e.g., Windows: C:\Users\walter\moefiles\svl\ or Unix: ~/moefiles/svl/)
3) Restart MOE to load the new file

Notes:
- The directory must be created if it does not already exist.
- $HOME can be determined at the SVL Commands windows. Type:
svl> HOME


USAGE:
The new descriptors are available from the Calculate Descriptors panel
(DBV | Compute | Descriptors | Calculate).
Use ECFP or FCFP FIngerprints in MOE
Date 2018-10-11
Author Markus Kossner (CCG Support)
Category Pharmacophores and Fingerprints
Downloads 333
Details
Rogers et al., (ECFP)
J. Chem. Inf. Model. 2010, 50, 742-154;

Differences to the Pipeline Pilot implementation may arise from:
- differences in treating charge-seperation of some moieties (Nitro etc.)
- hypervalent atom treatment (e.g. Sulphur and Phosphorous oxides)
- a different aromaticity perception

update 10-Oct-2018 (ma) E/FCFP now available as MOE descriptors

!!!
NOTE: This latest version (last change: 04-feb-2016 (ma))of the script generates fingerprints that are incompatible to earlier versions
!!!
Open and Save XYZ files
Date 2018-09-20
Author Richard Bartelt
Category Informatics and File I/O
Downloads 2
Details
This is a simple XYZ parser which uses the plug-in system of the MOE Open and Save panels.

Please note that there are multiple XYZ format descriptions. The one used here is:

5

C 0.0000 0.0000 0.0000
H 1.0900 0.0000 0.0000
H -0.3633 0.7267 0.7267
H -0.3633 -0.9926 0.2660
H -0.3633 0.2660 -0.9926

This is mostly an example of how to use the plug-in systems in MOE.

INSTALLATION:
- Copy the file to $HOME/moefiles/svl/ ($HOME is your home folder).
- Restart MOE.
- The XYZ file format should now be available in the Open and Save panel.
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Use MOE and Gaussian to calculate, visualize and fingerprint electrostatic potentials
Date 2018-09-12
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 12
Details
Starting with a database of small molecules:
1- Generate all Gaussian files needed to calculate electrostatic potentials (*.cube format)
2- Execute Gaussian via a single script automatically generated
3- Import all results to MOE
4- Visualize electrostatic potentials on molecular surface or as isosurfaces
5- Generate fingerprints for ESP grids
6- Search for similarity of ESPs

A PDF tutorial is included.

Extract the zip file to $HOME/moefiles and restart MOE.

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Bio-MOE: Custom MOE Biologics Applications
Date 2018-09-10
Author Maximilian Ebert
Category Basic Molecular Tools
Downloads 49
Details
The Bio-MOE package contains a series of custom SVL applications that are used for biologics modeling. These applications, accessible from the Sequence Editor and the Database Viewer menus, help automate regular homology and antibody modelling process, aid importing and exporting collections of sequences, as well as visualizing protein properties and coloring antibody motifs.

The attached file contains only the manual. To receive the full download instructions for this package please contact support@chemcomp.com.
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Example workflow showing the usage of the MOE docking nodes
Date 2018-09-03
Author Guido Kirsten
Category KNIME
Downloads 221
Details
Workflow for Exercise 8 "Small Molecule Docking" as described in the documentation of the MOE Extensions for KNIME version 2.4.0
See documentation for further details.
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Adds Text Highlighting to Sublime Text 3
Date 2018-08-17
Author Maximilian Ebert
Category SVL Utilities
Downloads 7
Details
Simply unzip the contents to your sublime folder Packages/User/. After restarting Sublime 3 you will have at the bottom right a new language from the drop-down list:

Scientific Vector Language

Sublime should also be able to autodetect SVL files by their extension .svl.
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FlexAlign a database of molecules to one molecule
Date 2018-08-07
Author Dimitri Bondarev
Category MOE/batch
Downloads 610
Details
Automatic flexible alignment for all molecules in a database against reference
molecules from the main MOE window. This function uses the FlexAlign []
function. If an output database filename is not supplied then it
will be based on the input filename. For instance if the input database
was in.mdb, the output database would be in_align_all.mdb.

If you set the molecule source to "MOE" then it runs as in the normal
Flexible Alignment panel in MOE.

USAGE

Save this file to your hard disk. For it to be available for use by all
of the users of MOE, create a directory called $MOE/lib/svl/custom/run
and save this file to that directory. eg on Windows and Linux,
this might be: c:\moe\lib\svl\custom\run\align_all.svl
/usr/local/moe/lib/svl/custom/run/align_all.svl

For the script to be available for use by a single user, then it
is best to create a directory in your home directory called svl,
and create a directory called run in that directory. Save this
file into that directory. eg on Windows and Linux, this might be:

c:\Documents and Settings\user_name\svl\run\align_all.svl
/usr/people/user_name/svl/run/align_all.svl

(a) From the MOE | File | Open panel, select this file
and click the "Run" button.

(b) Alternatively, at the SVL command line, type:
run 'align_all.svl'

The underlying SVL function is align_all. To use this, "load" this
file and at the SVL command prompt, type a command like:

svl> align_all []
svl> align_all ['in.mdb', 'out.mdb', options]
svl> align_all ['in.mdb', ', [heavy_rms:0.1, nfail:40]] //refinment only
svl> align_all ['in.mdb', 'out.mdb', [file:']]

- If you use MOE batch, then you have to pass the name of the input MDB file or
the script will fail. eg
moebatch -exec "run['align_all.svl', ['in.mdb',',[nfail:10]]]"

Align_all options are the following:

esel: 0, // use selected entries only
nsolns: 0, // no. of output solutions
mfield: ', // molecule field
dump: 1, // suppress CLI output if 0
fixed: 1, // fix template coordinates
write_template: 1 // 1: write only aligned pose to output (Pose)
// 2: write both in one field (Alignment)
// 3: write pose and template to diff fields (both)

To run the script with the "refine only" option, pass an option with file:'.
For other flexible alignment options see FLEX_DEFAULTS below.


*References*
An Alternative Method for the Alignment of Molecular
Structures: Maximizing Electrostatic and Steric Overlap
Tetrahedron Computer Methodology, Vol. 3, No. 6C, pp615-633, 1990

A New Approach to Probing Conformational Space with
Molecular Mechanics: Random Incremental Pulse Search
J. Am. Chem. Soc. 1989, 111, 4371-4378
D.M.Ferguson D.J.Raber
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Calculates CNS MPO from "Moving beyond Rules
Date 2018-07-26
Author Maximilian Ebert
Category Molecular Descriptors and QSAR
Downloads 21
Details
Calculates CNS MPO from "Moving beyond Rules:
The Development of a Central Nervous System Multiparameter Optimization
(CNS MPO) Approach To Enable Alignment of Druglike Properties;
Wager TT, Hou X, Verhoest PR, Villalobos A.
ACS Chem Neurosci. 2010 Jun 16; 1(6): 435-449"

1. Save this file in $HOME/moefiles/svl
2. Use DBV | Compute | Descriptors | Calculate
Imports the ZINC15 conformations into a MOE MDB
Date 2018-07-24
Author Maximilian Ebert
Category MOE Database Tools
Downloads 6
Details
The ZINC database is an excellent resource for structural information on small molecules. The script let's you import pre-calculated 3D conformations including relative energies from the DB2 format to a MOE Database. ZINC 2D structures can be downloaded as SDF file and imported using standard MOE tools (please contact support@chemcomp.com if you need further assistance).
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Workflow comparing the predictability of different QSAR methods
Date 2018-07-24
Author Guido Kirsten
Category KNIME
Downloads 22
Details
Workflow as built in Exercise 3 in the documentation of the MOE Extensions for KNIME.
See documentation for further details.
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Workflow calculating Interactions between Proteins
Date 2018-07-24
Author Guido Kirsten
Category KNIME
Downloads 19
Details
Workflow as built in Exercise 4 in the documentation of the MOE Extensions for KNIME.
See documentation for further details.
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A simple Polypharmacology workflow
Date 2018-07-13
Author Guido Kirsten
Category KNIME
Downloads 21
Details
Workflow as built in Exercise 7 in the documentation of the MOE Extensions for KNIME.
See documentation for further details.
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A tool that links ligands via the shortest pathway along the receptor van der Waals interaction surface. The linker poses are scored to help the design of new bivalent ligands.
Date 2018-06-04
Author Andrew Henry
Category Basic Molecular Tools
Downloads 19
Details
Bivalent ligands are increasingly important such as for targeting G protein-coupled receptor (GPCR) dimers or proteolysis targeting chimeras (PROTACs).

This script builds models for the linker between two ligands, bound in two binding sites.

There is more information in the Open Access paper:

Pérez-Benito, Laura, et al. "The Size Matters? A Computational Tool to Design Bivalent Ligands." Bioinformatics.
https://doi.org/10.1093/bioinformatics/bty422

Additional information is in the supplementary information for the pap
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Extract or merge molecular objects of molecule type fields and store them in a new field.
Date 2018-05-22
Author Yoshirou Kimura, MOLSIS Inc.
Category MOE Database Tools
Downloads 20
Details
Usage:
(1) Load this function
(2) At the SVL command line, enter

svl> db_moledit []

(3) Select target MDB file at the panel.

For more information, please see the bubblehelps.
This program may be useful if you want to extract ligand, receptor, or contacting solvent from molecule type field in MDB of molecular dynamics output.
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Search PSILO from MOE
Date 2018-03-23
Author Hooman Shadnia
Category SVL Utilities
Downloads 44
Details
Run PSILO searches from MOE

New in this version:
- Pocket Similarity Search
- Highlight hit atoms and meters for 3D interaction search
- Bugfixes

The following searches are currently implemented:
- Full Text Search
- Ligand Search (via SMILES /MOL)
- Small Molecule Name
- Protein Sequence Search
- Protein Name
- Title (PDB)
- Project Code
- PSILO Family
- Similar Pockets
- CIF Field
- 3D Search


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This node executes the SD2Frag shell script on a molecule stream.
Date 2018-03-14
Author Guido Kirsten
Category KNIME
Downloads 27
Details
This node can be used to create new linker/fragment libraries from input molecules.
The node will execute the sd2frag protocol.

Installation:
MOE Extensions at least version 2.2.0 are required.
Copy the svl file into $HOME/moefiles/knime and add that directory to the custom node directories in KNIME Preferences|KNIME|Chemical Computing Group.
The node will show up in the node repository in the category MOE:Custom the next time KNIME is started.
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Plugin to run MOE inside KNIME. The extension contains a compiler that can convert SVL files into nodes at KNIME start.
Date 2018-03-14
Author Alex Clark & Guido Kirsten
Category KNIME
Downloads 193
Details
The MOE Extensions for KNIME are available from support@chemcomp.com.
Please send us an email and we will send you the
download and installation instructions.

The latest MOE Extensions for KNIME are version 2.4.0. They have been tested with MOE 2018.01 and KNIME 3.5.2.
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Workflow for updating a molecule collection with a new set of molecules
Date 2018-03-14
Author Guido Kirsten
Category Basic Molecular Tools
Downloads 12
Details
Workflow for Exercise 1 "Compound Library Management" as described in the documentation of the MOE Extensions for KNIME version 2.4.0
See documentation for further details.
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This node calculate a flag for graph-based C2 symmetry of molecules
Date 2018-03-14
Author Guido Kirsten
Category KNIME
Downloads 21
Details
This node can be used to detect graph-based C2 symmetry in a molecule.

Installation:
MOE Extensions at least version 2.2.0 are required.
Copy the svl file into $HOME/moefiles/knime and
add that directory to the custom node directories in KNIME Preferences|KNIME|Chemical Computing Group).
The node will show up in the node repository in the category MOE:Custom the next time KNIME is started.
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This node extracts the atom positions and writes them into new columns.
Date 2018-03-14
Author Guido Kirsten
Category KNIME
Downloads 40
Details
For each molecule the 3D positions of either all or heavy atoms only are written to new columns.

Installation:
MOE Extensions at least version 2.2.0 are required.
Copy the svl file into $HOME/moefiles/knime and add that directory to the custom node directories in KNIME Preferences|KNIME|Chemical Computing Group.
The node will show up in the node repository in the category MOE:Custom the next time KNIME is started.
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Removes duplicate conformations from an MOE database
Date 2017-12-14
Author CCG Support
Category MOE Database Tools
Downloads 324
Details
Description:
Application to detect duplicate conformations in a MOE database.
Use cabn set RMSD theshold for unique conformations. Option of
eithe selecting of deleting duplicate conformations

Note: ALL entries must not be empty!

Usage:
(A) GUI
If you run this code from a MOE File Open panel(click on "Run SVL"),
a GUI will appear. Use the Browse button to select the input
database. Specify the molecule and (optional) mseq fields
(in the case of databases with multiple conformations).
Molecular symmetry will be taken into account.

Choose the actions for the duplicates - either select in the
database viewer or delete. Press OK to perform teh operation.

(B) Command Line:
The operation can be run using the SVL command:

svl> conf_unique opts

where opts is a tagged vector of options:

opts = [
dbfile:'database_filename',
mfield:'molecule field name'
mseq:'mseq field'
RMSD:'rmsd threshold in A'
action:'Select' or 'Delete' -> action to perform on duplicate
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DOCKTITE is the SVL implementation of a highly versatile covalent docking workflow into MOE.

The formation of a covalent bond with a target protein is essential for a number of successful drugs but computational tools for covalent docking without significant restrictions regarding warhead or receptor classes are rare. DOCKTITE is a highly versatile workflow for covalent docking combining automated warhead screening, nucleophilic side chain attachment, pharmacophore-based docking and a novel consensus scoring approach. DOCKTITE is a fast and user friendly method for covalent docking without restrictions upon warhead or receptor classes and is predestined to deal with large-scale virtual screening tasks. Furthermore, advanced users may modify the open source program to suit their demands.
Date 2017-10-30
Author Christoph Scholz and Sabine Knorr
Category Simulations
Downloads 177
Details
Installation Instructions Updated for MOE 2016

Please refer to the provided manual for details of usage.

To stay up to date about future updates, please subscribe to our newsletter: http://eepurl.com/_PqlD

How to cite Docktite:
Scholz, C.; Knorr, S.; Hamacher, K.; Schmidt, B., DOCKTITE — A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in the Molecular Operating Environment. J. Chem. Inf. Model. 2015, 55, 398-406
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A workflow for creating QSAR models allowing easy creation of training and test sets, comparison of Q2 and R2 for PLS/PCR component selection, and leave N out cross validation.
Date 2017-10-04
Author Simon Grimshaw
Category Molecular Descriptors and QSAR
Downloads 206
Details
This is a workflow for creating QSAR models in MOE. The process works like so:

1. Load (and optionally back up) an MDB of molecules with an activity field
2. Calculate descriptors and specify the name of the activity field
3. Split the database (optional step) into training and test sets. Various methods are available, including k means clustering and selection from binned activity values.
4. Select descriptors. The selection can be pruned by looking for low variance or highly correlated descriptors. In addition the training and test sets can be compared in PC space based on the current descriptor selection.
5. Build the QSAR model. Currently only the PLS and PCR methods are available.
6. Validate the model; a variety of methods, including MOE's standard Leave One Out method, are available.
7. If a test set has been created, the model can now be applied to the test set.

In the zip file you download you will find a PDF explaining how to use the Wizard and the SVL file itself. To start a QSARWizard session, simply save the SVL to your hard-drive and run it e.g. using the MOE | File | Open panel, browse to qsarwizard.svl and click OK.
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RECON TAE Histogram, Topological Autocorrelation (TRAD) and 3D Autocorrelation Descriptor (RAD) generator
Date 2017-10-02
Author Curt Breneman and N. Sukumar
Category Molecular Descriptors and QSAR
Downloads 100
Details
RECON Descriptors

RECON is an algorithm for the rapid reconstruction of molecular charge
densities and charge density-based electronic properties of molecules,
using atomic charge density fragments precomputed from ab initio
wavefunctions. The method is based on Bader's quantum theory of Atoms
in Molecules.

A library of atomic charge density fragments has been built in a form
that allows for the rapid retrieval of the fragments and molecular
assembly. The RECON algorithm reads in a molecular database, determines
atom types and environments, assigns the closest match from the library
of atom types and combines the densities of the atomic fragments to
compute a large set of new and traditional QSAR descriptors. QSPR and
QSER indices for large pharmaceutical databases or proteins can be
computed within seconds.

This is an SVL implementation of MOE RECON TRAD. A much faster linux
executable with additional features is available by license through the
RPI office of Technology Commercialization http://www.rpitechnology.com

Relevant references:

S. Oloff, S. Zhang, N. Sukumar, C.M. Breneman*, and A. Tropsha*,
"Chemometric Analysis of Ligand Receptor Complementarity: Identifying
Complementary Ligands based on Receptor Information (CoLiBRI)",
Journal of Chemical Information and Modeling, 46 (2), 844-851, 2006.

B.K. Lavine, C.E. Davidson, W. Katt, C.M. Breneman*, "Analysis of
odor structure relationships using electronic Van der Waals surface
property descriptors and genetic algorithms," ACS Symposium Series
(2005), 894 Chemometrics and Cheminformatics, 127-143.

B.K. Lavine, C.E. Davidson, C.M. Breneman*, W. Katt, "Electronic van
der Waals surface property descriptors and genetic algorithms for
developing structure-activity correlations in olfactory databases"
Journal of Chemical Information and Computer Sciences, 43 (6):
1890-1905, Nov-Dec 2003.

C.M. Breneman* and M. Rhem, "A QSPR Analysis of HPLC Column Capacity
Factors for a set of High-Energy Materials Using Electronic Van der
Waals Surface Property Descriptors Computed by the Transferable Atom
Equivalent Method." J. Comp. Chem. 18(2),182-197, 1997.

http://www.drugmining.com/files/RECON/recondoc/WinRecon.html

Installation of RECON TAE Molecule Descriptors

Create the directory $MOE/custom/svl/ (if necessary)
Copy the q_recon_tae.svl file to $MOE/custom/svl/

For instance, if MOE is installed in c:\moe on a Windows PC, this would be
c:\moe\custom\svl\q_recon_tae.svl

If MOE is installed in /usr/local/lib/moe on a Unix system, this would be
/usr/local/lib/moe/custom/svl/q_recon_tae.svl

Copy entire 'reconBin' directory to a nice location (e.g. $MOE)

Set system variable 'recon_moe_root' to the reconBin directory (remember
to include the final '\' or '/' in your variable!) e.g.

recon_moe_root = c:\moe\reconBin\


An alternative to setting a system environment variable is to
replace line 2295 in q_recon_tae.svl with with a line that
points to the reconBin directory. Examples of this could be

local RecRoot = 'c:/moe/reconBin/';
or
local RecRoot = '/usr/local/lib/moe/reconBin/';

Note that paths within MOE use / forward slashes, on both Windows and Unix.
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Calculates Central Nervous System Multiparameter Optimized Index
Date 2017-10-02
Author Jens Lätt
Category Molecular Descriptors and QSAR
Downloads 31
Details
Calculates Central Nervous System Multiparameter Optimized Index from

"Moving beyond rules: the development of a central nervous system multiparameter optimization (CNS MPO) approach to enable alignment of druglike properties."
Wager TT, Hou X, Verhoest PR, Villalobos A.
ACS Chem Neurosci. 2010 Jun 16;1(6):435-49. doi: 10.1021/cn100008c. Epub 2010 Mar 25.
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Search sequences from MOE via PFAM website (http://pfam.xfam.org) and annotate in MOE
Date 2017-04-21
Author Hooman Shadnia
Category Protein Tools
Downloads 18
Details
This scripts sends protein sequences to PFAM website and pareses the resulting hits, colors various detected domains and creates MOE 'sets' to access the domains as detected.
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This is a basic interface to the ORCA QM package written by F. Neese.
Date 2017-01-21
Author Richard Bartelt
Category Basic Molecular Tools
Downloads 4
Details
This is a basic interface to the ORCA QM package written by F. Neese. It allows to read and write ORCA coordinates (.xyz) and facilitates the creation of input files for reaction coordinate scans and constrained calculations.

USAGE:
MOE | File | Open -> ORCA_coordinates.svl

If you want to start ORCA from the panel the following executables and paths need to be specified in the script:
ORCA_DIR, QUEUE_TMP_DIR, MPI_EXE_DIR, MPI_LIB_DIR

The profiles allow you to create a series of input files with identical header and footer. E.g. calculation of NMR shieldings for different compounds with identical settings.

Press [Show] at the very bottom of the panel to get the input file w/o starting it locally or on a queing system.

For ORCA options etc. please refer to the ORCA documentation.

The output of ORCA calculations can be read by the script (geometric data only!). Scan calculations are imported to an MDB file and can be visualized using MOPAC_rb_energyTable.svl (uploaded to SVL exchange as well).

I do NOT guarantee that this script will work with future releases of ORCA and MOE.
Tested with MOE2015/2016, ORCA3.0.3 in a Linux environment and a SUN grid engine derivative.
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A collection of svl scripts for the purpose of creating MOPAC input files as well as interpreting and visualizing the results.
Date 2017-01-21
Author Richard Bartelt, Wolfgang Brandt
Category Basic Molecular Tools
Downloads 35
Details
UPDATE for MOE2016

All scripts have been tested with MOE2016.08 in a Linux environment.
MOE built-in public domain MOPAC does NOT work due to missing support of mixed cartesian and internal coordinates.

This collection consists of 5 svl scripts:
- MOPAC_rb_createInput.svl
- - create a MOPAC input file for 1D and 2D calculations
- MOPAC_rb_interpretOutput.svl & MOPAC_rb_lib.svl
- - extract structures and energies from MOPAC output file, import them into an .mdb
- MOPAC_rb_energyTable.svl
- - use the extracted structures and energies to visualize an "energy hypersurface"
- MOPAC_rb_applyFixed.svl
- - restore fix-flags when using a MOPAC output geometry as input for a new MOPAC calculation

These scripts are stored in a .zip file.


=== MOPAC_rb_createInput.svl ===
FEATURES:
- creates a MOPAC input file
- fixed atoms get no-optimization flag
- "normal" atoms will keep their cartesian form
- reaction coordinate atom(s) will be transformed into internal coordinates and appended to the "normal" atoms
- for restoration of atom-names and residues a .mmeta-file will be generated which can be used in

BEFORE running this script:
- adjust the constants MOPAC_EXE, MOPAC_LIC and MOPAC_LIB

USAGE:
- prepare the system you want to use as input (all atoms will be used - that is: every atom in Atoms [])
- run this svl-script via 'File' - 'Open'

=== MOPAC_rb_lib ===
- library functions for MOPAC_rb_interpretOutput.sv

=== MOPAC_rb_interpretOutput.svl ===
FEATURES:
- imports structures and energies of MOPAC output file
- if present, uses a .mmeta file to restore atom names and residues

BEFORE running this script:
- adjust the constant MOPAC_RB_LIB to point the location of the library file

USAGE:
- run this svl-script via 'File' - 'Open'


=== MOPAC_rb_energyTable.svl ===
FEATURES:
- visualizes an "energy hypersurface" of a MOPAC grid/scan calculation

USAGE:
- run this svl-script via 'File' - 'Open'
- select the .mdb file (needs to be same format as output of MOPAC_rb_interpretOutput.svl)


MOPAC_rb_applyFixed.svl
In MOE molecular databases (.mdb) are no information whether an atom is fixed or not (fix flag). For every no-optimization flagged atom present in the MOPAC input .dat-file this script looks for an atom of the same element at the same position in the MOE system, and fixes this atom.

FEATURES:
- restores the fix flags of an MOPAC output scene loaded from an .mdb

USAGE:
- load the MOPAC scene from the .mdb
- run this svl-script via 'File' - 'Open'
- select the .dat-file (MOPAC inputfile which has been used to generate the scene)
- PLEASE, check the results: 'Select' - 'Potential' - 'Fixed
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Define planes through sets of atoms. Then measure the distance between an atom and the plane, the angle between planes, and reflect atoms in
the plane.
Date 2016-12-07
Author gkirsten
Category Basic Molecular Tools
Downloads 20
Details
INSTALLATION

1) Copy this file to $HOME/moefiles/svl/run/, where $HOME is the user’s home directory (e.g., Windows: C:\Users\walter\moefiles\svl\run\ or Linux/Unix/macOS: ~/moefiles/svl/run/)

2) Start the script using, from the SVL command line or a menu:
run 'plane_gui.svl'

Notes:
- The directory must be created if it does not already exist.
- Alternatively, drag-and-drop this SVL file in MOE window to run.
- $HOME can be determined at the SVL Commands windows. Type:
svl
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Extends the functionality of MOE's text editor. (Revised 24th Oct 2016.)
Date 2016-10-26
Author CCG Support
Category SVL Utilities
Downloads 116
Details
Installation

1. Unpack the zip file in any directory.
2. Copy the two folders (menu and svl) to your $HOME/moefiles folder.
Now you should have $HOME/moefiles/svl/ted_extensions.svl and
$HOME/moefiles/menu/menu-ted_2016. Please be aware that the menu will over-ride
the default MOE text editor menu and any other modifications to those menu
you might have made.
3. Restart MOE.

Added Features

SVL Search (TED | Find | SVL Search or Ctrl + f in the TED window) - runs the SVL search utility. This allows a more fully featured search either in the current file or in MOE or User directories (as defined in step 4 of the installation process). Searches in file may fail if the file has been modified; please save then search if problems are encountered.

Manual Page (TED | SVL | Manual Page or Ctrl+m) - to enable this function, first type _UPDATE_ in a text editor window, highlight the text and choose TED | SVL | Manual Page. Once the index has been built (you can monitor the indexing in the SVL Commands Window), the manual page for an SVL function can be launched by highlighting the function name and choosing TED | SVL | Manual Page.

Default text blocks: Insert Header (Ctrl+h) and Database Looper Motif will insert a standard SVL file header (as seen in MOE SVL files) and a sample db_NextEntry-style database loop.

Block indent (Ctrl+. indents in, Ctrl+, indents out) - allows easy formatting of SVL. Select a few lines of text and indent it further right or left to make your code easier to read.

Block commenting (Ctrl+I comments out, Ctrl+Shift+I comments back in) -
allows easy commenting in/out of multiple lines of code in a similar manner to block indenting.

Move cursor back one word with Ctrl+b.

Unload the currently viewed SVL file from MOE by TED | SVL | Unload

TED | File | Save, TED | SVL | Save and Load, and TED | SVL | Save and Run all perform a "two stage" save, i.e. the last saved version is copied to a file with the same filename apart from an additional ~ suffix, then the main file is saved.

TED | Edit | Copy doesn't clear the clipboard if no text is selected

TED | Edit | Paste will delete any selected text before pasting at the cursor position.

TED | SVL | Save and Read Menu File will save the current file, reload the standard MOE menus then load the current file with the ReadMenuFile SVL command.

TED | SVL | Execute Command will execute any selected text, or if there is no selected text it will open a command line in the current text editor. This makes it fairly easy to step through a function executing one line at a time. Selected text is automatically expanded to complete lines. If the first line starts with "local", "global", "static", or "const" then that word is removed (this only affects the first line).

TED | SVL | Insert Date inserts today's date at the cursor position

TED | SVL | History Browser launches a listbox containing the contents of your history[]. Commands can be executed by selecting one or more of them and clicking "Execute", or can also be executed by double-clicking. Selected commands can be sent to a MOE text editor by clicking on "Make script".
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This application highlights pharmacophore features that can be used to maximize selectivity for a protein target vs a chosen set of off-targets.
Date 2016-10-11
Author Hooman Shadnia
Category Protein Tools
Downloads 98
Details
This application uses a collection of proteins aligned using a common ligand and will highlight pharmacophore features that can be used to maximize
selectivity for each individual protein. An experimental scoring table (provided in the dabatase file imatrix.mdb) is used for this.

The resulting visuals can be used to modify the ligand to increase selectivity, i.e. to improve the activity on the chosen target while reducing the activity on others.

Sample files provided for quick testing.

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Script to write MD snapshots from a databse to BMP files
Date 2016-10-11
Author Sarah Witzke
Category Graphics and Rendering
Downloads 13
Details
This script will take as input the MDB from an MD simulation and write out every nth frame as a BMP file.
The user needs to set up the visualization before hand.
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The smooothed protein ribbon representations sometimes pass a short distance
from the C alpha atoms. If the sidechain and C-alpha atoms are shown, they
appear disconnected from the ribbon.

This script creates a copy of a chain, adjusts the position of the
C alpha atoms so they are close to the protein ribbon. The ribbon
is shown for the original chain, with the sidechain and C alpha atoms
from the temporary chain.

The temporary chain should only be used to create images of the structure,
and not for any calculations which rely on the 3D coordinates.

The C alpha atoms positions are only adjusted for residues which have a
ribbon displayed. Residues with C alpha trace ribbons are also ignored
as the ribbon already passes through the C alpha atom positions.
Date 2016-09-20
Author Andrew Henry
Category Basic Molecular Tools
Downloads 41
Details
Load the protein in MOE and display ribbons. The "run" this script.
By default all the receptor chains with protein ribbons will be
modified. Chain keys can be supplied as an argument to adjust
only specific protein chains.

(a) From the MOE | File | Open panel, select this file
and click the "Run" button.

(b) Alternatively, at the SVL command line, type:
run 'ribbon_sidechains.svl'
run ['ribbon_sidechains.svl', protein_chains]
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Some game you may already know.
Date 2016-07-11
Author Richard Bartelt
Category Miscellaneous
Downloads 57
Details
This implementation of the classic game tetris is published for demonstration purpose only and does NOT contain any scientific relevant methods etc.

For those of you, who need to relax some minutes ... enjoy

(Updated to work with file locking in MOE 2015.1001)
SVL Syntax highlighting for the NEdit text editor
Date 2016-03-07
Author Andrew Henry
Category SVL Utilities
Downloads 14
Details
Syntax highlighting for the NEdit text editor for Motif/X11 available from https://sourceforge.net/projects/nedit/

To use this, download this file and save it to ~/.nedit/nedit.rc
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Run MOE database entries of a folder of files through any third party code, collect the results in MOE database
Date 2016-01-20
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 19
Details
Summary:
- Reads a MOE database or a folder containing MOE recognized structures
- Converts all files or database entries to the format give in 'Internal Format'
- Uses a simple mark-up syntax to generate command line required to call third party binary
- Uses the same format to designate the output files expected from third party binary
- collects the results in a MOE database.

It can also create batch scripts (unix only, for now) to do this offline.
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A few tweaks to Giovanni's excellent scene manager.
Date 2015-10-30
Author Byron Delabarre modification to Giovanni C's previous submission
Category Graphics and Rendering
Downloads 35
Details
The Scenes_Manager is a great way to enable collaboration between MOE users.
This will allow a user to save "scenes" in a fashion similar to other molecular viewers. Saved scences can be shared electronically via a .mse and accompanying .moe file.
Set amide bonds to 180 degrees. Interactive (3D) window and MDB versions
Date 2015-08-27
Author Emilio Xavier Esposito
Category SVL Utilities
Downloads 11
Details
It is common for small drug-like compounds and peptides that are constructed from SMILES strings and even SDfiles to have amide bonds where the hydrogen of the nitrogen atom and the oxygen of the carboxyl group result in a dihedral angle of approximately 0 degrees. This function sets all amide dihedral angles to 180 degrees and provides the option for energy minimization (this functionality is not implemented in the MDB version because of the energy minimization function with the MDB framework). The interactive (MOE 3D window) version allows the user to select the amide bond of interest.

The MDB version of this function provides the option to overwrite the original molecule or create a new column (field) for the compounds. The MDB version does indicate how many amide bonds were corrected. It is recommended that after changing the amide dihedral angle(s) within a database of compounds that the MDB energy minimization (MDB | Compute | Energy Minimize) function be performed using the desired molecular force field.

Note: Amide groups within rings are not modified.

The default values are:

No energy minimization for MOE 3D window (nrgOpt:0)
Column (field) with molecule is 'mol' (molField:'mol')
Save corrected compound to a new column 'modMol' (newMolField:'modMol')
Maximum peptide length is set with 'maxPeptideLength' (maxPeptideLength:15)

Instructions

Load this function
load '~/code/svl/utilities/db_SetAmide180.svl'

For a compound in the MOE 3D window (either a single small-organic drug-like compound or a selected molecule)
SetAmide180[]

For a compound in the MOE 3D window with energy minimization of the new conformation
SetAmide180[nrgOpt:1]

For a collection of compound in a MDB saving the new conformation to the originating column of the compound
db_SetAmide180['drugLike_compounds.mdb', [molField:'mol', newMolField:']]
The 166 MACCS keys as molecular descriptors
Date 2015-08-27
Author Emilio Xavier Esposito
Category Basic Molecular Tools
Downloads 27
Details
This function counts the occurrence of the 166 MACCS keys for each molecule in a MOE database (mdb). The number of each key's occurrence is written to a user specified CSV file. The option to include the compounds' names and endpoint values in the CSV file is an option from the opts variable.

The default values are:

Column (field) with molecule is 'mol' (molField:'mol')
Include the endpoints if the endpoint column name is provided (endpointField:')
Include the compound's name or SMILES string. Not indicating a compound name file (nameField:') uses the compound's name returned with cName Chains[] or the compound's SMILES string if no name is present.
Column headers for MACCS keys will be returned in lower case letters (uppers:0)

Instructions

Load this function
load '~/code/svl/utilities/MACCSkeyCounts.svl';

Calculate the MACCS Key Counts for a MDB of compounds
MACCSkeyCounts['Selwood_dataset.mdb', 'Selwood_MACCSkeyCounts.csv', [molField:'mol', endpointField:'pEC50', nameField:'name']]

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Docking for MOEWeb
Date 2015-08-20
Author Hooman Shadnia
Category MOE/web
Downloads 84
Details
Sketch ligands or load from a database and dock into prepared protein targets in MOEWeb

(revised for MOEWeb 2014)
(revised to use JavaScript JSME,JSMOL)
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MOE/web Molecular Viewer (jsmol)
Date 2015-08-20
Author Hooman Shadnia
Category MOE/web
Downloads 35
Details
Display a MOE readable structure (*.moe, *.pdb, etc) via internet browser.

Requires jsmol. Please contact support@chemcomp.com if you have any difficulty installing jsmol.


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Useful for evaluating solvent exposure differences between bound and free proteins. For example, to define the structural epitope on an antigen by evaluating the solvent exposure difference of antigen residues with and without the bound antibody.
Date 2015-06-19
Author Randal R. Ketchem
Category Protein Tools
Downloads 22
Details
residuesOfInterest = Residues[] |
cNumber rChain Residues[] == 2 or cNumber rChain Residues[] == 4;
atomEnvironment = Atoms[] |
cNumber aChain Atoms[] == 2 or cNumber aChain Atoms[] == 4 or
cNumber aChain Atoms[] == 5 or cNumber aChain Atoms[] == 6;
solvent_exposure_difference[
residuesOfInterest:residuesOfInterest,
atomEnvironment:atomEnvironment,
diffCutoff:0,
colorResidues:0,
printAtoms:1,
outfileSADiff:'solvent_exposure_difference.txt'];
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This is an add-on to the standard interface in MOE. The additional buttons contain simplified graphical panels for molecule alignment and pharmacophore design.
Date 2015-04-10
Author CCG Support
Category Z- Obsolete Code
Downloads 128
Details
DESCRIPTION:
The buttons contain: a molecular builder with added handling of chirality constraints, a simplified interface for flexible alignment of structures, a simplified interface for Contact Potentials and a pharmacophore query editor.

USAGE:
Save the attached files in your working directory (along with your molecule files) and open the moe-menus.pharmacophores file with the MOE File Open panel. A new set of buttons will appear at the left side of the MOE window.

D. Bondarev
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Conformational search application for MOEWeb
Date 2015-03-27
Author Hooman Shadnia
Category MOE/web
Downloads 71
Details
Allows performing conformational search via a web browser. The structures can be sketched, or read from PDB/SDF files.

The global minimum conformation is displayed in 3D. The energy distribution of conformations are shown on a 2D plot. The entire generated conformations can be downloaded as MDB or SDF files.

Installation notes:
unpack the archive under $MOE/web.

Revised for MOEWeb 2014
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Run Torsion Scan via internal MOPAC engine (Update for External MOPAC2012)
Date 2015-03-02
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 34
Details
Run Torsion Scan via internal MOPAC engine.


USAGE:

1. Load a desired small molecule structure in MOE.

2. Energy minimiza using MOPAC at AM1 level using
MOE | Compute | Energy Minimize | QM

3. Save this file to your working folder and run it by using
MOE | File | Open

then select 'torscan_mopac.svl' and press 'OK'

The code will run a '1scf' job via MOPAC and will display the zmatrix
created in MOPAC. Heavy atoms in main MOE window will be labelled
accordingly.

4. Select the desired dihedral from the list by clicking on the corresponding
line, then press 'Dihedral'.

ATTENTION: please verify that the selected atoms in main MOE window
correspond to a valid dihedral torsion. Currently we make no attempt
to verify this.


5. Press 'Run MOPAC'.

The script will use the internal MOPAC engine to run a torsion scan and
will plot the results.

The MOPAC input/output files can be displayed by checking 'Open Results
in Text Editor'.

These files are written into temp folder. To find the temp folder, Open
the SVL command window and type TMP. All files are named mopac*.*.

The current version uses external MOPAC such as MOPAC2012 for the actual
torsion scan, since some bugs in MOPAC7 affect certain structures.
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Calculate, Isolate, and Display Networks of Hydrophobic Interactions in Proteins and other Complexes
Date 2015-02-26
Author Hooman Shadnia
Category Protein Tools
Downloads 87
Details
Given a structure and a threshold in kcal/mol, the script first detects all "links". A link exists when two neighbouring residues have hydrophobic interaction stronger than the given thresholds.

The script then detects and isolates networks made solely via hydrophobic links as described. Users can include or exclude non-protein residues, multi chain interactions, etc.

An interactive histogram of all links in the system is also displayed, to help users set the hydrophobic threshold value.
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Computes grid based Tanimoto similarity score between a molecule loaded in the MOE window and a database of ligands.
Date 2015-02-24
Author Jon Heal
Category Molecular Descriptors and QSAR
Downloads 250
Details
This code computes an electrostatic similarity value between a molecule in the MOE window and (each of)a database of compounds previously aligned with the target molecule (for example, resulting from a FlexAlign procedure). It is observed that compounds with higher electrostatic similarity values may show similar biological activities. Thus this procedure may be used to rank docking poses where a known ligand is the target molecule, or can be used for ranking alternate scaffolds from a lead hopping program such as BREED. Electrostatic similarity is computed by solving the PB equation for both target and query compounds and computing a grid based Tanimoto (Tes) between the resulting grids. Thus results are in the range -1->1, with 1 = identical field and -1 = inverse field. This code uses the original PB solver in MOE prior to re-write in 2005.09 release and thus these dependent MOE functions are included in the script to work with versions of MOE released after 2004.

Usage :
(1) Load a molecule into the MOE window and compute MMFF charges. Also calculate MMFF charges for database ligands. nb all code has been tested using MMFF charges so these are recommended for correct use.
(2) Run db_ElectroSim[mdb,molfield] where the mdb contains a set of molecules in 'molfield' (defaults to mol if absent) to compute values for. Procedure outputs scores in field 'Tes' (range -1->1, where 1 = identical field)
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Download the entire PDB from RCSB or from a local mirror into volumes of databases. Updates the existing databases and adds new entries on subsequent runs
Date 2015-01-15
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 30
Details
Simply open the script if MOE: MOE | File | Open and you will get a graphical panel that allows you to pick the source, target, and number of entries per database.

Upon future execution, use the same output folder, it scans for already downloaded items and only downloads the new ones, and appends them to the last volume.
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Edit mode for jEdit including Syntax highlighting (MOE 2014.09)
Date 2015-01-08
Author Guido Kirsten
Category SVL Utilities
Downloads 130
Details
Syntax highlighting for the jEdit editor available from www.jedit.org

Save the xml file in JEDIT/modes and add the following lines at the end of JEDIT/modes/catalog

<MODE NAME="SVL" FILE="svl.xml"
FILE_NAME_GLOB="*.svl" /
Detects and encode the missing sequence information for peptides
Date 2014-12-12
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 34
Details
If a peptide structure is built via SMILES, or read-in from a *.sdf file, it will lack the residue information and thus appears as a small molecule in MOE.

This script will detect and encode the sequence information.

Dec 2014 update: N/C terminal caps are detected as well.
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Ligand-pocket interaction forces and energies.
Date 2014-11-05
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 322
Details
Starting with a force-field energy minimized complex, the program calculates and displays the atomic interaction forces between the ligand and the pocket, as well as the per residue interaction energies of such interactions.

Originally published in Interaction force diagrams: new insight into ligand-receptor binding, H. Shadnia, J.S.Wright, J.M.Anderson Journal of Computer Aided Molecular Design, Vol. 23, No. 3, 1573,185-194, 2009.
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A fingerprint based on triangles of EHT-defined projected features
Date 2014-07-23
Author Simon Grimshaw
Category Pharmacophores and Fingerprints
Downloads 50
Details
Description
Use the EHT pharmacophore scheme to calculate where the Don2, Acc2, Aro and
Hyd features are, bin the distances along the triangle edges and convert to
fingerprint indexes. Hyd-Hyd-Hyd triangles are removed, and rings that are
both Hyd and Aro are only counted as Aro.

Usage
Load this file into MOE, e.g. save to $HOME/svl and restart MOE.
Use the fingerprint tools as normal, search for FP:EHTTAT.
Calculates a matrix for the number of compounds each database has in common with each of the other databases based on either structure or fingerprints.
Date 2014-07-16
Author kgrabowski
Category Basic Molecular Tools
Downloads 81
Details
DESCRIPTION:

db_nb_mols_incommon calculates a matrix for the number of compounds each database
has in common with each of the other databases based on either structure or
fingerprints.

db_compare_fp can be used to output the average tanimoto between two databases
based on fingerprints if called with

db_uniqBits_fp calculates a matrix for the number of unique fingerprint bits per
database, i.e.the number of bits not present in both compared databases

USAGE:

1. Save and load this function

2. A) At the SVL command line prompt type the following

svl> db_nb_mols_incommon [mdbs, outfile, opt]

where,

mdbs is a vector of tokens of filenames of the databases to
operate on
outfile is a token representing the filename of the output file
opt is a tagged vector of options
[
fp_flag: flag,
thresh: threshold,
fp_code: fingerprint code,
sim_code: similarity code,
average_Tani: flag,
write_cpds: flag,
cpds_outfile: cpds_outfile
]
- fp_flag: if 1 then similarity is calculated based on fingerprints
default is 0 (based on structure)
- molecules with similarity above the value of threshold are
regarded to be the same

- average_Tani: if 1 the the average similarity between two
databases is calculated instead of the number of molecules which
are regarded to be the same. fp_flag will be set to 1 automatically
(the average similarity is calculated in the following way: take the
maximum value for each row (so the highest similarity for each entry
to any other compound in the comparison database), then the average
value for those row-wise maxima.)

- fp_code and sim_code are the fingerprint and similarity metrics
to be used in the comparison. A list of fingperprints can be found
using the command ph4_FingerprintList []
Default options are fp_flag:0, thresh:0.85 using bit-packed MACCS
keys and the tanimoto coefficient.

- write_cpds: if 1 then another textfile is written containing all
compounds and the databases that contain the compound; if a cpd is
only found in one db, then it is not written to the textfile
- cpds_outfile: name of the output file for the above

2. B)
svl> db_uniqBits_fp [mdbs, outfile, opt]

mdbs is a vector of tokens of filenames of the databases to
operate on
outfile is a token representing the filename of the output file
opt is a tagged vector of options, in this case only the fp_code option,
e.g.: [fp_code:'FP:MACCS'] or [fp_code:'FP:piDAPH4']
A list of fingperprints can be found using the command
ph4_FingerprintList []

EXAMPLE:

db_nb_mols_incommon [['db1.mdb', 'db2.mdb', 'db3.mdb'], 'MatrixOut.txt']

// for all databases that are open in the database viewer
db_nb_mols_incommon [dbv_KeyList[], 'MatrixOut.txt']

// use fingerprint similarity
db_nb_mols_incommon [dbv_KeyList[], 'Matrix.txt',
[fp_code:'FP:MACCS', sim_code:'tanimoto', thresh:0.95, fp_flag:1]]

// output average tanimoto between two databases based on fingerprints
db_compare_fp[['a.mdb', 'b.mdb', 'c.mdb'], 'Matrix.txt',
[fp_code:'FP:MACCS', sim_code:'tanimoto', average_Tani:1]]

db_uniqBits_fp [['db1.mdb', 'db2.mdb', db3.mdb], 'Matrix.txt',
[fp_code:'FP:piDAPH4']]
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Browse the SVL exchange recent submissions straight from MOE.
Date 2014-07-07
Author Simon Grimshaw
Category Miscellaneous
Downloads 12
Details
A demonstration of MOE's url reading and XML parsing functions: given a list of RSS feed URLs (hard coded in the constant URL), read the XML and show the feed's contents as a set of buttons displaying title and first 140 characters of each feed's description. Clicking on the buttons should launch the relevant webpage in your browser.

I've included the SVL Exchange as the first feed; if clicking the button doesn't jump you straight to the item, first log in to the Exchange so the cookie is set in your browser then try again.

MOE can import .png format images, so I might be able to get those into the buttons one day.

Usage:

Run this file, e.g. use the File | Open panel, browse to rss.svl and click OK.
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Align protein chains in MOE using external alignment tool MUSCLE
Date 2014-06-18
Author Hooman Shadnia
Category Protein Tools
Downloads 40
Details
Align protein chains in MOE using external alignment tool MUSCLE (http://www.drive5.com/muscle)
Calculate the number of bad and rare bond lengths, angles, torsions and lengths using MOGUL.
Date 2014-06-10
Author Simon Grimshaw
Category Basic Molecular Tools
Downloads 24
Details
DESCRIPTION:
MOGUL descriptors - get descriptors for the number of rare and unusual bond angles, lengths and torsions.


USAGE:
1. Save and load this function
2. Compute Descriptors:
DBV | Compute | Descriptors | Calculate
3. Search in the descriptor list for mogul
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Simultaneously browse corresponding residues of aligned sequences
Date 2014-06-02
Author Hooman Shadnia
Category Protein Tools
Downloads 17
Details
Simultaneously browse corresponding residues of aligned sequences. This utility uses MOE's selection language to define what to browse, what to hide, and what to keep displayed. It should be useful in comparing corresponding structures such as various crystal structures belonging to the same protein family.
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Calculate and display twist angle between two planes, each defined via three atoms
Date 2014-02-17
Author Hooman Shadnia
Category Graphics and Rendering
Downloads 23
Details
Calculate and display twist angle between two planes, each defined via three atoms
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Print mutation codes of a given protein chain vs a reference chain
Date 2014-02-17
Author Hooman Shadnia
Category Protein Tools
Downloads 21
Details
Print mutation codes of a given protein chain vs a reference chain. Output in SVL command window and text file.
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Export RISM grids from *.RISM files to *.CCP4 format
Date 2014-02-17
Author Hooman Shadnia
Category Utilities
Downloads 18
Details
Export RISM grids from *.RISM files to *.CCP4 format so they can be displayed via MOE Grid Analyzer etc.
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Constraint (staple) alignment of protein chains to current state
Date 2014-02-17
Author Hooman Shadnia
Category Protein Tools
Downloads 21
Details
Constraint (staple) alignment of protein chains to current state
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Builds Kinase Homology Models using input files for template and sequences. Allows various fusion modes
Date 2014-02-14
Author Hooman Shadnia
Category Protein Tools
Downloads 35
Details
Builds Kinase Homology Models using input files for template and sequences.

Allows various fusion modes described in the accompanying PDF document.
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Graphical panel to run sdfrag from MOE.
Date 2014-02-14
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 53
Details
Graphical panel to run sdfrag from MOE. This generates a database of fragments using six possible methods listed on the panel.
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Renders the protein backbone as a graphical object
Date 2014-02-10
Author Hooman Shadnia
Category Protein Tools
Downloads 18
Details
Renders the protein backbone as a graphical object
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Display forcefield potential status of atoms in MOE window and SVL command prompt
Date 2014-02-10
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 22
Details
This script display the force-field potential status of the system in SVL text window and creates graphical text labels. It can be used to verify
whether atoms are fixed, inert, or tethered.
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Creates restraints on alpha helix hydrogen bonds
Date 2014-02-10
Author Hooman Shadnia
Category Protein Tools
Downloads 19
Details
Creates restraints on alpha helix hydrogen bonds
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Change protein ribbon transparency via CTRL+F8
Date 2014-02-10
Author Hooman Shadnia
Category Protein Tools
Downloads 25
Details
Cycle transparency setting of all or selected atoms. Automatically assigns CTRL+F8 on keyboard to execute itself.
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Finds molecules in a database that match a SMARTS pattern and connects them to a specified position in a scaffold molecule.
Date 2014-02-01
Author Christoph Scholz
Category Basic Molecular Tools
Downloads 28
Details
This is a script to connect molecular fragments from a database with a connection point of a scaffold.

For defining the connection point in
the database a SMARTS pattern is used, whereas the first atom in the SMARTS filter is the connection point.

The scaffold has to be loaded in MOE and its connection point atom has to be named "CON".

Only fragments with exact one connection point are written to the output database.
An mseq integer for every entry in the input database is required!

For use in MOE_Batch use a tagged vector. Tags are:
'smfilter' for the SMARTS Filter.
'dbinuput' for the input file.
'dboutput' for the output file.
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Allows multi-processor utilization for LowModeMD and Stochastic Conformational search (jan 2014 update)
Date 2014-01-24
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 170
Details
Allows multi-processor utilization for LowModeMD and Stochastic conformational search.

Instructions:

For single user mode, place these files under $HOME/svl/run and restart MOE. If unsure about location of the $HOME folder, please run MOE and in the SVL command window type HOME and press enter. Please notice that the 'svl' and 'run folders may not exist under $HOME and should be created.

To install for all users, place under $MOE/lib/svl/custom/run and restart MOE.

For a single machine multi-processor mode use the command:
MOE -mpu N

Where N is the number of parallel processes. For best performance this should be set equal to the number of physical processors available. For example for a dual core machine use MOE -mpu 2 . Similarly for a Core i5 or Core i7 machine N should be 4 or 6 respectively. For network multi-processor mode please refer to MOE help pages under 'Installing and Running MOE/smp' .

Next, you can run the conformational search via
MOE | Compute | Conformations | Conformational Search ...

and choose LowModeMD or Stochastic search to run the search.
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The script give the user the ability to save "scenes" and recall them easily via a graphical interface
Date 2013-08-22
Author giovanni cianchetta
Category Utilities
Downloads 51
Details
The script uses a GUI to manage the scenes. To start the GUI, type "Scenes_Gui []" in the command line or you can add a button to the menu.
Once you have a view of the atoms in the graphical window that you want to save, you can add it to the list of the saved ones by clicking "Append" or "Prepend". The program will ask you for a unique name and the you'll see the name in the list.
Clicking on the name will bring the scene back on the screen: visibility, colors, surfaces, ribbons and so on.
If the animation between the scenes is too slow, you can deactivate it or decrease the sleep time between frames in the Options.
Scenes can be deleted, moved, modified and renamed easily with the buttons in the GUI.

When saving the scenes (Save button in the Gui), the script saves two files: one with all the molecules in the system (.moe extension) and another one with the information about the visibility and color of the objects (.mse extension); this means that you can load the scenes only through the GUI by clicking on Load.
This means also that, if you want to share the scenes, you have to send both files.
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A measure of molecular flatness
Date 2013-07-29
Author Simon Grimshaw
Category Molecular Descriptors and QSAR
Downloads 56
Details
DESCRIPTION:
Calculates a descriptor, Plane of Best Fit, after Firth et al., Plane of best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules, JCIM 2012, 52, 2516-2525.

USAGE:

1. Save and load this function, e.g. save to $HOME/svl and restart MOE
2. In the database view menu, choose DBV | Compute | Descriptors | Calculate
3. Look for a descriptor called PBF (type it into the Filter: line)
An interface to allow substructure searching of a MOE database with the
substructure defined by an external sketcher rather than SMARTS.
Date 2013-01-23
Author Simon Grimshaw
Category MOE Database Tools
Downloads 80
Details
Description
An interface to allow substructure searching of a MOE database with the substructure defined by an external sketcher rather than SMARTS.

When this tool is run for the first time, the ten slots for stored searches will be empty. Click on New Sketch to launch the sketcher and create a substructure search; once transferred back to MOE, the sketch will appear in the first available slot. Click on the sketch search the selected MOE database for that substructure. If all ten slots are full, the first slot will be emptied to make room. Alternatively, Ctrl-click on a slot to remove that sketch from the history.

Usage
Run this SVL file, e.g. use the MOE | File | Open panel, browse to db_substructuresketch.svl and click OK.
Determine a set of key physicochemical protein properties that are of interest in protein engineering applications, and a protein-protein interaction report.
Date 2012-12-20
Author Simon Grimshaw
Category MOE/web
Downloads 73
Details
The MOE Protein Properties application calculates a set of key physicochemical protein properties that are of interest in protein engineering applications.

If there is more than one receptor (protein) chain, a protein-protein interface interaction report is generated. For each pair of interacting residues there is a listing of the atom, residue and UID along with the type of interaction (HB, pi-pi etc), the distance and the strength.

To install the MOE/web application, unzip it into your $MOE/web folder and (re)start the MOE/web server. Alternatively unzip it to a different directory, e.g. webapps, then start the MOE/web server with the -app option:

$MOE/bin/moebeb -app webapps
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An implementation of: Xu, Jun; A New Approach to Finding Natural Chemical Structure Classes; J. Med. Chem. 2002, 45, 5311-5320 http://dx.doi.org/10.1021/jm010520k
Date 2012-09-26
Author Guido Kirsten
Category Molecular Descriptors and QSAR
Downloads 312
Details
The scripts finds all scaffold in a database, writes them to a separate database and calculates the complexity and cyclicity of the molecules like described in the paper. Also the frequency of the scaffold in the original database is written to the scaffold database.

Usage: load 'sca.svl' then use: db_SCAclassify['databasename',opt] where opt = 0 means that chiral constraints are not taken into account and 1 means they are taken into account. You may also run the script in GUI mode. In this case you will be prompted for a database and you can select how chiral constraints should be handled.
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Allows the definition of custom units for SA/Report, enabling the visualization of arbitrary phys/chem properties or activities. This latest version fixes bugs and removes restrictions on the order of the low, medium and high thresholds for each unit, allowing the "low" value for say CLogP to be higher than the "high" value.
Date 2012-08-19
Author Alain Deschenes, CCG
Category SA/Report
Downloads 34
Details
The MOE SA/Report tool uses a file ($MOE/web/sareport/units.txt) to determine both the units (eg. pIC50, IC50, percent) that a column in your data can have, and also regular expression style patterns in the column name that enable MOE to guess its type (eg. *PIC50 implies it is a PIC50). The format of the units.txt file is a little cryptic and difficult to edit by hand. Hence, this module allows the user to define new units or change the regular expression patterns, names or matching order of already defined units.

Place the module in $MOE/lib/svl/custom so it is loaded on startup, and run it without arguments from the SVL command line:
SAreport_range_editor [];

The GUI allows you to define, for each unit being edited, the following information:

* Autotype fields: a limited regular expression syntax consisting of asterisks at the beginning or end (or both) of a match string, and with multiple patterns separated by commas. Eg. *pK*,*pXC50*
* Name: a name for the new unit
* Type: activity (eligible for analysis by SAReport) or property (not eligible). Most new units should be defined as activities (even "properties" like MW or ClogP), unless you don't want to allow SA/Report to analyze them.
* Minimum, Mid-point and Maximum numeric points of the range for this data type. These will correspond to red, yellow and green colors respectively in the standard SA/REport three-color scheme, and values between these three thresholds will be interpolated.
* Multiplier/Offset/Function: scaling, addition and functional (eg. log) transforms applied while interpolating numbers between low/medium/high thresholds. I.e. y = f(ax+b)

PS: this module is referenced in the MOE UGM poster and ACS Philadelphia talk given by Deepak Bandyopadhyay of GSK in 2012.
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Alter residue UID or position in the sequence editor.
Date 2012-08-10
Author Simon Grimshaw
Category Protein Tools
Downloads 99
Details
When run, a menu is created in the Sequence Editor that allows the user to choose the set of residues to be acted upon and the renumbering action (whether it is on the alignment position or the residue ID) to be performed. This is useful for preparing a set of protein-ligand complexes for input into PLIF and Ligand Interactions, as those applications rely on a consistent rUID scheme across all receptors.

Additionally, antibody structures can be renumbered to a canonical scheme.

To use the code, run it, e.g. use the MOE | File | Open panel, browse to resIDfns.svl and click OK, or use this SVL command:

run 'renumber_residues.svl'
42 counts of simple structural features implemented as descriptors in MOE.
Date 2012-08-10
Author Markus Kossner
Category Molecular Descriptors and QSAR
Downloads 46
Details
Classification of Organic Molecules by Molecular Quantum Numbers
Kong T. Nguyen, Lorenz C. Blum, Ruud van Deursen, and Jean-Louis Reymond
ChemMedChem (2009), 4:1803-1805
DOI: 10.1002/cmdc.200900317

USAGE:
1. Save and load this function
2. The 42 mqn_* Descriptors will be available in MOE
Surfaces get moved along with the atoms that define them.
Date 2012-07-01
Author Martin Santavy
Category Graphics and Rendering
Downloads 32
Details
Run the file. A task called 'SurfSync' will show in the Cancel menu (and stay there). If you have a surface around some atoms and then move the atoms, the surface will move with them.

- If only a subset of defining atoms is moved, the surface will try to superpose itself on all the defining atoms but will not change shape. (To change the shape of the surface, you must select it in the surfmap panel and press Apply).

- The surfaces will follow atoms only while the task (named 'SurfSync') is running.

- A new instance of SurfSync will destroy any previous instances and will reset all surfaces according to the current positions of atoms that define them.
RDF descriptors in a variety of flavours
Date 2012-06-13
Author Markus Kossner
Category Molecular Descriptors and QSAR
Downloads 36
Details
DESCRIPTION:

Prediction of three-dimensional molecular structures using information
from infrared spectra
Hemmer, MC and Gasteiger, J
Analytica Chimica Acta 420 (2000) 145-154

NOTE: Different scaling factors can be found in the literature.
This code does not apply any scaling facor, i.e. both, factor
"f" and "B", as sometimes refered to in the literature,
are both set to one.



This code implements RDF descriptors in a variety of flavours:
1.) Distance:
- topological distances: tRDF*
- geometric distances: gRDF*

2.) Properties encoded:
- none/unweighted: ?RDF*u
- atomic mass: ?RDF*m
- atomic volume: ?RDF*v
- electronegativity: ?RDF*e
- SMR increments: ?RDF*s
- SLogP increments: ?RDF*L
- VSA values: ?RDF*a
- partial charge: Q_?RDF*c
- positive partial charge: Q_?RDF*c++
- negative partial charges: Q_?RDF*c--
(NOTE: partial charges need to be calculated
via DBV|Compute|Molecule|Partial Charge)

- E-Hueckel based strength parameters for hydrogen bond donors
or acceptors: ?RDF*ha and ?RDF*hb



USAGE:

1. Save and load this file
2. The descriptors will be available via DBV|Compute|Descriptors...
3. You can find them by typing "tRDF" or "gRDF" in the
filtering textbox
Moreau/Broto's Autocorrelation vector descriptors
Date 2012-06-13
Author Markus Kossner
Category Molecular Descriptors and QSAR
Downloads 37
Details
DESCRIPTION:

Moreau/Broto's Autocorrelation vector descriptors
Moreau, G.; Broto, P. NouV. J. Chim. 1980, 4, 359-360.



This code implements ATS descriptors in a variety of flavours:
1.) Distance:
- topological distances: tATS*
- geometric distances: gATS*

2.) Properties encoded:
- none/unweighted: ?ATS*u
- atomic mass: ?ATS*m
- atomic volume: ?ATS*v
- electronegativity: ?ATS*e
- SMR increments: ?ATS*s
- SLogP increments: ?ATS*L
- VSA values: ?ATS*a
- partial charge: Q_?ATS*c
- positive partial charge: Q_?ATS*c++
- negative partial charges: Q_?ATS*c--
(NOTE: partial charges need to be calculated
via DBV|Compute|Molecule|Partial Charge)

- E-Hueckel based strength parameters for hydrogen bond donors
or acceptors: ?ATS*ha and ?ATS*hb

USAGE:

1. Save and load this file
2. The descriptors will be available via DBV|Compute|Descriptors...
3. You can find them by typing "ATS" in the filtering textbox
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An implementation of Sterimol descriptors
Date 2011-12-23
Author Guido Kirsten
Category Molecular Descriptors and QSAR
Downloads 199
Details
Calculates the Sterimol descriptors L, B1, B2, B3, B4, B5.
Load file into MOE. The six new descriptors will appear in the Descriptor panel.
Descriptors are calculated for the whole molecule if no attachment point (A0) is found. If an attachment point is found L is measured along the substitution axis and B1-B4 orthogonal to the substitution axis. (see picture)
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GAMESS-FMO interface for MOE
Date 2011-12-19
Author Shinya Nakamura
Category Basic Molecular Tools
Downloads 87
Details
MOE-FMOutil consists of several tools and DEMO files.
> Structure preparations (Truncation around the ligand, etc.)
> Input-file preparation (Suport: PIEDA, FMO/PCM, FMO-D optimization, partial MP2 PIE etc.)
> Read and validate GAMESS-FMO inputfile
> Import optimize coodinates into MDB file
> Output Analysis (Summation of Pair Interaction Energy for insisted fragments, Visualize Charge transfer, etc.)

USAGE:
Load fmoutil.svl and type FMOutil []
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Custom Cartoon Display of Molecular Fragments Incl. Carbohydrates and Nucleic Acids
Date 2011-12-09
Author Hooman Shadnia
Category Graphics and Rendering
Downloads 42
Details
This script draws cartoons of molecular fragments, to provide non-atomic visualization of macromolecules. The molecular fragments and the corresponding cartoons are read from a customizable dictionary. The current dictionary includes some carbohydrates and nucleic acids.
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This provides algorithms for automatically assigning standard triple resonance NMR spectra on proteins to the amino acid sequence.
Date 2011-11-02
Author Gordon Crippen
Category Protein Tools
Downloads 20
Details
As described in the accompanying documentation, SEBAS is a program for automatically assigning NMR spectra to a given amino acid sequence. Peak files in standard Sparky and/or NMRPipe format are curated with possible interaction with the user. The curated files are used to construct generic spin systems (GS), and then these are assigned to the given sequence (in FASTA format). Possibly multiple assignments are written out as an Excel spreadsheet for easy examination by the user. Several different assignment algorithms are offered, some being suited to extensive examination of all possible assignments of high quality data, and others are better suited to finding any sort of consensus of assignment from noisier data coming from fewer different triple resonance experiments.
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Draws a cone to indicate the dipole moment of the molecule.
Date 2011-11-01
Author Andrew Henry
Category Graphics and Rendering
Downloads 141
Details
Usage: Simply choose MOE | File | Open then double click on
visualize_dipole.svl

For it to be available for use by all of the users of MOE, create a directory called $MOE/lib/svl/custom/run and save this file to that directory. eg on Windows and Linux, this might be:

c:\moe\lib\svl\custom\run\dbimport.svl
/usr/local/moe/lib/svl/custom/run/dbimport.svl

For the script to be available for use by a single user, then it is best to create a directory in your home directory called svl, and create a directory called run in that directory. Save this file into that directory. eg on Windows and Linux, this might be:

c:\Documents and Settings\user_name\svl\run\dbimport.svl
/usr/people/user_name/svl/run/dbimport.svl
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This plugin computes the change in exposed surface area upon ligand binding to the receptor.
Date 2011-10-07
Author C. Williams
Category Protein Tools
Downloads 314
Details
DESCRIPTION:

This plugin computes the change in exposed surface area upon ligand binding to the receptor.

USAGE:

Select the ligand atoms and run this code. The results will be printed into the Commands Window: exposed surface area for a 'free' ligand in its current conformation, and the exposed surface are for the ligand in its complex with the receptor.
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Workflow showing the usage of the Scaffold Replacer Node
Date 2011-09-19
Author Guido Kirsten
Category Basic Molecular Tools
Downloads 27
Details
Simple workflow that shows the usage of the Scaffold Replacer Node.
Requires MOE Extensions 2.0.2 and KNIME 2.4.0
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Plot ROC "receiver operating characteristic curves
Date 2011-08-15
Author CCG Support
Category Molecular Descriptors and QSAR
Downloads 94
Details
Description:
Calculate the ROC curve based on a real activity field and a
predicted activity field. The user has the option of ascending ranks
(small is good) or descending ranks (big is good - default) in both
the real and predicted activity fields. If the used specified
a prediction threshold, a confusion matrix of predicted active/
inactive vs. actual active/inactive is calculated based on the
threshold.

Usage:
(1) Run this file (TED | SVL | Save and Run...)
(2) You will be prompted for a database
(3) The ROC Plot panel will open.
(4) Use the option pull-downs to specify the real and
predicted activity fields. Set the thresholds for each if appropriate.
(5) Press 'Calculate' to perform the matrix calculation.
(6) Use the Radio button at the bottom of the panel to
display the results as either absolute numbers or percentages.
(7) Various statistics are also displayed.
(8) Press the 'Dump Plot to Text' to produce a tab-delimited
file that can be imported in to Excel
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Plot ROC "receiver operating characteristic curve
Date 2011-08-15
Author CCG Support
Category Z- Obsolete Code
Downloads 248
Details
ROC "receiver operating characteristic curve" see following links

http:www.statsoft.com/textbook/glosr.html#ROC
http:www.anaesthetist.com/mnm/stats/roc/

Given a database with predicted active and true activity,
the function plots an ROC curve. Sample data from one of the
above links is given at the end of this file.

Usage:
(1) Load this function
(2) Open the database with the activities and predictions.
(3) Enter

svl> ROC_Plot[]

at the SVL command line

(4) Choose the predicted active and the true active fields
(5) Set the thresholds so that compounds where

'Activity Field >= Activity Threshold'

'are deemed "active"' and compounds where

'Prediction Fiels >= Prediction Treshold'

are deemed 'predicted active'

(6) Press 'Plot' to plot the ROC curve.

HITS are CORRECT PREDICTIONS
MISSES are INCORRECT PREDICTIONS

The area beneath the curve is also reported

(7) Press 'Report' to produce a text report including
area calculation and TPF vs. FPF data
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Converts .kont files into MOE's grid format. The output files can be visualized with Surfaces and Maps
Date 2011-07-27
Author Guido Kirsten
Category Basic Molecular Tools
Downloads 50
Details
Start the program with "Run SVL File". The program will ask for a .kont file. All grids contained in the .kont file will be exported as .grid files in MOE grid format into the directory of the .kont file.
The exported grid files can be visualized with MOE's Surfaces and Maps.

Please note: The binary GRID format conversion is still "experimental". If you encounter problems please contact gkirsten @ chemcomp.com
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A low footprint GUI to set various atom properties on a per chain basis, e.g. visibility, render mode. The interface is based on an original idea by Francis Atkinson and Andrew Leach (GSK). (Revised 18 July 2011)
Date 2011-07-18
Author Simon Grimshaw
Category Basic Molecular Tools
Downloads 118
Details
DESCRIPTION:
A low footprint GUI to set various atom properties on a per chain basis, e.g. visibility, render mode. The interface is based on an original idea by Francis Atkinson and Andrew Leach (GSK).

The application allows you to set the visibility for particular chains (or show only one chain, or show all or no chains), set chain names and tags, select individual or all chains, change the rendering mode from line bonds to stick bonds and alter the potential settings (none, fixed, inert). Which hydrogen atoms are shown can also be changed, and carbon atoms can be coloured by chain or by unique chain tags.

The application will remember if you have hidden atoms in a particular chain, e.g. if you are showing only the pocket atoms from a receptor. If you wish to reset the set of hidden atoms for a particular chain, simply hold down the Shift key and click on the visibility toggle button. If you wish to reset the whole system's hidden status, Shift click the "Show" button at the top.

See the bubble help for the action of each button by holding the mouse pointer over it for a few seconds.

Note:
If there are more than a certain number of chains, the buttons are spread over a set of pages, controlled by < and > buttons in the bottom right of the panel. Currently the maximum number of rows, 18, is hard coded within the script in line 88.

You can make the Chain Manager window stay in the same place when it is recreated after creating or removing chains, set the SAVEPOS constant to 1 in line 89.

USAGE:

1. Save this function
2. Run the SVL, e.g. use the MOE | File | Open panel, browse to chainmanager.svl and click OK.
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Includes instructions and files necessary to install MOE on Solaris 10
Date 2011-04-26
Author Andrew Swann
Category Z- Obsolete Code
Downloads 7
Details
MOE2005.06 does not support installation on Solaris 10 (due to the fact it was released prior to Solaris 10). The included files will be necessary to install MOE on a machine with Solaris 10, as well as register the license manager as a Solaris 10 service.

Files included in MOE_Solaris.tar:
readme.txt - these instructions
install.sh - MOE install script
arch.sh - MOE architecture redirection script
lmgrd.xml - lmgrd service file

Instructions:
1. Install MOE with the included install.sh file with the -i option. For example, if the install.sh file is at the current directory, and the MOE CD is mounted, type:
./install.sh -i /cdrom/moe_2005_06

2. Replace $MOE/bin/arch.sh with the included arch.sh file.

3. Install the license manager as follows:

a. Edit the paths to your MOE/bin, license file, and log file directories on each of the "exec" lines. In this particular file, MOE is installed at /usr/moe, and the log file resides in the root MOE folder.

b. Copy lmgrd.xml to /var/svc/manifest/application/lmgrd.xml (this is not essential, but this is where all of the other service manifest reside)

c. Type "svccfg import /var/svc/manifest/application/lmgrd.xml"

d. Type "svcadm enable application/lmgrd"

e. The service is now registered and started. It will start on each boot. To stop the license manager, type "svcadm disable application/lmgrd", and to reread the license file, type "svcadm refresh application/lmgrd". To restart the license manager, type "svcadm restart application/lmgrd"

OR
a. Copy the "lmgrd_init" file from the SGI architecture included in MOE to /etc/rc3.d/S95lmgrd_init (replacing the appropriate variables in the script).

b. Treat it as you would any other legacy (pre-Solaris 10) service.


Known Issues:
1. lmgrd is run as root. This can be easily changed by adding "username -c " to the beginning of the commands preceded by "exec" in lmgrd.xml

2. The log file is continuously written, so it may get too large. Simply make a copy of the current log, delete it, and restart the license manager.
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Post conformational analysis tool: plots observed values of multiple dihedrals in a molecule.
Date 2011-04-08
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 44
Details
This application facilitates exploration of the conformations generated via a conformational search method, including LowModeMD.

It scans a database of conformers and displays the global minimum geometry in the MOE window. Then it display a 2D plot of observed values of 'important'
dihedrals. Next, it allows selection of one or more observed dihedrals and displays the values and some statistics in the MOE window, and selects the
corresponding conformations in the database viewer.
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Fingerprint using pharmacophore typing with distances calculated over a reduced molecular graph.
Date 2011-02-09
Author Simon Grimshaw
Category Pharmacophores and Fingerprints
Downloads 51
Details
Fingerprint using pharmacophore typing with distances calculated over a reduced molecular graph, after JCIM 2006, 46, 208-220 (DOI: 10.1021/ci050457y)

USAGE:

1. Save and load this function e.g. using MOE | File | Open, browse to ph4erg.svl and click "Load SVL".
2. Calculate fingerprints using DBV | Compute | Fingerprints: the new fingerprint will be available, called FP:ErG. Searches can be performed using the DBV | File | Similarity Search tool.

At the moment the amount of fuzzy incrementation has a default of 0.3. To alter this, set the value of a variable called ERG_FUZZY at the command line, for example:

svl> ERG_FUZZY = 0.2

Fuzzy incrementation as implemented here differs slightly from that described in the paper. The paper suggests that for a particular bit that has e.g. three matching paths in the molecule, that bit and its two neighbours would be:

3*FUZZY, 3, 3*FUZZY

In this implementation that has been changed to:

FUZZY, 1 + FUZZY, FUZZY

In addition each bit can only be incremented once, so if bits A and C were matched in the molecule, bit B would only be incremented once. This has been done in order for the similarity scores to more closely match the ones presented in the paper. If the scheme described in the paper is used, similarity scores are too low due to the large value in the main bit.

The correlation between the scores from this SVL and the paper are still not 100% - I am looking into the reason for this. In my tests with thiscode, the similarity scores are always slightly too low.

The collapse of hydrophobic ring systems into a single Hf feature will occur if any two or more ring systems share more than two atoms.

There is no limit to the number of flip-flop atoms (atoms that are both donor and acceptor). Instead, a descriptor is included in the code (accessible via the MOE tool DBV | Compute | Descriptors, called "flipflop". This allows the user to filter their databases manually prior to fingerprint calculation.

_Normalising the fingerprint_
A database can be used to calculate a normalisation vector, that is a set of numbers by which each fingerprint bit will be multiplied when comparing similarities. This allows the effect of overly-represented bits to be reduced. To create a file of normals, use this command:

svl> CalculateErGNormalisation [mdbfile, normalsfile]

Where both mdbfile and normalsfile are tokens containing the filename of the input MDB file and the output text file. If normalsfile is null then the filename will be {mdbfile}_ergnormals.txt.

A file of normals can be "loaded" into MOE using this command:

svl> LoadErGNormals normalsfile

This will then be used when performing similarity searches.

_Visualisation and Reverse Fingerprinting_

Diagnostic tools are available in this code:

1. If you load a molecule into the main MOE window and run this SVL (e.g. use the MOE | File | Open panel, browse to ph4erg.svl and click OK) then the feature types assigned to the molecule will be drawn in the system. In addition the list of features and the distance matrix of features will be printed in the SVL Commands Window. Only the first feature distance matrix is printed in the case that the molecule contains flipflop atoms. If there are flip flop atoms then for each possibility a different graphic object is created. These can be viewed individually using the Graphics Object Manager.

2. With this SVL file loaded into MOE you can see the scores for each property-distance-property triplet with a molecule loaded in MOE using this command:

svl> Reverse_ErG_Fingerprint ph4_ErG_Fingerprint Atoms[]

Fuzzy incrementation is applied, but weighting is not.

This code is also compatible with the MI reverse fingerprinting package, although as of 10th Sept 2009 it does not elaborate flip flop atoms.

3. ErG Bit Descriptors
This will create a new column for each of the bits in the ErG fingerprint (default settings will create 315 new fields). These are then filled with the counts for each bit. Fuzzy incrementation is applied, but only once, i.e. if a bit is matched three times, that bit and its two neighbours would be:

1*FUZZY, 3, 1*FUZZY

To use this tool, enter the following SVL Command:

svl> ErG_Bit_Descriptors mdb

where mdb is a token containing the filename of an MDB, e.g. 'test.mdb'.

4. ErG Bit Descriptor Heat Map
This will load the descriptors calculated using the previous command from the database and create a graphic object showing the counts as a heat map coloured using a black-body palette.

svl> ErG_Bit_HeatMap mdb

The graphic can be saved in various image formats (JPG, PNG, etc) by clicking the Export button in the Heat Map panel.
Calculate the chirality of the distribution in space of some atomic property.
Date 2010-12-30
Author Gordon Crippen
Category Chirality Tools
Downloads 13
Details
Wildman & Crippen, J. Chem. Inf. Comput. Sci., 43, 629-636 (2003).

Given the 3xN array of Cartesian coordinates of N atoms plus N associated "weights" or property values of the atoms, calculate a chirality value for the distribution of the weights in space. The weights must be positive.

This corresponds to CIP chirality when the weights are the atomic weights or priorities of the four substituents of a chiral center, and the coordinates are the coordinates of the substituents. If the four substituents are coplanar or if two weights are the same, the calculated chirality is zero. The mirror image of the configuration gives the opposite sign chirality.

The difference is that this chirality measure is a continuous function of the coordinates and the weights of four or more points. Not only does it give the same value when the coordinates are transformed by a translation or proper rotation, but the value is unchanged when the coordinates or the weights are multiplied by a positive constant.
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SMARTCypMOE predicts positions in drug-like molecules that are likely sites for metabolism by cytochromes P450. It acts as a wrapper for the SMARTCyp java program.
Date 2010-11-08
Author Patrik Rydberg
Category Basic Molecular Tools
Downloads 124
Details
SMARTCyp predicts positions in drug-like molecules that are likely sites for metabolism by cytochromes P450. It acts as a wrapper for the SMARTCyp method within MOE.

SMARTCypMOE processes single molecules loaded in the main MOE window or groups of molecules stored in a MOE molecular database. Molecular databases can be processed interactively from MOE’s Database Viewer or in batch mode via the moebatch program. Reactivity ranks and scores are added to the molecular database and the results can be viewed graphically in the MOE Database Browser.

Using a heme model system,Rydberg et al. computed transition state energies for more than 200 fragments and from these energies and one accessibility-like descriptor a very simple scoring function was deduced which is used to score and rank atoms in a molecule. The model covers all common reactions in P450s and has a good performance for all P450 isoforms except 2C9 and 2D6.

Score = Reactivity – 8 x Accessbility

Where Reactivity is the activation energy in kJ/mol and the accessbility is the span descriptor which measures the relative topological distance to the end of the molecule (which always is between 0.5 and 1).

Prerequisites:
The SMARTCyp executable jar file which can be downloaded at http://www.farma.ku.dk/smartcyp/

The distribution is a zip archive containing the SVL script (cypscore.svl), entries for the moe-menus file (moe-menus-cypscore) and a manual (SMARTCypMOE.pdf), which provides full details on how to install and use the script.

References:
Patrik Rydberg, David E. Gloriam, Jed Zaretzki, Curt Breneman and Lars Olsen (2010) "SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism" ACS Med. Chem. Lett., 1, 96-100
Patrik Rydberg, David Gloriam and Lars Olsen (2010) "The SMARTCyp cytochrome P450 metabolism prediction server" Bioinformatics, DOI: 10.1093/bioinformat
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Calculates data for histogram for a numerical field in an MDB and save the histogram data in a separate MDB enabling
1) to sample the representatives from the bins with an uniform width
and
2) to plot the histogram of huge database with a commonly used spreadsheet program in which the readable data size is limited, e.g.,
with Microsoft Excel it is limited to 65536 rows and 256 rows.
Date 2010-11-08
Author Ryoichi Kataoka
Category MOE Database Tools
Downloads 49
Details
Divides numerical data into bins defined by the lower bounds, the upper bonds
and width. Optionally, bins are divided by the number of bins if the width is
not set. The values normalized to the lower bounds of bins will be written in
the input MDB and the lower bounds and the frequencies of bins will be output
to the other MDB.

The histogram of the values of fieldname and their lower bounds
within their bins in Gaussian distribution will be plotted.

Installation:

(a) Place dbv_histogram.svl in $MOE/lib/svl/custom/ directory
and invoke MOE for the general use
(b) Place dbv_histogram.svl in $HOME/svl/ directory
and invoke MOE for the personal use
(c) From the MOE | File | Open panel, select this file
and click the "Load" button for the temporal use.

USAGE:

moe> db_Histogram [filename: '/home/userid/work/filename.mdb', \
nfname: 'SlogP', \
esel: 0, lb: -9, ub: 9, w: 0.5]
('\' stands for the continuation, i.e., enter these in a single line)

or

1. Select a field in MDB on DBV,
2. DBV | CLI | dbv_Histogram [lb: -9, ub: 9, w: 0.5]

where the parameters are:

filename: the mdb filename
If not specified, the filename of the default view will
be used.
nfname: the numeric field name to calculate
The default is the first numerical field name.
esel: calculate only on the selected entries
lb: the value of the lower bound
The default is the minimum value in the field.
ub: the value of the upper bound
The default is the maximum value in the field.
w: the width of the bins
If not specified, (ub - lb) / nbin will be used.
nbin: the number of bins
The default value is 10.
If w is specified, (ub - lb) / w will be used.
openodb: If on, open the output database in database viewer
The default is 1 (on) for GUI
and 0 (off) for batch mode.
drawhis: If on, draw the histogram
The default is 1 (on) for GUI
and 0 (off) for batch mode.

e.g.,

DBV | CLI | dbv_Histogram [nfname: 'SlogP', lb: -9, ub: 9, w: 0.5]

or

1. Select a field,
2. DBV | CLI | dbv_Histogram []
3. Set optional parameters and click OK

if w is given, nbin will be ignored.

The outputs are:
filename.mdb:
l_fieldname: the lower bound of the descriptor in each bin

filename_fieldname_histogram.mdb
l_fieldname: the lower bound of the descriptor in each bin
f_fieldname: the frequencies of the entry in each bin

The histogram between the values of fieldname and their lower bounds
within their bins in Gaussian distribution will be plotted.
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Generates input and reads output for Z-matrix optimisations and electrostatic potential calculation in Gamess.
Date 2010-10-28
Author Michael Charlton
Category Utilities
Downloads 35
Details
There are three main routines you can call :

gamin 'gamess.log'
Update co-ordinates and charges of current Moe molecule with those from the gamess output file. You MUST have the appropriate molecule already read into Moe or the results will be unpredictable.

gampotgui 'gamess.log'
Read the molecular electrostatic potential (MEP) from the gamess output. Contour the MEP on a grid around the molecule using a Gui to control the three contour levels. Works with the 2010 version of Gamess (WinGamess 10).

gamess_input_gui []
Produces a Gui to generate basic Gamess input files. input is a 6-31G** Hartree Fock calculation. You will need to change the basis set manually but you can select an option in the Gui to perform a B3-LYP calculation. The input file is generated when you enter a file name and press return. A .moe file of the current structure is saved at the same time. This is needed when you come to analyse the results.

There is an option to select a Z-matrix (i.e. internal co-ordinate) input file / optimisation rather than the cartesian input normally produced by Moe. This can lead to faster optimisation - I achieved optimisation of 3-Me pyridine in 7 cycles rather than 42 with cartesian, so quite a useful saving.

It is possible to select a partial Z-matrix optimisation in which some degrees of freedom (DoFs) are frozen at their input values. This is handy for calculating strain energies, where you can freeze all torsion angles and allow the bonds and angles to relax. A Gui is generated which allows interactive selection of the frozen DoFs.

The input file for the MEP calculation can also be generated. This option generates a grid of points around the molecule which can be manipulated using a Gui to give the size of grid you need to observe features of interest.

Note : optimisation will move the molecule slightly from the starting point, so you may want to optimise first and then do a second calculation without opt. to calculate your MEP.
Z-matrix optimisation moves the atoms to the co-ordinate origin, so your grid WILL be in the wrong place.

The default version of Gamess limits you to only 100 grid points. You will need to recompile it. Go to the source directory in the unpacked distribution and edit prplib.src. Global replace MXPTPT=100 with MAXPTPT=99999. Then save and follow the compilation instructions. (Easier on linux than windows as you will need compilers, which only come free with good operating systems).
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This script has functions that perform simple but useful database related tasks such as:
- select every nth entry in a MOE database
- index a group based on a field identifier
- select duplicate entries in a specified field
- replace exiting entries in a specified field
Date 2010-10-28
Author Kaushik Raha
Category MOE Database Tools
Downloads 100
Details
How to use the script:

In MOE command window:
load 'selectNentry.svl'

Individual functions can be used as follows:

selectNtry [num_entry, which_entry, entry_option]
examples:
selectNtry [20,0,0] for selecting every 20th entry of the database
selectNtry [20,1,0] for selecting every 21st entry of the database
selectNtry [20,2,0] for selecting every 22nd entry of the database
selectNtry [5,0,1] for selecting every 5th entry and creating a new group for it


indexgroup [fieldname, indexname]
Where:
fieldname: name of the field that needs to be indexed
indexname: name of the index field that will be created
example: indexgroup ['mseq','Rank']

selectdups [fieldname]
Where:
fieldname: name of the field in which duplicates will be selected
example: selectdups ['CMPDID']
Note: The field should be sorted before running the command

replacentry [fieldname, searchstrng, replacestrng, esel]
Where:
fieldname: name of the field in which the string to be replaced will be searched for.
searchstrng: this string will be searched in the fieldname of the database
replacestrng: this string will replace the search string in all entries of the database
esel: if set to 1 will operate on selected entries otherwise entire database
example: findentry ['HIT_TYPE',"HTS1","HTS2",1]
Note: string for searching and replacement should be in double quotes "
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load the restraints from a tab-delimited file or save from MOE to such a file. Also: compare the restraints vs current system.
Date 2010-09-20
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 24
Details
DESCRIPTION
This utility allows import/exporting MOE-Restraints from/to tab-separated-text files. It also compares the existing MOE-restraints vs. the currently loaded
structures and saves the 'unsatisfied' restraints to a text file.
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Breed operation on aligned structures of A-B-C formula where B is a ring system.
Date 2010-09-20
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 18
Details
This function allows BREED operations on aligned structures with general formula of A-B-C where B is a ring system. For n input structures, it generates all A(n)-B(n)-C(n) combinations. A demo input file is provided (_rb_demo.moe).
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Marks protomers generated via sdwash operations. Can be used to separate them from tautomers.
Date 2010-09-20
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 32
Details
The -protomer switch in sdwash creates the tautomers along with protomers.In case enumerating new tautomers from the input structures is undesirable this program can be used to mark the protomers in the enumerated database, so that they can be separated from the tautomers.

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An interface to the CEPOS InSilico Ltd. programs ParaSurf and ParaFit.
Date 2010-09-10
Author David Whitley
Category Basic Molecular Tools
Downloads 23
Details
This is a set of scripts that allow the CEPOS InSilico Ltd. programs ParaSurf and ParaFit to be run from within MOE. ParaSurf generates molecular surface properties based on semi-empirical molecular orbital calculations. ParaFit superposes and compares molecules using the spherical harmonic expansions of the molecular surface and properties calculated by ParaSurf. The scripts enable the user to run ParaSurf on single molecules or molecular databases; use ParaSurf descriptors and rotationally invariant fingerprints (RIFs) in MOE QuaSAR; visualize ParaSurf surfaces and properties; align molecules with ParaFit based on their ParaSurf properties; and produce ParaFit 'canonical' alignments.

Prerequisites:
ParaSurf and ParaFit are available from CEPOS InSilico Ltd. (www.ceposinsilico.com). ParaSurf requires the results of semi-empirical molecular orbital calculations, which can be provided either by VAMP or by a public domain version of MOPAC that is available for free download from www.ceposinsilico.com.

The distribution is a zip archive containing the SVL scripts, entries for the moe-menus file and a manual in PDF format that provides full details on how to install and use the scripts.

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RDF Descriptors
Date 2010-08-02
Author Guido Kirsten
Category Molecular Descriptors and QSAR
Downloads 62
Details
Radial Distribution Function Descriptors
based upon:
Hemmer, M. C.; Steinhauer, V.; Gasteiger, J.
J. Vibrat. Spect., (1999), 19, 151-164
The Coefficients f and B have been derived from fits against literature data.
This is an independent implementation of J.Bajorath's structural/property keys, as published in J.Chem.Inf.Sci. 2003
Date 2010-07-21
Author CCG Support
Category Pharmacophores and Fingerprints
Downloads 346
Details
This is an independent implementation (D.Bondarev) of the reference below:

J.Chem.Inf.Comput.Sci. 43(4), pp. 1151-1157, 2003
Design and Evaluation of a Molecular Fingerprint Involving the Transformation of Property Descriptor Values into a Binary Classification Scheme. Ling Xue, Jeffrey Godden, Florence Stahura, Jurgen Bajorath.

USAGE:
Load this file with the MOE File Open panel (click OK).

You can then use MOE fingerprint tools as usual.

Compute the MPMFP fingerprint or use any fingerprint tools (including any scripts from this website). The fingerprint code is MPMFP, the similarity metric code is avg-tanimoto.
Implementation of the CypScore method to predict positions in drug-like molecules that are likely sites for metabolism by cytochromes P450.
Date 2010-07-06
Author David Whitley
Category Basic Molecular Tools
Downloads 114
Details
This is an implementation of the CypScore method devised by Hennemann et al. for the prediction of cytochrome P450 reactive sites in drug-like molecules. The script processes single molecules loaded in the main MOE window or groups of molecules stored in a molecular database. Molecular databases can be processed interactively from MOE’s Database Viewer or in batch mode via the moebatch program. Reactivity scores are added to the molecular database and the results can be viewed graphically in the MOE Database Browser.

For six oxidation reactions, Hennemann et al. derived linear models predicting an atom’s reactivity from the values of descriptors calculated by ParaSurf, with each model producing reactivity predictions on an individual scale. The original paper described a procedure to establish a common reactivity scale for all the models, providing a CypScore value for each atom in the range from 0 (stable) to 100 (reactive), and implemented this procedure for a proprietary data set. Unfortunately, Hennemann et al. do not include sufficient detail to define completely the relationship between the original model values and the scaled scores, and it is not possible to reproduce the missing information as the data from which it was derived is not available publicly. To overcome this, this script employs a common reactivity scale that is a close approximation to the one used by Hennemann et al., derived from secondary information in the original paper through a process described in the accompanying manual. Consequently, the results obtained will approximate closely, but not match exactly, those in the original publication.

Prerequisites:
The CypScore predictions are based on molecular surface descriptors calculated by ParaSurf, which is available from CEPOS Insilico Ltd. (www.ceposinsilico.com). ParaSurf requires the results of semi-empirical molecular orbital calculations, which can be provided either by VAMP or by a public domain version of MOPAC that is available for free download from www.ceposinsilico.com.

The distribution is a zip archive containing the SVL script (cypscore.svl), entries for the moe-menus file (moe-menus-cypscore) and a manual (CypScoreMOE.pdf), which provides full details on how to install and use the script.

Reference:
M. Hennemann, A. Friedl, M. Lobell, J. Keldenich, A. Hillisch, T. Clark and A. H. Goller. CypScore: quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory. ChemMedChem, 2009, 4
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2010.02.13 version of Genetic Algorithm based QSAR
New Features in ver.2006.08.12
- Added 'Write Script' button to output script file for batch calculation without running interactively.
- mdb2fit[] command allows users to convert model to .fit file (Note:.fit file cannot support model with operant such as sqr, log etc.)
- Automatically plot important descriptors in plot area of _trj.mdb output.
New Features:
-essential descriptor option
-support non-linear model with lots of SVL functions such as sqr, sqrt, log....
-Dynamic link to database viewer
Date 2010-07-01
Author junichi goto
Category Molecular Descriptors and QSAR
Downloads 715
Details
Usage:
(1) Load this function
(2) Enter

svl> GA[]

at the SVL command line

You can get linear model, perform cross validation and
save your models in mdb file format from this panel.

To evaluate new molecules with your model, enter

svl> ModelCalc[]

-----------
TUTORIAL:

'$MOE/sample/mol/blood_brain.mdb' may be used as a tutorial.

(1)Calculate 32 VSA descriptors and TPSA
(2)Run QuaSAR-Evolution with default parameters
Equation file 'ga_*_eq.mdb' and trajectory file 'ga_*_trj.mdb' will open
(3)Plot SMR_VSA4 and SlogP_VSA0 in plot area of trajectory file.
and observe how equations evolve
(4)Calculate TPSA descriptor
(5)Click 'CONTINUE'
(6)Plot TPSA and observe equations
You will see that the combination of SMR_VSA4
and TPSA is very important for good model
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A nonparametric statistic that can detect linear and nonlinear functional relationships in bivariate data samples.
Date 2010-06-09
Author Gordon Crippen
Category Miscellaneous
Downloads 24
Details
Given a sample of (x,y) points where x values are not necessarily uniformly spaced, kappaxyval [x, y] returns 0 if there are just two tight clusters of points, 1 if y is a linear function of x, >1 if y is a nonlinear function of x and/or there is some noise, and 2 if the points are a uniform random scatter inside some rectangular region. This can be handy for automatically detecting linear and nonlinear relations in samples of points, whereas the usual correlation coefficient may be nearly zero for nonlinear relations. This also lends itself to fitting nonlinear and/or noisy samples of points. yfit = fitKxy [x,y] gives a fitted y value for each sampled x value. The yfit values form a relatively smooth curve.

All this is described in: G.M. Crippen, Computational Biology and Chemistry, 33, 357-360 (2009).
An interface for easy editing of torsion angles in the main MOE window.
Date 2010-04-12
Author CCG Support
Category Basic Molecular Tools
Downloads 35
Details
Simply run the function, e.g. by choosing MOE | File | Open then double click on torsion_editor.svl. Once the application is running one needs to select two atoms that constitute a rotatable bond. This is done by selecting the first atom then the second atom (by holding down the shift key). Atoms attached to the second selected atom will be the ones that move when the bond is rotated (Alt - left drag).

- to visualize which half of the molecule will rotate once a selection is made, toggle on Show bond arrow. The arrowhead points toward the movable portion

- to reverse which half of the molecule will rotate click on the Reverse button

- to see the current value of the selected torsion toggle on Show meters. Note the values run from 180 degrees to -180 degrees in a clockwise sense when the rotatable atom is in front

- to add a torsion to the list, select a valid set of atoms then click on Create. The atoms that comprise the torsion, the original angle (when the torsion was added to the list) and the current angle is shown. Now whenever this value changes, it will be updated in the list (and the meters as well if Show Meters is toggled on)

- to reselect a torsion in the list, simply click on it and the corresponding atoms will be selected in MOE

- to set a torsion back to its original value, select it in the list and click Reset. (The original torsion angle is value that existed when the torsion was added to the list.)

- to delete a torsion form the list, select it then click on the Delete button

Important Note: This application works by FIXING (MOE | Edit | Potential | Fix) atoms in space to force the required portion of the molecule to rotate. If you decide to minimize the system while the editor is running please make sure that no atoms are selected as the application may create sets of fixed atoms.
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Sets environment values for a database so that the database browser, will
show the ligand and receptor pocket atoms. The molecules are read from
fields for the ligand and receptor. A score for the docked pose can also
be specified.

A number of sets of receptor, ligand and scores can be specified. However,
a single field can only belong to one of these sets. If you want the same
data to appear in different sets (for instance a Corporate ID as the score),
you need to copy the field.

Fields must always be specified for the ligand and receptor. The score field
is optional.
Date 2010-04-09
Author Andrew Henry
Category MOE Database Tools
Downloads 72
Details
1. Save this script to your hard disk.

2. (a) From the MOE | File | Open panel, select the db_mol_setenv.svl
file and double click with the left mouse button.

(b) Alternatively from the SVL command line, type:

run 'db_mol_setenv.svl'

3. To make these changes from MOE/batch, use the following syntax:

$MOE/bin/moebatch -exit -exec "run ['db_mol_setenv.svl', ['dock.mdb',
['ligmol', 'ligmol1'], ['recmol', 'recmol1], ['score1',[]]]]
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Show and colour by sequence similarity and identity in the Sequence Editor. Output alignment and scores to HTML report.
Date 2010-03-31
Author Simon Grimshaw
Category Protein Tools
Downloads 92
Details
Score the sequences in the main MOE window by similarity. The similarity matrix is used from the default setting for the MOE system (blosum62 by default), but you can pick a different one from the list. The identity and similarity between two chains is shown in the panel. If you select the "Color Residues" checkbox then the residues will be colored so that similar residues are green and dissimilar residues are red. If you have any chains selected, the colouring and sequence similarity and identity scores are restricted to selected chains.

If you click the "Report" button, then an HTML file is written out with the sequence alignment and the similarity matrix, comparing all the sequences against all the others.

This matrix is not symmetrical - in one half of the matrix the scores are divided by the number of amino acids in one sequence. In the other half of of the matrix, the scores are divided by the length of the other sequence.

If you have any residues selected in the Sequence Editor when you click the "Report" button, then the rest of the residues in the same column will be selected. The similarity matrix in the HTML file will only consider the residues in those columns. In the sequence alignment, the residues which had been selected will be shown in bold and upper case. Unselected residues will be in the
normal font and lower case.

The rPos residue numbers for the whole alignment and the rUID numbers for the first sequence are shown at the top of the alignment.

In the rPos residue numbering the residue number is shown for the residues where the rPos is a multiple of 10. The residue number is positioned so that the unit digit from the number is above the residue. Residues where the rPos number ends in 5 are shown with a : character.

Similarly, the rUID residue numbers are shown for residues where the rUID is a multiple of 10. If there is an rINS insertion character for the residue, then this is shown. Otherwise if the rUID number ends in 5, then this is shown with a : character. If there is another residue it is shown with a - character. If there is a gap in the sequence for that structure, then a space is shown. rUID residue numbers may not be consecutive or unique.

For instance if you had a stretch of amino acids where the rLetter, rPos and rUID values were as below:

rLetter rPos rUID
A 1 18
C 2 19
D 3 19A
E 4 20
F 5 20A
G 6 25
H 7 26
I 8 27
K 9 27A
L 10 27B
M 11 27C
N 12 28
P 13 29
Q 17 30
R 18 31
S 19 32
T 20 33

----:---10----:---20
--20A:--ABC-- 30---
ACDEFGHIKLMNP---QRST

Note:

The rINS for residue 19A is not shown as it is overwritten by the label for residue 20. The rINS value is shown for residue 20A. There are no residues where the rUID is 21, 22, 23 or 24 so these are missing from the rUID numbering line. There are 3 gaps in the alignment, but there are only 2 spaces shown in the rUID numbering line as the label for residue 30 overwrites one of the spaces.

USAGE

1. Save this file to your hard disk.

For it to be available for use by all of the users of MOE, create a directory called $MOE/lib/svl/patch/run and save this file to that directory. eg on Windows and Linux, this might be:

c:\moe\lib\svl\patch\run\seq_sim_monitor.svl
/usr/local/moe/lib/svl/patch/run/seq_sim_monitor.svl

For the script to be available for use by a single user, then it is best to create a directory in your home directory called svl, and create a directory called run in that directory. Save this file into that directory. eg on Windows and Linux, this might be:

c:\Documents and Settings\user_name\svl\run\seq_sim_monitor.svl
/usr/people/user_name/svl/run/seq_sim_monitor.svl

2. Run this file.
(a) From the MOE | File | Open panel, select this file and click the "Run" button.

(b) At the SVL command line, type:

run 'seq_sim_monitor.svl
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A Method for the Alignment of Molecular Strucures: Maximizing Electrostatic and Steric Overlap
Date 2010-03-31
Author CCG Support
Category Z- Obsolete Code
Downloads 716
Details
A Method for the Alignment of Molecular Strucures: Maximizing Electrostatic and Steric Overlap.
Fifty 3D QSAR descriptors from the paper:
A. Cherkasov, Z. Shi, M. Fallahi, G. Hammond. Successful in Silico Discovery of Novel Non-Steroidal Ligands for Human Sex Hormone Binding Globulin. J. Med. Chemistry, 48, 3203, 2005
Date 2010-01-06
Author Artem Cherkasov
Category Molecular Descriptors and QSAR
Downloads 259
Details
1. Load this file. eg
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

2. In the Database Viewer select the Compute | Descriptors menu.
The new descriptors will be added to the list. If you type
IND_I in the "Filter" box at the bottom of the panel, then just
these descriptors will be shown.

Select the descriptors the you want to calculate and click the OK
button.

Warning: When unparameterised atoms are found, the electronegativity
will be set to -999 and the covalent atomic radius to 0. A warning will
be printed to the SVL command line.
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Provides a GUI to highlight areas of secondary structure within a protein and then allows you to (de)select the residues associated with the region.
Date 2010-01-05
Author Michael Charlton
Category Protein Tools
Downloads 39
Details
You can choose which chain you want to select from with the pull-down. The tool then allows you to visualise specific parts of the secondary structure by adjusting the two sliders.
Residues between the sliders (red) are selected, residues outside the sliders (green) are unselected. You can skip forward or backward one residue using the single arrow buttons. The double arrows take you to the start/end of the current structural feature (e.g. back to the start of the current helix).
Once you have identified the feature you are interested in, you can (de)select the residues in the sequence editor using the buttons at the bottom. You can then show/hide residues or use the Synchronise option etc. in the normal way.
Pressing "done" will return the 2ary structure rendering to how it was when you started.

To use the code, load it into Moe and type SSS []
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Automatic generation of candidate structures from a
pharmacophore pattern.
Date 2009-11-22
Author Vincenzo Tschinke
Category Basic Molecular Tools
Downloads 194
Details
NEWLEAD is a computer program for the automatic
generation of candidate structures. The input for the program
is a set of fragments in the three-dimensional orientation
corresponding to a given pharmacophore model. The treatment
consists in connecting the fragments with spacers assembled
from small chemical entities (atoms, chains or ring moieties).

The results are new structures containing the fragments in
the orientation defined in the input. The program offers
the opportunity of rapidly applying a pharmacophore model
in drug-design by generating automatically a set of chemical
sructures conforming to the model.

This distribution contains several files enabling the use of
NEWLEAD within MOE.

Tschinke, V.; Cohen N.C. The NEWLEAD Program: A New Method for the Design of Candidate Structures from Pharmacophoric
Hypotheses. J. Med.Chem. 1993, 36, 3863-3870.

Binary executable files for NEWLEAD are available for Linux, OS/X and Windows at

http://www.ccl.net/
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GI-MOE is a full-featured SVL-based interface for integrating
quantum calculations into MOE using Gaussian 03.
Date 2009-09-16
Author Andreas Lambropoulos, Ghislain Deslongchamps
Category Utilities
Downloads 98
Details
GI-MOE is a full-featured SVL-based interface for integrating
quantum calculations into MOE using Gaussian 03 as computational back-end. Calculations can be performed on single molecules or on multiple structures (in either .com or MOE .mdb format). Bypassing the cryptic Gaussian command line, various calculations can be performed in GI-MOE including: ground state and transition state calculations (3 methods), checkpoint file restarts, potential scans (with or without geometry optimization), full ONIOM implementation (2-layer and 3-layer), frequency calculations, solvation, and automated RESP charge fitting. Tools for .com file inspection and z-matrix conversion are included. All GI-MOE parameters can be saved and read from a settings file. Calculations can be performed on a local installation of Gaussian or via the GI-MOE remote computing window, which allows for automatic login and submission of GI-MOE jobs to a distributed computing cluster. A complete user manual is provided.
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Performs spectral clustering, as outlined in M.L. Brewer, J. Chem. Inf. Model, 2007 (47), 1727
Date 2009-08-11
Author Michael Charlton
Category MOE Database Tools
Downloads 63
Details
Performs Spectral Clustering, based upon
M.L. Brewer, J. Chem. Inf. Model, 2007 (47), 1727
Code written by M.H. Charlton at Chroma Therapeutics, 2007.

To use this code, load it into MOE and type :
specclus_gui []
Pressing Calculate performs the computation and writes the cluster information to an mdb field '$CLUSTER'.
The code uses precalculated fingerprint fields, but if none is present, it will calculate MACCS FPs for you.
The code needs the tanimoto metric to be applicable to the FP you select.

The code uses two methods of filtering the clusters, as outlined in the paper. The default "threshold" method using a value of 0.85 seems to be quite reliable, although dropping it to 0.65 is often good in the "Diverse Islands" situation (molecules in the clusters are relatively similar, but the clusters are well separated).

Note on timings : the code uses MOE's eigenvector solution function and can get quite time consuming for large sets, potentially scaling with the third power of the number of compounds.
Sample timings 2.66 GHz Xeon, MACCS FPs :
n_mol: 206 500 1000 1500 2000
t(s): 1.1 6.0 24.5 65.4 135.7
fitted line : t=1.14e-08(n^3) + 8.86e-06(n^2) + 4.80e-03(n) - 0.268

Times for larger mdbs depend on the value of the threshold used, but compare well with MOE's standard FP clustering :
~6s for 500 cpds, 25s for 1,000 cpds.
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Thaw' a PDB file: performs a steered energy minimization to preserve the active site
Date 2009-08-11
Author Hooman Shadnia
Category Protein Tools
Downloads 56
Details
A major problems in energy minimization of the raw PDB files is the lack of hydrogen atoms in the crystallographic coordinates. Software packages including MOE can add the hydrogens in ‘default’ orientations, which lead to many steric clashes. At this point, a regular energy minimization will lead to significant perturbations and movements of hydrogens as well as the heavy atoms.

One way to decrease such perturbations is to try to ‘shift’ them towards less important areas in the protein, i.e. residues which are far from active site. The ‘PDB-Thawing’ program works on this concept.

See the online
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Browse pages of depicted molecules
Date 2009-06-30
Author Simon Grimshaw
Category MOE Database Tools
Downloads 172
Details
Update 12-09-08: fixed navigator button sensitivity

The inspiration for this application is to create an interactive version of the DBV | File | Print panel.

To use this script, save the file to your hard drive then run it, e.g. using MOE | File | Open, browse to db_bigbrowser.svl and click OK.

Once the Big Browser window is open, the basic browsing functionality provided by the arrow buttons at the bottom of the panel is the same as for the standard DBV | File | Browse application:
|< moves to page 1
< moves back a page
> moves forward a page
>| moves to the last page

At the top right, the page position is shown as "n/pages". Clicking that button allows one to jump to a specific page number.

The Subject menu allows one to choose a molecule field.

Define template allows a common substructure to be entered based on atoms in the main MOE window. To use this, click Define Template, then either build the scaffold using the Builder or simply click a molecule to toggle it into MOE. Select the scaffold atoms and click Load in the "Define Template" window. Adjust the depiction (rotation or X/Y flip) and click Apply.

Set Data Fields allows the user to choose a set of data fields to be shown as text. Also a numeric field can be shown as a colour-coded square; use the Activity Indicator drop down menu to select the field.

The Action button allows the user to change what happens when a molecule is clicked in the Big Browser panel. If Toggle MOE is selected, the molecule is either created or destroyed in the main MOE window. If Toggle Sel is chosen, the entry selection state will be toggled. If Mark is chosen, the value in the text field will be written to the field specified in the drop down menu'

The Clear button clears whatever the action is currently set to, i.e. if the action is MOE, all molecules sent to the main MOE windows are deleted; if action is Select the entry selection in the database is cleared. There is no effect for Mark mode.

The Grid drop down menu sets the number of molecules depicted; the grid is defined horizontal x vertical.

The Size menu sets the size of each cell; 1 is smallest, 5 is largest.

Browse Selected sets the browser to show only the entries that were selected when the box was checked. This means that if you are browsing a set of selected molecules and you deselect one of the entries, it will not be removed from the browser. To remove it, you will need to turn off "Browse Selected" then re-enable the option.

The application is not sensitive to changes in the database (e.g. creating or deleting fields or entries); making such changes is liable to result in the application crashing. I aim to address this in a future revision. Please send any bug reports or feature requests to sgrimshaw@chemcomp.com.
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Given a database with a molecule identifier, extracts conformations
from one or more other databases and writes the output to a new database.
There is an option to only write the molecules from the selected entries
in the initial database. A threshold can be set for the size of the
output files. New output databases will be created once this limit has
been passed.

When the script starts, there is a prompt to select the MDB database
with the 2D molecules. This needs to have fields with the identifier
for the molecule, and the filename which has the conformations. These
will be set to "MOE_ID" and "file" if fields exist with that name.
Next the databases with the conformations should be specified. The
data fields in the input files are listed. If some of the fields are
selected, only that data will be written to the output. If none of the
fields are selected, all will be written to the output, so long as
data is present for some of the molecules.
Date 2009-06-04
Author Andrew Henry
Category MOE Database Tools
Downloads 58
Details
Save this file to your hard disk. For it to be available for use by all
of the users of MOE, create a directory called $MOE/lib/svl/custom/run
and save this file to that directory. eg on Windows and Linux,
this might be: c:\moe\lib\svl\custom\run\extract_conformations.svl
/usr/local/moe/lib/svl/custom/run/extract_conformations.svl

For the script to be available for use by a single user, then it
is best to create a directory in your home directory called svl,
and create a directory called run in that directory. Save this
file into that directory. eg on Windows and Linux, this might be:

c:\Documents and Settings\user_name\svl\run\extract_conformations.svl
/usr/people/user_name/svl/run/extract_conformations.svl

(a) From the MOE | File | Open panel, select this file
and click the "Run" button.

(b) Alternatively, at the SVL command line, type:
run 'extract_conformations.svl
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Fragments molecules by cutting out the scaffold and a adjustable number of adjacent bonds.
Date 2009-03-17
Author Guido Kirsten
Category Combinatorial Chemistry
Downloads 107
Details
Reference:
Oyarzabal, Julen; Howe, Trevor; Alcazar, Jesus; Andres, Jose Ignacio; Alvarez, Rosa M.; Dautzenberg, Frank; Iturrino, Laura; Martinez, Sonia; Van der Linden, Ilse
Novel Approach for Chemotype Hopping Based on Annotated Databases of Chemically Feasible Fragments and Prospective Case study: New Melanin
Concentrating Hormone Antagonists
J. Med. Chem. Articles ASAP March 16, 2009
SQL > SVL > 3D SDF generation
Date 2009-01-21
Author Daniel Butler whilst at Inhibox
Category Informatics and File I/O
Downloads 39
Details
This set of tools was developed for Inhibox by Daniel Butler in conjunction with excellent UK CCG support.

The user can develop an SQL statement using their favourite (Oracle) cartridge and these scripts will generate a 3D SDF from the submitted SQL statement which is a very handy and efficient way to use the MOE tokens available within a given organisation.

The SVL modules are tied together with a script (MOE_SQL_TO_SDF.sh or MOE_SQL_TO_SDF.bat) which prompts the user for the relevant information and a SMILES column and primary key column must be specified. If the primary key is of type number then this must be converted to a varchar using oracle to_char function (if not oracle then equivalent). If running on linux you may need to run dos2unix on the files for them to work.

Enjoy + I hope it makes a difference!

Daniel Butler.
Jan 2009







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This code is now obsolete. It is best to use MOE | File | Save and select the Picture format. Use the POV-Ray checkbox to automatically export the data to POV-Ray format and run the ray tracer for very high quality images. The POV-Ray program is free and can be obtained from www.povray.org. MOE requires the features of POV-Ray 3.7, which is in beta testing.

This is a prototype for a function to write a POV-Ray scene from a MOE session. Export of POV-Ray files is likely to be a new feature for the 2008 release of MOE using code from the R&D group at CCG.
Date 2009-01-20
Author Andrew Henry
Category Z- Obsolete Code
Downloads 266
Details
POV-Ray is a freeware ray tracing program. See http://www.povray.org for more details. This script writes a POV-Ray scene from MOE. It creates spheres for atoms, cylinders for bonds and triangles for surfaces for MOE graphical objects. The advantage of using a ray tracing program like POV-Ray is that you get much more control over the appearance of the image, with the option to use settings which would be too slow for use in an interactive program. You can also output the images in any size you like (eg for publications, posters or an exhibition stand), with no loss of crispness.

At the moment it does not draw anything for a backbone representation. The trace representation is easy (cylinders between the CA atoms). For the cartoon and tube representations, you can use $MOE/sample/cartoon.svl This creates a graphical object that is then rendered the same as a surface.

The script now handles graphic objects with a dotted, line and solid surfaces.

The position of the camera is not exactly correct, so the perspective view looks a little different to the MOE window. Any suggestions would be gratefully received.

The positions of the lights in the POV-Ray scene are also static. Edit the coordinates and add extra lights as you see fit. You can also modify the textures of the objects with POV-Ray commands (eg to make a surface shiny, smooth, bumpy, etc).

TO DO

Clean up code (error checking, comments, split into functions)

Load positions of camera, lights and scale

Cartoon, Tube and C-Alpha Trace Backbone

Double/triple bond sticks (including SO2, NO2)

Pick up display settings from MOE

Textures

Stereo views

Display labels and meters

USAGE

1. Load a view in MOE which has the surfaces, atoms and bonds displayed as you want in the output. If you want backbone representations, then use $MOE/sample/cartoon.svl.

2. Load this script using one of these methods:

(a) From the File | Open panel, click on this with your left mouse button and click the "load" button to the left hand side of the panel

(b) At the SVL command line type
load 'write_pov.svl'

(c) Set an environment variable MOE_SVL_LOAD that points to a subdirectory like $MOE/local_svl and save this file into that subdirectory. It will then be loaded the next time that MOE starts.

3. At the SVL command line type: Write_POV 'out.pov'

4. Load the out.pov file into POV-Ray and render it.
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This is a plugin for making molecular movies.
Date 2009-01-09
Author CCG Support
Category Z- Obsolete Code
Downloads 271
Details
DESCRIPTION:
This plugin saves an MOE screen picture several times per second into .bmp image files, while you manipulate a molecular system in MOE. It is a MOE video recorder, rather than a 'macro recorder'.
You can then create a video file from these movie frames.

USAGE:
1. MOE | File | Open | "Run SVL"
2. Once you have finished recording, use a third-party program to join the .bmp image frames into a video file. One such program (there are others as well) available at the time of writing, is bmp2avi
http://www.divx-digest.com/software/bmp2avi.html

D.Bondarev
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Computes root mean square deviation between conformers of structures in two molecular fields in an MOE database and writes out the optimal superposition.
Date 2009-01-09
Author CCG Support
Category Basic Molecular Tools
Downloads 328
Details
Calculates pairwise rmsd in a database between mols in first two adjacent mol fields or to fields
indicated by the fields parameter. WE ASSUME these are pairs of conformers arbitrarily positioned in space and that these have atoms in the same order.

Usage:
1) Save and Load the file pairwise_rmsd_superpose.svl
2) Type the following at the CLI

svl> pairwise_rmsd_superpose []

This will work on any open database containing two fields of molecules in different conformations. Te explicitly set the database and fields to operate on, type:

svl> pairwise_rmsd_superpose ['myDB.mdb', ['mol_field1', 'mol_field2']]

where 'myDB.mdb' is the database to work on and 'mol_field1' and 'molfield2' are fields in the database containing molecules to operate on.
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Process many files in batch mode anf calculate the diversity between two databases using clustering and PCA.
Date 2008-12-23
Author Suzanne Sirois
Category Z- Obsolete Code
Downloads 185
Details
Output

Overlap

=======

With in-house With it-self

============= ============

25.4% 17.1%



Number of Clusters

==================

Total number of entries: 101040.0

Total number of inhouse entries: 125170.0

Total number of outside entries: 9600.0



Number of cluster from outside libraries
having more than one compound 1034.000
Number of entries that overlap with reference database 2441.0
Number of entries that overlap with itself 1639.0

Number of cluster from outside libraries
having one compound 7043.000



Number of cluster from inhouse libraries
having more than one compound 16156.000
Number of cluster from inhouse libraries
having one compound 78679.000

====================

outside freq_outside

0 92963
1 7043
2 750
3 193
4 44
5 23
6 10
7 7
9 2
10 3
14 1
16 1


====================

reference freq_inhouse

0 6205
1 78679
2 10682
3 2898
4 1059
5 548
6 320
7 151
8 113
9 91
10 59
11 44
12 33
13 29
14 21
15 15
16 17
17 8
18 5
19 6
20 6
21 4
22 6
23 4
24 4
25 2
26 2
27 3
28 1
29 2
30 1
31 1
32 2
34 4
35 1
37 1
38 1
39 1
42 1
43 2
48 2
50 1
56 1
58 1
60 1
61 1
67 1

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Convenient access to FlexX/FlexSIS for evaluation purposes (e.g. re-docking). Updated for FlexX 3.x
Date 2008-10-16
Author Marcus Gastreich
Category Utilities
Downloads 58
Details
guides the user through a few simple steps to perform a FlexX computation:

- check for a valid FlexX installation
- load a protein
- protonate properly
(optionally using the new protonate3D)
- launch the FlexX-in-MOE interface
with pre-configured default settings
- determine a reference ligand
for optional RMSD calculation

The results will be ready for post processing
in a MOE mdb database.
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db_COMBINE calculates the components of ligand-residue interaction energies as a part of COMBINE descriptors (Ortiz, et al., 1995). The interaction energies per residue are divided into van der Waals and electrostatic contributions as described in Arakawa et al. (2008). The Born solvation contributions are also calculated with the constant or distance-independent dielectric constant with the value of 1 if the Generalized Born implicit solvation model is selected as the solvation model.
Date 2008-09-18
Author Kinya Toda and Ryoichi Kataoka
Category Molecular Descriptors and QSAR
Downloads 95
Details
db_COMBINE calculates the components of ligand-residue interaction energies as descriptors like COMBINE descriptors (Ortiz, et al., 1995). The interaction energies per residue are divided into van der Waals and electrostatic contributions as described in Arakawa et al. (2008). The Born solvation contributions are also calculated with the constant or distance-independent dielectric constant with the value of 1 if the Generalized Born implicit solvation model is selected as the solvation model. The changes in the internal conformation energies of the ligand and the receptor included in the original COMBINE descriptors are not calculated. Cutoff for the non-bonded interaction energies is set to off to ensure calculating non-distorted energies contributed from distant receptor atoms. Receptor residues are defined as the residues with selected atoms in MOE window if there are selected atoms, or the all residues if no atoms are selected.

Installation:
1. Load db_combine.svl in MOE. Or save it in $MOE/lib/svl/rsi.svl/ or $MOE/lib/svl/patch directory to automatically load it when MOE is invoked.

Usage:
1. Click Window | Potential Setup and select Born as Solvation in the Potential Setup window if you want to include the contribution from the solvation energy of Generalized Born implicit solvation model.
2. Read a receptor into MOE.
3. Select atoms to limit the residues to be calculated. If no atoms are selected, all atoms in MOE window will be taken into account.
4. Open a ligand MDB in DBV.
5. DBV | CLI | db_ COMBINE []

The fields for contributions of van der Waals, electrostatic and, if selected, solvation interaction energies per residue will appear in MDB.

References:
[1] A.R. Ortiz, M.T. Pisabarro, F. Gago, R.C. Wade, Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis, J. Med. Chem. 1995 38, 26812691.
[2] M. Arakawa, K. Hasegawa and K. Funatsu, Tailored scoring function of Trypsin-benzamidine complex using COMBINE descriptors and support vector regression, Chemom. Intell. Lab. Syst. 2008 92, 145-151.
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Tutorial, example files, and SVL codes to calculate and compare ligand-receptor interaction forces of different complexes.
Date 2008-07-15
Author Hooman Shadnia
Category Protein Tools
Downloads 86
Details
PDF tutorial, step by step, illustrated.

Example files on Way244

SVL utility for template-based superposition and alignment.

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PostDock: A Novel Visualization Tool for the Analysis of Molecular Docking
Date 2008-06-24
Author Ashley Wiley and Ghislain Deslongchamps
Category Graphics and Rendering
Downloads 166
Details
PostDock is a new visualization tool for the analysis and comparison of molecular docking results. It processes a docking database and displays an interactive pseudo-3D snapshot of multiple ligand docking poses such that their docking energies and docking poses are visually encoded for rapid visual assessment. The docking energies are represented by a transparency scale whereas the docking poses are encoded by a color scale. The submission includes postdock.svl, a user manual, as well as a reprint of the publication.
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Hierarchical Scaffold Classification
Date 2008-05-06
Author Guido Kirsten
Category MOE Database Tools
Downloads 333
Details
The current version is using a revised rule set. In rule 7 the aromaticity definition is used in a more strict manner than in previous versions. Rule 8 and 9 now include heteroatoms connected by double bonds to carbocycles to distinguish between carbo cycles.
The resulting clustering should be improved compared to the original rule set.

Implemenation based on:

Schuffenhauer, Ansgar; Ertl, Peter; Roggo, Silvio; Wetzel, Stefan; Koch, Marcus A.; Waldmann, Herbert
The Scaffold Tree - Visualization of the Scaffold
Universe by Hierarchical Scaffold Classification
J. Chem. Inf. Model. (47) 2007, 47-58

Calculates a hierarchical scaffold tree analysis for a database of compounds. Writes out statistics for frequencies of scaffolds in
actives and inactives.
For cyclic compounds the algorithm is based on the paper mentioned above. For acyclic compounds I have used my own rules.
Rules can be overwritten by a priorityscaffold. This Scaffold will be kept together until no other ring is present.

USAGE: run 'ScaffoldTree.svl' to start the analysis or display previously calculated results

Or load this file and use:
db_ScaffoldTree [database, opt]
where opt is a tagged vector:
[molecules: molfield, activity: activityfield,
threshold: activitythreshold,
operator: activityoperator as token,
prioscaff: SMARTS token]
runs the analysis in batch. operator may be '<' or '>'
if no activity field is specified use 'none' or []
prioscaff is the SMARTS for a prioritzed scaffold
(leave ' if none) only molecules is a required tag!

To extend an existing scaffold tree:
db_ResumeScaffoldTree [database, opt]
opt is defined as for db_ScaffoldTree but has the additional tag 'SCT_Output' for the scaffold database.

See pdf file for more details.
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Superpose a molecular library onto a given substructure.
Date 2008-04-22
Author CCG Support
Category MOE Database Tools
Downloads 746
Details
Description:
-similar to the conformational superpose, except that
selected atoms determine a molecular subfragment that is
used to perform the superpose. This is useful when superposing
a set of ligands on to a common substructure

Usage:
(1) First, load a reference ligand into the 3D MOE
window. The ligand should contain the common core
and be in the correct absolute coordinates (if appropriate).
The coordinates of this structure will be used to superpose
the database ligands
(2) Run this function -a GUI will appear. Use the browse button
to select the database of ligands to align.
(3) The alignment may be performed based one of two
criteria for specifying superposition point correspondence:
(i) A SMILES/SMARTS match of the conserved core
(ii) Atoms with unique names throughout the database
(4) (i) Superposing with a SMILES/SMARTS string.
To superpose on a SMILES/SMARTS string of the conserved
core, select the atoms of the consered core and
press the 'Extract' button. A SMILES string of the
selected atoms will be produced. This can be edited to
include wildcards, etc. Then press
'Align by SMARTS'
(ii) Superposing by unique atom name
When the database file is specified, the program will scan
through the first molecule field in the database and
automatically detect 'unique atom names' i.e. (C1, N2),
which are names that occur with only one instance in
any molecule, and occur in every molecule.
The names will be listed in the Alignment Points box.
To superpose on these named atoms, load a template
3D reference structure which has the appropriate
atom names. Select the named atoms in the MOE window
AND in the Alignment Points list. Then press
'Align by Name'

(5) A new field named transformed_mol_field will appear in the
database, with the transformed structures. A comment field
will also be generated, indicating if a the point mapping
and transformation were successful.
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Calculates InChI's for molecules in a database.
Date 2008-02-06
Author Guido Kirsten
Category Utilities
Downloads 59
Details
This is an interface to the InChI molecule identifier calculator available at:
http://www.iupac.org/inchi/download/InChI-1.zip

When the program is started for the first time you have to browse to the command line version of the InChI tool in the 'Settings & Options' panel to set the path to the executable.
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Fingerprint based on Shannon Entropy Descriptors
Date 2007-11-16
Author Guido Kirsten
Category Pharmacophores and Fingerprints
Downloads 129
Details
REFERENCE:
Gregori-Puigjane, Elisabet; Mestres, Jordi
SHED: Shannon Entropy Descriptors from Topological Feature Distributions
J. Chem. Inf. Model. 2006, 46, 1615-1622

USAGE: load 'fp_shed.svl'
FP:SHED is added to fingerprints and to the database browser. Molecules in the main window are drawn in black. The current entry is colored in red.
To create a shedplot of all molecules in the main window use SHED_Plot[]. Chain color is used for the plots of different molecules.
Calculates enhanced CATS vectors (Schneider et al, Angew Chemie, 38, 2894-2896)
Date 2007-11-16
Author Michael Charlton
Category Molecular Descriptors and QSAR
Downloads 93
Details
Calculates CATS vectors, based upon Schneider et al, Angew Chemie, 38, 2894-2896 with augmentation to included aromatic atom types based upon unpublished work by M.H Charlton, M.L. Brewer and P.N. Mortenson carried out at Evotec.
This code written by M.H. Charlton at Chroma Therapeutics, 2007.

To use the code, load it into MOE and type :
db_cats []
Alternatively, to use a specific molecule field (e.g. mol_wash), type :
db_cats ['mol_wash']
Published version normalises the CATS vectors by the number of heavy atoms. To achieve this, use :
db_cats ['mol_wash', 1]
Doing this will produce 210 fields of type float. Not setting the second argument produces a simple count of the various CATS features (210 * integer).
Failing to provide a molecule field will default to the first such field in the database.
Code uses MOE's definitions of various Ph4 types (e.g. anion, cation) and is therefore best used after washing the molecules to ensure these features are recognised.
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Setup the light directions using trackballs
Date 2007-10-22
Author Kinya Toda
Category Graphics and Rendering
Downloads 28
Details
Usage>
1. Load 'lightdirection.svl'
2. Type the "LightDirection[]" instruction in CLI

Now light directions can be setted by [MOE|Render|Setup...]. But because we need to input the values of the vector, it is little difficult.

By using this program, you can adjust them smoothly.
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With fragment_rmsd.svl you have to select the atoms in the template structure that you want to calculate the RMS deviation for. When you run the script, it prompts you for a MOE database of compounds to compare against. It writes a new field in the database with the RMS deviation of the atoms in the structure with the selected atoms in the template structure.
Date 2007-10-16
Author Andrew Henry
Category MOE Database Tools
Downloads 275
Details
Usage:
(1) Open the template structure that is in the
correct reference position. Select the atoms of the
common sub-structure against which you wish to use
to calculate for the RMS deviation.
(2) Open the database of structures you wish to align
(3) run fragment_rmsd.svl
(4) Alternatively, load fragment_rmsd.svl and enter
svl>database_molecule_rmsd ['database.mdb']
(5) A new field 'RMS_Deviation#' will be produced where #
is an integer that increments to generate a unique field name
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Code that fills a box with any solvent using a Monte Carlo-like algorithm.
Date 2007-08-02
Author Andrew Swann
Category Basic Molecular Tools
Downloads 82
Details
This code fills a box with a given solvent in a random manner. It also minimizes and saves the final system.

Inputs:
1. Name of *.moe file to save final structure to
2. Solvent, as SMILES string or file name
3. Two of the three:
a. Number of solvent molecules
b. Box dimensions
c. Density (g/cm**3)
4. Maximum energy difference (maxDE)

How it works:

From the inputs, the number of solvent molecules and box dimensions are calculated if they are not given. If the solvent is given by a SMILES string, the solvent is created and minimized, and this is the structure that is used as the solvent. If the solvent is given as a file, the structure in the file is used as a solvent. The uses a Monte Carlo-like algorithm. A solvent molecule is inserted and positioned randomly in the box. The energy difference between the system pre- and post-solvent addition is calculated. If this difference is less than the maxDE variable, the move is accepted, otherwise, it is rejected and a new attempt is made. This is done until the box is full, after which a final minimization is performed.

The code slows down at higher densities/lower maxDE values. Increasing the maxDE as density goes up allows the filling to occur fast while not allowing molecules to overlap. The final minimization will generally take out any high energy regions caused by the increased maxDE.

If, for some reason, the code is stopped, there is no real data loss, as the system is saved to the designated file after every accepted move (it will not be minimized, however).

Usage:
Described in the file header. The basic syntax is:

SoakPanel[] to display the panel and

Soak[soak_file, solvent, opt] for command line and batch usage.
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Form View panel for mdb file
Date 2007-07-03
Author junichi goto
Category Informatics and File I/O
Downloads 103
Details
Automatically create Form View panel for any mdb file. Panel consists of 3 parts, namely molecular structure, numeric data and text data.
You can browse entire mdb file with slider in Browse Mode and search by queries in Search Mode.
Usage:
load formbrowser.svl and type FormBrowser[]
or
just run formbrowser.svl in the directory where you have mdb files.
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Display, Save and Load Force Vectors
Date 2007-07-03
Author Hooman Shadnia
Category Basic Molecular Tools
Downloads 41
Details
This utility is designed to help studying atomic / residual forces. For tutorial and support, please goto www.shadnia.com
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Implementation of the method in:

In silico prediction of blood-brain barrier permeation using
the calculated molecular cross-sectional area as main parameter.
Gerebtzoff, G., Seelig, A. J. Chem. Inf. Model. 46, 2638-2650 (2006).
Available at http://www.biozentrum.unibas.ch/aseelig/aseelig_pub.html
as a PDF file.

The main differences between this implementation and the method in the
paper are that the atom hydrophobicities are derived from SlogP
(Wildman,S.A., Crippen,G.M.; Prediction of Physiochemical Parameters
Atomic Contributions. J. Chem. Inf. Comput. Sci. 39(5), 868-873, (1999))
and not the XlogP values. Also the TPSA values in MOE ignore the
values for S-ethers, sulphones and phosphorous bonded to 4 heavy
atoms. Ertl specified parameters for these in J. Med. Chem., 43,
pp3714-3717, 2000, but using the parameters listed in the paper
did not match the example calculations. The additional parameters
are commented out in "TPSA" in $MOE/lib/svl/quasar.svl/q_surf.svl


This script reads conformations from a MDB database and calculates the
axis between the centres of mass of the hydrophobic and polar atoms.
There is an option to adjust the position of the centre of mass of the
polar atoms using the pKa values, read in from the output of ACD/pKa
DB prediction.

The database with the pKa information needs a field with molecule
identifiers that are also found in the database of conformations.
The names of these fields do not have to be the same.

It writes new fields into the conformation database with the cross
sectional area and a new molecule field, where the molecule is rotated
along the axis that was used for the calculation. In this view, there
are dummy atoms for the centres of mass of the polar and hydrophobic
atoms and also for the grid points which were used to calculate the area.

This view of the molecule also has a "molecule" showing the axis between
the hydrophilic and hydrophobic centres of mass. These are shown as a
Cl-O molecule, where the Chlorine atom is at the hydrophobic centre
and the Oxygen is at the hydrophilic centre. These atoms should be deleted
before running an energy calculation for the molecule.
Date 2007-06-27
Author Andrew Henry
Category Molecular Descriptors and QSAR
Downloads 125
Details
USAGE

Save this file to your hard disk. For it to be available for use by all
of the users of MOE, create a directory called $MOE/lib/svl/patch/run
and save this file to that directory. eg on Windows and Linux,
this might be: c:\moe\lib\svl\patch\run\db_amphiphilic_xsa.svl
/usr/local/moe/lib/svl/patch/run/db_amphiphilic_xsa.svl

For the script to be available for use by a single user, then it
is best to create a directory in your home directory called svl,
and create a directory called run in that directory. Save this
file into that directory. eg on Windows and Linux, this might be:

c:\Documents and Settings\user_name\svl\run\db_amphiphilic_xsa.svl
/usr/people/user_name/svl/run/db_amphiphilic_xsa.svl

(a) From the MOE | File | Open panel, select this file
and click the "Run" button.

(b) Alternatively, at the SVL command line, type:
run 'db_amphiphilic_xsa.svl
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Colour carbon atoms of the selected molecule and render in stick form
Date 2007-06-22
Author Andrew Henry
Category Graphics and Rendering
Downloads 110
Details
Colour carbon atoms of the selected molecule and render in stick form

USAGE

1. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL
command line, type a command like

ColMol 'cyan'

2. Save the moe-menus file to your home directory, such as:
C:\Documents and Settings\your_user_name\moe-menus
/usr/people/your_user_name/moe-menus

With Linux and Unix systems, you can also call the file
/usr/people/your_user_name/.moe-menus which will then be
hidden from a normal directory listing. If you have both
moe-menus and .moe-menus in your home directory, the moe-menus
file will be used.

If you already have a moe-menus file in your home directory,
append the contents of this file to the existing file.

Do not replace $MOE/lib/moe-menus with this file.
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Open Images in MOE
Date 2007-06-19
Author Alain Deschenes
Category Informatics and File I/O
Downloads 39
Details
This tool allows the user to open an image file (*.png, *.gif, *.jpg, etc...) and view it in a popup window. The images can be in grayscale or in color. Transparency is also supported.

If one of the dimensions of the image exceed 800 pixels, the image will be scaled down so that the maximum dimenion is 800. Users with high resolution displays can increase the value of MAX_SIZE constant in the code.

Usage:
- Save this file in your ~/svl/run folder
- Run the file with:

svl> run 'ImageViewer.svl
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Prints a vector with nested entries indented and split over several lines.
Date 2007-06-10
Author Andrew Henry
Category SVL Utilities
Downloads 75
Details
Usage:

1. Load the function.

1(a) You can do this by saving the SVL file to your hard disk. From the MOE File | Open panel, click on the pretty_print.svl file and click the Load button).

1(b) Set an environment variable MOE_SVL_LOAD and save the pretty_print.svl file to that directory.

2. At the SVL command line, type either

pretty_print vector

or

ppr vector

e.g.

ppr ['a', ['b', ['c', 'd'], 'e']]
ppr mol_Extract Atoms[]
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For each molecule in a database, plot the distance between the centre of mass for the ligand to the oxygen atom of the water molecules.
Date 2007-06-10
Author Andrew Henry
Category Simulations
Downloads 71
Details
The ligand and solvent atoms are defined using the
same code that is used in the MOE | Selection | Ligand and MOE | Selection | Solvent menus.

If a database is not specified, then there is a prompt to open one. If some database entries are selected, then only those entries
will be used for the plot. If no entries are selected, but some are hidden, then only the visible entries will be used.

USAGE

1. Run this file.
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.
2. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL
command line, type a command like

db_WaterRadialDistribution []
db_WaterRadialDistribution [mdb_key, input_mol_field]
mdb = db_Open 'in.mdb';db_WaterRadialDistribution [mdb, 'mol']
Takes an input token and opens the relevant documentation from the MOE function index $MOE/html/fcnindex.html. If you pass it a token such as '*cat*' then it runs sym_find on the token and displays any documentation for those functions.
Date 2007-06-10
Author Andrew Henry
Category SVL Utilities
Downloads 45
Details
USAGE

1. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

2. This zip file includes a copy of menu-ted that adds a
TED | SVL | Function Help menu to the text editor.
Save this file to $MOE/lib/menu-ted
Then if you highlight text in the text editor and launch the
TED | SVL | Function Help menu, the help files for those
functions will be opened.

3. At the SVL command prompt, type commands like:
help 'cat'
help '*cat*'
help 'if length pack (string input_tok[i] =="*") then'

When the last of these commands runs, it produces the
following output:
svl> help 'if length pack (string input_tok[i] =="*") then'

No help for : "input_tok", "i", and "then".

Displaying $MOE/html/svl/fcnref/s_stmt.htm for "if".
Displaying $MOE/html/svl/fcnref/length.html for "length".
Displaying $MOE/html/svl/fcnref/packetc.html for "pack".
Displaying $MOE/html/svl/fcnref/types.htm for "string".

ISSUES

$MOE/html/fcnindex.html does not index every MOE function.
The function loops through a database and assigns partial charges to molecules without performing MM minimizations.
Date 2007-06-10
Author Chris Williams
Category Z- Obsolete Code
Downloads 96
Details
The function loops through a database and assigns partial charges to molecules without performing MM minimizations.
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Configure the VIM VI-like text editor to color SVL by its syntax. Includes new functions for MOE 2006.08
Date 2007-06-10
Author Andrew Henry
Category SVL Utilities
Downloads 172
Details
VIM is an editor based on VI, but with some improvements. For instance, with the Windows version the main Windows keyboard shortcuts work (eg to cut, paste, copy, undo etc), you can select text with the mouse. It installs itself so that if you right click on a file in the Windows Explorer, there is a link to open the file in vim. You still have the power of the original VI commands, so you can do regular expressions that look like line noise. Where the "improvements" to vi get in the way of something, then you can usually turn them off with options.

Its available on all the major platforms from http://www.vim.org/download.php

It is a Charityware program, so you can install and use it wherever you like for free, but you are requested to make a donation to a Children's home in Uganda.

Another feature is that you can colour programming languages by their syntax. I've created an SVL syntax file that is based on the one for C. The C syntax file has some bits that are horribly complicated and I don't claim to understand exactly what they do, but it does do a really nice job for things like highlighting comments in code. I've left these in for the SVL syntax file unless I was sure that they weren't going to be of use.
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PSPad is a freeware text editor Windows. These files allow SVL code to be colored by syntax.
Date 2007-06-10
Author Johannes Maier
Category SVL Utilities
Downloads 46
Details
- download the zipped editor package (for instance, a file like pspad452en.cab) from http://www.pspad.com/

- Unpack the zipped file in any directory
- copy SVL.ini from the pspad.zip into the "Syntax" subdirectory of the editor directory
- launch PSPAD.exe
- in the program settings choose "Highlighter Settings":
click on first entry "<not assigned>";
in the "Use Highlighters" list: choose SVL
"OK"
- exit PSPad
- copy content of pspadini.txt into clipboard
- open "pspad.ini"
- replace the section SVL with content of clipboard
- save pspad.ini and launch pspad.exe
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This script generates conformations for a database of compounds. It uses the "Bond Rotation" method that is used in the MOE 2005.06 Pharmacophore Elucidator and in the Docking code (when the maximum number of conformations to 1000).

The default method for conformation generation with both of these is "stochastic", but if you have a compound where the initial bond rotation steps generates fewer than the "maxconf" setting, then they will all be enumerated. There are also options for systematic or random conformers.

The default settings do not remove duplicates. Change the removeDuplicates option to 1 to enable this.
Date 2007-06-10
Author Andrew Henry
Category Simulations
Downloads 115
Details
DESCRIPTION

Given a database filename, dbfile, function loops through the database and performs a bond rotation conformation search on each entry.

The output is written to a single database with the basename of the input database followed by _bond_rot.mdb (eg if the input database is input.mdb, the output will be input_bond_rot.mdb

This file will have all of the data from the input database.
If the input database has data in the same field name as the output from the conformational search (E, dE, chi) then these will be overwritten with the information from this conformational search. The mseq field in the output has the index of the molecule from the input (ie an mseq value of 10 means the compound came from the 10th entry in the input database).

dbfile is the file name of the source MOE database, and search_options is a tagged vector of the stochastic search options.

USAGE

Save this file to your hard disk. For it to be available for use by all of the users of MOE, create a directory called $MOE/lib/svl/patch/run and save this file to that directory. eg on Windows and Linux, this might be: c:\moe\lib\svl\patch\run\db_bond_rotation.svl
/usr/local/moe/lib/svl/patch/run/db_bond_rotation.svl

For the script to be available for use by a single user, then it is best to create a directory in your home directory called svl, and create a directory called run in that directory. Save this file into that directory. eg on Windows and Linux, this might be:

c:\Documents and Settings\user_name\svl\run\db_bond_rotation.svl
/usr/people/user_name/svl/run/db_bond_rotation.svl

(a) From the MOE | File | Open panel, select this file
and click the "Run" button.

(b) Alternatively, at the SVL command line, type:
run 'db_bond_rotation.svl'
run ['db_bond_rotation.svl', [dbfile, search_options]]
run ['db_bond_rotation.svl', ['in.mdb',[maxconf:10, method:'systematic']]

To use it from MOE/batch, use the following syntax:
$MOE/bin/moebatch -exec "run ['db_bond_rotation.svl', 'in.mdb']
Reads in a blast alignment of two chains,
writing to FastA format in the process.
Date 2007-06-10
Author Raelene Lawrence
Category Protein Tools
Downloads 66
Details
This function allows the user to load a BLAST
generated alignment into MOE. A fasta file
containing the alignment is also written since to
open the BLAST alignment into MOE, it is first
converted into fasta format. There are a couple
of preparation steps and notes before you can use
this svl function.

1. This function is designed to deal with an
alignment of only 2 chains; a query and a subject.
It will not work for any more than 2 chains.

2. This function does not load any structure that
may be affiliated with the alignment. It loads
the sequence alignment ONLY. Once the BLAST
sequence alignment is loaded into MOE, it is up
to the user to load any structure file and set its
residue positions to the residue positions from
the alignment.

3. Prepare the blast file according to the example
at the beginning of the SVL file.

USAGE:
1. Save and load the svl file.
2. At the SVL command line, enter:

svl> blast_2_fasta ['blastfile', 'fastafile']

where blastfile is the filename of the text file
containing the BLAST alignment and fastafile is
the name of the fasta file that is written.
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Joins two protein chains with a peptide bond. If started with a null vector, then the Sequence Editor is opened and the user is prompted to click on the chains to be joined, and to select the first and last residues from the linker. The conformation of the linker will be optimised, leaving the rest of the protein conformations fixed. Finally the linker chain will be joined with the other chain. If it is not clear which chain should be used for the information like the chain name and chain tag, then the user will be prompted to click on the chain to use for this in the sequence editor.
Date 2007-06-09
Author Andrew Henry
Category Protein Tools
Downloads 70
Details
Usage
Either run the SVL file, or load it and then launch the Join_ProteinChains function
Run this file.
From the MOE | File | Open panel, select this file and click the "Run" button.
At the SVL commmand line type

run 'Join_ProteinChains.svl'
Load this file:
From the MOe | File | Open panel, select this file and click the "Load" button.
Create an environment variable MOE_SVL_LOAD that points to a subdirectory such as $MOE/local_svl and then save this file into that subdirectory.
In an SVL function, in a MOE menu file or at the SVL command line, type a command like:

Join_ProteinChains []
Join_ProteinChains [nter_chain, cter_chain, linker_start_res, linker_end_res]
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For each molecule in a MOE database, load into the main MOE window and calculate various forcefield terms in the context of the atoms in the main MOE window.
Date 2007-06-08
Author Andrew Henry
Category Molecular Descriptors and QSAR
Downloads 58
Details
By default it will use
the following SVL functions for the various forcefields terms
as described in $MOE/html/moe/fcnref/potfcn.htm

pot_angEnergy
pot_eleEnergy
pot_oopEnergy
pot_resEnergy
pot_solEnergy
pot_stbEnergy
pot_strEnergy
pot_torEnergy
pot_vdwEnergy

The values are reported for Etot (the whole system), Eint (the value for the database ligand) and Einteract (the interaction between the ligand and the rest of the system in the main MOE window.

USAGE

1. Run this file.
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.
2. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL
command line, type a command like

db_EnergyAnalysis []
db_EnergyAnalysis [mdb_key, input_mol_field, options]
mdb = db_Open 'in.mdb';db_EnergyAnalysis [mdb, 'mol']
db_EnergyAnalysis ['in.mdb', [], [pot_vdwEnergy:'Einteract']
db_EnergyAnalysis ['in.mdb', 'mol', [
energies:['Etot','Einteract'],
pot_terms:['pot_vdwEnergy', 'pot_angEnergy']
]
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See through surfaces that are facing away from
the viewer using back-face culling.
Date 2007-06-08
Author Martin Santavy
Category Z- Obsolete Code
Downloads 195
Details
This utility effectively removes those portions of a molecular surface pocket that obscure the view of the docked ligand.

Running the program starts a monitoring tasks that periodically examines each surface and removes the portions of the surface that face away from the viewer. In computer graphics, this technique is called "back-face culling". As a result, we can "see through" the walls of a molecular surface pocket when looking at them from the "receptor side".

The program must be terminated explicitly from the Cancel menu.
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Creates restraints for dihedral angles for one or more amino acid residues, based on the current geometry, specified phi, psi and omega angles, or the ideal values for secondary structure types such as a 'strand' or '3-10-helix'. If this file is "run", then a GUI panel will be created. Otherwise you can call the underlying SVL function directly.
Date 2007-06-08
Author Andrew Henry
Category Basic Molecular Tools
Downloads 61
Details
USAGE

1. Save this file to your hard disk.

For it to be available for use by all of the users of MOE, create a directory called $MOE/lib/svl/patch/run and save this file to that directory. eg on Windows and Linux, this might be:

c:\moe\lib\svl\patch\run\2o_struct_restrain.svl
/usr/local/moe/lib/svl/patch/run/2o_struct_restrain.svl

For the script to be available for use by a single user, then it is best to create a directory in your home directory called svl, and create a directory called run in that directory. Save this file into that directory. eg on Windows and Linux, this might be:

c:\Documents and Settings\user_name\svl\run\2o_struct_restrain.svl
/usr/people/user_name/svl/run/2o_struct_restrain.svl

2. Run this file.
(a) From the MOE | File | Open panel, select this file and click the "Run" button.
(b) At the SVL command line, type:
run '2o_struct_restrain.svl'

3. To execute the SVL function, without launching the GUI panel

In an SVL function, in a MOE menu file or at the SVL command line, type a command like

restrain_protein [residues, torsions, opt]

restrain_protein [
SelectedResidues[],
pro_BackboneDihedrals SelectedResidues[],
[force:100, tolerance:10]
];

where residues is a list of residue keys, torsions is a vector with dihedral angles in the format returned by pro_BackboneDihedrals, weight is the weight for the restraint, and tolerance is the angle in radians that the torsion can rotate before the restraining force is applied (in the GUI panel, the tolerance is specified in degrees). All of these parameters need to be passed to the script.
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Read a MOE database from a homology model. Display a ribbon structure for one of the structures, with the ribbon thickness scaled by the cartesian mean of the RMS deviations between each of the models and the displayed structure.
Date 2007-06-08
Author Andrew Henry
Category Graphics and Rendering
Downloads 79
Details
USAGE

1. Run this file:
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.
2. Alternatively, load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL
command line, type a command like

ribbon_by_rmsd []
ribbon_by_rmsd 'promodel.mdb
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This imports an ASCII text file into a new MOE database, calculates the LogP for each record and then writes out another ASCII text file.
Date 2007-06-08
Author Andrew Henry
Category Molecular Descriptors and QSAR
Downloads 113
Details
Reads an ASCII text file with the format like
"mol","name"
"1ccccc1","benzene"
The file is read into a temporary database, logP is calculated and the data is written back out to an ASCII text file.

USAGE

From the File | Open panel in the main MOE window, select ascii_logp.svl and click on the Run button. This will then prompt you for an input file.

Alternatively, from the File | Open panel in the main MOE window, select ascii_logp.svl and click on the Load button. Then at the SVL command prompt, type
ascii_logp.svl 'input.txt'
or
ascii_logp.svl []

The output will be written to input_logp.txt, or if this filename already exists a digit will be added until the output filename is unique (eg input_logp1.txt).
Kier and Hall chi2 descriptor
Date 2007-06-08
Author Chris Williams
Category Z- Obsolete Code
Downloads 102
Details
Descriptor calculation of Kier and Hall 2nd order connectivity
indicies.

Usage:
(1) Load this function
(2) Open the QuaSAR-Descriptor panel (DBV | Compute | Descriptor)
(3) New entries for the following indices will appear

[ 'chi2', 'Cond Connectivity Index (order 2)', '2D', []],
[ 'chi2v','Bond Valence Connectivity Index (order 2)', '2D', []]


Reference:
Hall, L.H., Kier, L.B.
The Molecular Connectivity Chi Indices and Kappa Shape Indices in
Structure-Property Modeling.
Reviews of Computational Chemistry. Vol 2, (1991)

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Applies different partial charge models to selected atom subsets
Date 2007-06-08
Author CCG Support
Category Z- Obsolete Code
Downloads 88
Details
Apply different charge models to selected subsets
of the system

Usage:
(1) Load this function
(2) Enter

svl> partial_charges []

at the SVL command line
(3) A GUI will appear, prompting the user to
select different partial charge models and apply them to
set partial chagres on different subests of the system.
(4) There are also buttons to quickly show and hide the labels
on the selected subset
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Label atoms with a text graphic object
Date 2007-06-08
Author Andrew Henry
Category Graphics and Rendering
Downloads 96
Details
You can pass the script the text for the label or if you start
it with a null vector, it will prompt you for the text. The
atoms that will be labelled are the atom keys passed to
the script. If these are not set, then if any atoms are selected
these will be labelled. Otherwise the script will prompt the user
to click on an atom for the label.

USAGE

1. Run this file.
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.
1. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

2. In an SVL function, in a MOE menu file or at the SVL command line,
type a command like

Label_Atoms []
Label_Atoms ['Interesting label', Atoms[], 0x0080FF]
a = first Atoms[];Label_Atoms [aName a, a, 0x0080FF]

ISSUES

The labels are graphic objects which are seperate from the
atoms. If you move or delete the atoms, the labels will remain.
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This code is a modification of the interactive superpose function in MOE that uses chain
tags, rather than molecule identification, to identify and superpose sets;
This can be used for superposing ligands and bringing along the protein,
and for superposing based on centroids.
Date 2007-06-08
Author Chris Williams
Category Basic Molecular Tools
Downloads 115
Details
Usage for superposing two protein/ligand systems based on ligand positions:

(1) Load this function
(2) Load the 1st protein and ligand system.
(3) Double click on any atom in the system to bring up the the Atom Manager.
(4) Choose Compress All in the Atom Manager
(5) For each chain to be associated, click on the chain, then type a name
under Tag: (say System1)
(6) Load the 2nd protein and ligand system.
(7) Again choose Compress All in the Atom Manager
(8) For each of the remaining chain to be associated, click on the chain,
then type a name under Tag: (say System2)
(9) Save the system (just to be sure)
(10) Enter
svl> tag_Isuper []
at the SVL command line
(11) Choose 3 or more pairs of corresponding atoms between the two ligands
and remember to change the set number each time
(12) Press the Superpose button (ESC will cancel). Everything with the same
chain tag will be moved as a group.
Takes each graphic object in the MOE system and creates dummy atoms for each vertex. If you move these dummy atoms and click the "Rebuild" button, a new graphic object is created with '_edit' appended to the title. The old graphic object is hidden.

If you delete any of the dummy atoms before pressing the "Rebuild" button then that vertex and any of the lines and triangles that use it will be removed from the new graphic object. Changing the RGB colour of the dummy atoms will change the colour of the surface.
Date 2007-06-08
Author Andrew Henry
Category Graphics and Rendering
Downloads 65
Details
USAGE

1. Run this file.
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.
2. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL
command line, type a command like
edit_GObject
edit_GObject [graphic_object_keys]
This explains how MOE/smp can be used in conjuction with LSF in order to better manage distributed MOE batch processing jobs.
Date 2007-06-08
Author CCG Support
Category MOE/batch
Downloads 62
Details
Using LSF to run MOE/batch jobs enables the user to do things such as monitor the run through LSF and use LSF to make the host selection on behalf of the user, selecting machines which are "least loaded" according to the resource requirements of the job. The "machine.txt" file required by MOE/smp is generated from this selection.

This application not was downloaded from http://www2.platform.com/pdfs/appnotes/appnote_CCG_MOE.pdf
where there may be an updated version. It includes a a detailed description of how to integrate MOE with LSF.
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Implementation of Probe algorithm. Place a very small probe
(typically of radius 0.25A) at points along the van der
Waals surface of a ligand or a selected set of atoms and
determine if this probe also contacts atoms within a second
\"target\" set. Word, et al. (1999). \"Visualizing and
Quantifying Molecular Goodness-of-Fit: Small-probe Contact
Dots with Explicit Hydrogen Atoms\" J. Mol. Biol. 285, 1709-1731.
http://kinemage.biochem.duke.edu/software/software2.html#probe
Date 2007-06-08
Author Andrew Henry
Category Graphics and Rendering
Downloads 142
Details
view_probe runs the calculation once and displays the graphic
object.

With monitor_probe, the calculation is repeated if there is a
change in the atoms that are selected, or in the coordinates
of the ligand or residues in the surrounding pocket. To stop
the monitor_probe function cancel it from the "Cancel" dropdown
list in the top right hand corner of the main MOE window, Database
Viewer or Sequence Editor.

USAGE:

1. Run this file.
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.
2. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL
command line, type a command like

view_probe []
view_probe [ligand_atoms, cutoff, opt]
monitor_probe []
monitor_probe [ligand_atoms, cutoff, opt]

If no atom keys are passed in the ligand_atoms parameter, then
the selected atoms will be used as the "ligand". If no atoms are
selected, then the ligand will be selected using the code used
in the MOE | Selection | Ligand menu.

TO DO:

Output a mesh or solid surface for easier visualisation in a static image

Add hydrogens if not already present?
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Calculates accurately the number of rings per molecule for each entry in a database.
Date 2007-06-08
Author John Haltiwanger
Category Z- Obsolete Code
Downloads 114
Details
This particular method utilizes the ring-descritptions in SMILES strings to count the calculate the number of rings for a given molecule. Thus, it's utility relies on the stability and uniformity of moe's internal SMILES generation (more on this can be found in the file itself).

As of moe 2002.03 it is both fast and extremely accurate.

Also, thanks go to CCG for providing the sm_charge routine utilized within.

Usage:
Load file, then
db_ringc []
Select database. Ring counts will be added in new field 'Ringcount'.
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Create a setup.exe for MOE using the freeware Inno Setup compiler
Date 2007-06-08
Author Andrew Henry
Category Miscellaneous
Downloads 40
Details
Use the freeware Inno Setup Compiler http://www.jrsoftware.org/isinfo.php to

o Package a customised version of MOE.

o Options for a compact installation.

o Uninstall option.

o Easy installation of MOE and icons to start it.

o Launch MOE by file type association.

o Sensible defaults for the Current Working Directory in the MOE session.

o Please ask at support@chemcomp.com if you would like help in modifying these files to your own requirements.
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This plugin for MOE 2004.03 or later. It demonstrates how you can retrieve multiple compounds from a webpage on the intranet using a text query.
Date 2007-06-08
Author CCG Support
Category Informatics and File I/O
Downloads 94
Details
DESCRIPTION: (you need to install MOE 2004.03 or later to use this)

A medicinal chemist would type in a query by compound ID (for example, adrena*) and MOE would read off that webpage piece by piece and search for the given ID string. Each compound it finds is then converted to 3D and added to an MOE database file. A database viewer is then opened.

Please see it for yourself, run the attached plugin (MOE | File | Open, "Run SVL"). AS A SEARCH QUERY, put * for this case. I've put that html address there as an example. On that page, there's 10 SMILES.
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A modified version of Dynamics_Panel from MOE 2006.08, that takes a protein structure in the main MOE window and adds one molecule at a time from a MOE database. There are options to add explicit solvent, run a series of energy minimization jobs with forcefield tethers of decreasing strength, and the run molecular dynamics.

The GUI panel creates a text file with the configuration options for the job. The file includes a copy of the receptor structure. This can then be configuration file can then be run from MOE/batch. The settings in the configuration file can be overridden at this time (eg to run the simulation with another database of ligands, or with different parameters for the simulations. The output is written to a separate MOE database for each ligand. This output is in the same directory as the ligand database, with
a digit appended to the base of the filename (eg for input from ligands.mdb, the output will be written to ligands_1.mdb, ligands_2.mdb etc.
Date 2007-06-08
Author Andrew Henry
Category MOE/batch
Downloads 143
Details
The first stage is to write the configuration file. To use this "run" this script with no parameters in an interactive MOE session. For instance, from the MOE | File | Open panel, ighlight this file and double click on it, or at the SVL command line type:

run 'batch_md.svl'

The GUI panel is based on the MOE | Compute | Simulations | Dynamics and MOE | Edit | Build | Water Soak panels. There are buttons to open the MOE | Window | Potential Control panel, and to open a panel for setting options for energy minimization to run before the the dynamics.

To use the configuration file to launch the calculation, "run" this file with the name of the configuration file as an argument. eg

run ['batch_md.svl',[configfile, mdbfile, mfield, moefile, opt]]

where:
- configfile is the name of the configuration file
- mdbfile is the name of the MOE database with ligands
- mfield is the name of the molecule field in that database
- moefile is the name of a MOE file for the receptor
- opt are any other settings for the dynamics, minimization
or potential

The configuration file is essential. Any of the other parameters can be left as null and the values will be taken from the configuration
file. eg

run ['batch_md.svl', 'batch_md_config.txt']
run ['batch_md.svl', ['config.txt', 'lig.mdb', 'mfield']]
run ['batch_md.svl', ['config.txt', [], [],'in.moe', [gtest:1]]
run ['batch_md.svl', ['config.txt', [], [], [], [ensemble:'NPT']]

For MOE/batch on Windows, type a command like:

c:\moe\bin-i4w9\moebatch -exec "run ['batch_md.svl', 'config.txt']
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Enumerates all of the ligand-protein hydrogen bonds greater than a user-specified threshold in a database and then use the DBV Browser to visualise the ligand-pocket hbonds for each configuration.
Date 2007-06-08
Author Niall English
Category Basic Molecular Tools
Downloads 213
Details
For each molecule in a MOE database, load into the main MOE window and calculate ligand-receptor hydrogen bond strengths, angles and lengths in the context of the atoms in the main MOE window. These are recorded in the database. Then use the DBV Browser to view the hydrogen bonds for each database entry. The rendering defaults for the hydrogen bonds (e.g. colour) may be changed in DEFAULT_HBOND.
The algorithm for scoring the strength of a hydrogen bond is taken from Dimitri Bondarev's script scoring.svl at the SVL exchange. This has been modified by Niall English (July 2005, cf SVL Exchange) to ensure that H bonds are not between heavy atoms only (i.e. the H bond angles are now correct).
Detailed usage instructions appear in the comments lines above the code.
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SMILES Calculation in Database Viewer
Date 2007-06-07
Author Norihiro Seki & Ryoichi Kataoka
Category Z- Obsolete Code
Downloads 121
Details
Computes SMILES strings for a molecular database in DBV

1. load MDB onto DBV
2. DBV | CLI | run 'db_sm_extract.svl'
Calculation of donor/acceptor counts for Lipinsky-type descriptors
Date 2007-06-07
Author Chris Williams
Category Z- Obsolete Code
Downloads 140
Details
Calculates donor and acceptor counts for Lipinsky rules.

Lipinski, C.A., Lombardo, F., Dominy, B.W. and Feeney, P.J.,
Adv. Drug Deliv. Rev., 23 (1997) 3.

Acceptor: Any N or O with a free lone pair (i.e. *not* amide or indole
N's, but do count pyridine N's), any negatively charged atom

Donor: Any N, O, or S with at least one attached hydrogen

Usage:
(1)This is a QuaSAR-Descriptor enables function.
(2)Load this function
(3)Open the QuaSAR-Descriptor calculator as usual

(DBV | Compute | Descriptors )

(4) Two new descriptors

[ 'lip_don', 'Lipinsky donor', '2D', [] ],
[ 'lip_acc', 'Lipinsky acceptor', '2D', [] ]

will appear in the descriptor list
The RestoreSelection function restores up to sixteen levels of changes to the atom selections in the main MOE window
Date 2007-06-07
Author Andrew Henry
Category Z- Obsolete Code
Downloads 21
Details
RestoreSelection is an SVL function keeps a record of the last 16 changes to the atom selections in the main MOE window. It is a standard function in the MOE distribution and is documented. It is also available from the MOE | Selection | Restore menu.

It does not work if you make enable the MOE | Selection | Synchronize mode and change the residue selection in the main MOE window. If you only change the atom selection then it will update the residue selection like this. The GizMOE selection monitor from MOE 2004.03 and earlier also has the same problem. As far as I know, the worst that will happen is that you will click the button and nothing will change.

To add a button to the button bar to the right hand side of the main MOE window, save the attached moe-menus file into your home directory.

If you share a MOE installation with other users, that change will only be configured for you. If you want the change to be available for all the users of a single MOE installation, add in the text in this file to $MOE/lib/menu-bbar

The RestoreSelection is available in MOE 2002.03, 2003.02, 2004.03 and 2005.06 (at least). It is used in $MOE/sample/obsolete/csa.svl which is dated 1996.
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Substructure search panel for Database Viewer with tautomer support
Date 2007-06-07
Author junichi goto
Category MOE Database Tools
Downloads 112
Details
Load smilessearch.svl and type
dbv_SmilesSearch[]
in the command line of database Viewer.

SMILES strings for query is automatically extracted from the structure in the main window or you can directly type in SMILES column.
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Substructure matching in a database.
Date 2007-06-07
Author Dimitri Bondarev
Category MOE Database Tools
Downloads 407
Details
The script will identify molecules in a MOE database that contain the substructure displayed in the MOE Window. The substructure can either be a subset of selected atoms or, if no atoms are selected, the entire molecule will be used as a template.

The hit entries will be selected in the database viewer.

USAGE:
Bring a molecule into the Main MOE Window, select the substructure and run this file (MOE File Open panel, "Run SVL"). If you don't select any atoms, the full molecule will be used as a search template.
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Subset Manager is the program for creating the subset of atoms and changing the atatus of atoms by subset.
Date 2007-06-07
Author Kinya Toda
Category Basic Molecular Tools
Downloads 90
Details
As subset.zip is unziped, following 2 files are created.

(1) subset.svl
(2) SubsetManager_Manual.pdf

subset.svl is the svl program file. SubsetManager_Manual.pdf is the operation manual for subset.svl.

-You can name the subset.
-You can change the states, Selected/Unselected, Shown/Hide, Active/Inactive by subset.
-Output the subset lists to text editor
... and other convenient functions.

This program is created as enhanced Molecule Object Manager (J. Goto, RSI, 2003).
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A database of compounds can be filtered using Lipinski, Oprea or customized rules. Users may define their own rules using a set of descriptors, substructures, fingerprints or QSAR models. An interactive mode also exists to display the pass/fail criterion for a molecule in the MOE window.
Date 2007-06-07
Author Junichi Goto
Category MOE Database Tools
Downloads 206
Details
A database of compounds can be filtered using Lipinski, Oprea or customized rules. Users may define their own rules using a set of descriptors, substructures, fingerprints or QSAR models. The input file can either be in sd or mdb format. Two output databases are automatically created: inputfilename_pass which contains compounds that have passed the filter rules and inputfilename_fail for compounds which failed the filter rules. The output file format will be the same as the input file format. An interactive mode also exists to display the pass/fail criterion for a molecule in the MOE window.
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Surface area descriptors with directionality of polar/hydrophobic character.
Date 2007-06-07
Author Dimitri Bondarev / Mike Soss
Category Molecular Descriptors and QSAR
Downloads 178
Details
This code includes a set of two descriptors:
directional_pol_sa and directional_hyd_sa.

These two take into account the directionality of po/hyd character and compute the amount of polar and hydrophobic atomic accessible surface for a structure.
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Reads a numeric file.
Date 2007-06-07
Author Chris Williams
Category Z- Obsolete Code
Downloads 77
Details
Reads an entire text file based on a delimiter defined in the constant SEP (comma by default) and interprets the data as numeric.
Function returns a list of numeric vectors. Empty fields get assigned the value 0.
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Molecular Builder with UNDO button
Date 2007-06-07
Author junichi goto
Category Z- Obsolete Code
Downloads 91
Details
A simple modification of original code to allow
users to undo one step previous operation in this panel.

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Modified PCH scheme for use with RECAP fragment databases.
Date 2007-06-07
Author Niall English
Category Pharmacophores and Fingerprints
Downloads 42
Details
This code implements a modified PCH scheme for use
with RECAP fragment databases. In this 'PCHM' scheme,
the A0, A1, A2 etc attachment points are specified (by
atom name), along with the associated substitution atoms
(labelled by name as Z0, Z1 etc) prior to annotation.
Upon annotation, the Ax hydrogens are assigned a 'Ratt'
feature and the substitution atoms are designated as
'Rsub' annotation points). For construction of a query,
the user should assign Ax names to the attachment
points, and the PCHM scheme will assign the Zx names
to the adjoining substitution atoms, and then perform
the required annotation. For annotation of a RECAP
fragment database, the user must specify the 'name'
field in the Database Ph4 Annotation panel, along
with the PCHM scheme. The RECAP SMILES tokens in the
name field are used to label the Zx substitution points.
Prior to annotation, the Ax hydrogens are added exclusively
to the substitution atoms. After annotation, the modified
names are written out to the database, so that any Ax
and Zx names may be seen along with the query in the
MOE Window when using the Browser in the DBV for a
hit database output from a Ph4 search.

It is straightforward to use these modified code
versions permanently. You may choose to do so only for
yourself or a particular set of users, or you may opt
to do so for all users:

(a) Create a directory called svl in your HOME
directory (eg c:\Documents and Settings\username\svl
or /usr/people/username/svl) and save ph4s_pch_recap.svl
into that directory. Create a sub-directory called 'run'
(i.e. /usr/people/username/svl/run) and save ph4_edit.svl
and ph4_prep.svl therein, without changing the filenames.
When you restart MOE, the code will be loaded automatically,
but not for any other users of MOE from that installation.

(b) Save into the $MOE/lib/svl/patch directory (eg
c:\Program Files\moe\lib\svl\patch\ph4s_pch_recap.svl
or /usr/local/lib/moe/lib/svl/patch/ph4s_pch_recap.svl).
Create a sub-directory called 'run' (i.e.
$MOE/lib/svl/patch/run) and save ph4_edit.svl and
ph4_prep.svl therein, without changing the filenames.
This code will then be available for all the users of
that MOE installation, upon restarting MOE.

If you choose option (b), then you will need to
remember to copy the modified files in the 'patch'
directory if you need to re-install MOE, or if you wish
to use these in a future MOE release.
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Label atoms by their net formal charge.
Date 2007-06-07
Author CCG Support
Category Graphics and Rendering
Downloads 114
Details
Names the atoms according to formal charge

Usage:
(1) Load this function
(2) Enter

svl> label_by_formal_charge[]

at the SVL command line

Atoms with non-zero formal charge will be named by formal charge
at the labels will be turned on.
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Change the default web browser used for the MOE "help" function from netscape to firefox.
Date 2007-06-07
Author Josh Tasman
Category Z- Obsolete Code
Downloads 37
Details
Replace the $MOE/bin/rnetscape file with the downloaded file. That's it!
Export structures from a MOE database into single-molecule mol2 files.
Date 2007-06-07
Author CCG Support
Category Informatics and File I/O
Downloads 269
Details
DESCRIPTION:
Run this code to save structures from an MOE database to single-molecule mol2 files.

Compound names are taken from a char field 'name' or 'NAME' and become filenames. If there is no such field or the name is empty, filenames are automatically generated as entry numbers in the database.

USAGE:

1. Run this file.
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.
2. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL
command line, type a command like

db2mol2files []
db2mol2files 'in.mdb'
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Interactive data mining tool for database viewer.
Date 2007-06-07
Author junichi goto
Category MOE Database Tools
Downloads 164
Details
Usage:

1. load this file.
2. type MDB_Mining[] in the command line of database viewer.
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This plugin counts all hydrogen bonds within the molecular system in the main MOE window.
Date 2007-06-07
Author CCG Support
Category Z- Obsolete Code
Downloads 65
Details
DESCRIPTION:
This plugin counts all hydrogen bonds within the molecular system in the main MOE window.

USAGE:
1. Bring a system (one or more molecules) into the Main MOE window.
2. MOE | File | Open, highlight the program file on the list, "Run SVL".
The results are printed in the Commands Window (Ctrl-C to open).

Dimitri Bondarev

Performs a minimization of a molecular structure while restraining torsions within +/- 5 degrees of their given values and maintaining atoms near their starting coordinates in cartesian space.
Date 2007-06-07
Author CCG Support
Category Simulations
Downloads 170
Details
Performs a minimization of a molecular structure while restraining torsions within +/- 5 degrees of their given values and maintaining atoms near their starting coordinates in cartesian space. By default, chiral configuration is maintained during the calculation.

If you select some of the atoms in the structure, they will be kept fixed duting the calculation.

D.Bondarev
Run this code with the MOE File Open panel.
This is a list companies that sell screening compounds.
Date 2007-06-07
Author Andrew Henry
Category Z- Obsolete Code
Downloads 154
Details
The contact details may be for the UK representative for the company. Where there is a hyperlink, it works as of July 30th 2003. If I have received the catalogue on a CD, then the contacts details may now be out of date.

You may need to register with the company WWW sites to get a username and password before you can download the structures, but this has been free for me.

All together there are approximately 2 million unique compounds in these catalogues.
Colors residue carbons by a given scalar
Date 2007-06-07
Author Chris Williams
Category Z- Obsolete Code
Downloads 54
Details
Function colors all selected residue carbon atoms by the
input argument scalar (0 = purple, 1 = red). If no residues
are selected, the carbon atoms in all residues will be
colored by the scalar

Usage:
(1) In the Sequence Editor, select the residues whose
carbon atoms you wish to color

(2) Enter

svl>color_residue_carbons scalar

at the SVL command line. Here, scalar is a number between 0 and 1
that represents the RBG color scale. Experiment with different
scalar values to produce the color you desire


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Visualization and setting of chiral constraints
Date 2007-06-07
Author Martin Santavy
Category Chirality Tools
Downloads 129
Details
This utility visualizes chiral properties and chiral constraints of atoms of the loaded molecule. The chiral constraints can be also interactively modified from the associated GUI panel.

Chiral or chirally constrained atoms are annotated with a labeled square. The squares are color-coded: red means (S)-chiral, blue means (R)-chiral, gray means non-chiral or unconstrained. The color of the upper half of each square represents the chiral constraint on the atom, while the color of the bottom half represents the geometric chirality of the atom.

Labels R and S (in uppercase) denote chiral constraints; labels r and s (in lowercase) denote geometric chirality, label x denotes non-chiral or planar atoms.

The associated GUI panel contains four buttons used to affect chirality constraints of selected atoms. Buttons "R" and "S" set the chirality constraints to (R) and (S), respectively. Button "C" sets the chiral constraint according to the geometric chirality. Button X unsets the chiral constraint. (To "correct" all chiral constraints to reflect the current geometric chirality, select all atoms and press "C".)

Note: The chirality of an atom is determined by the SVL function aRSWaterChiral[]. The geometric chirality is measured by aRSWaterChirality[]. The chiral constraint is obtained by aForceRS[] and set by aSetForceRS[].

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Bond two selected atoms and reparent their residues/chains into one chain.
Date 2007-06-07
Author CCG Support
Category Z- Obsolete Code
Downloads 43
Details
DESCRIPTION:
Bond two selected atoms and reparent them into one chain.

USAGE:
Load this file (OK in the MOE File Open panel)
Select two atoms
type create_bond[]

Computes descriptors for an SD file and outputs another SD file
Date 2007-06-07
Author Chris Williams
Category Z- Obsolete Code
Downloads 111
Details
Given an SD file token and a list of descriptors, the function imports
the SD file, calculates the descriptors and exports the
results back to another SD file

Usage:
(1) Load thus function;
(2) At the SVL command line, enter

svl> batch_sd_desc [['d1,'d2',d3',..'d'],'sd_filename','out_file']

where 'd1' - 'dn' are descriptor tokens

Alternately, the file can be run from batch mode

moebatch -exec "run['batch_sd_to_ascii',[['d1','d2'],'sdfile','asciifile']]" -exit
Re-types atoms for all molecules in a MOE database, removes ring threading and fixes NO2 groups
Date 2007-06-07
Author Dimitri Bondarev
Category Z- Obsolete Code
Downloads 71
Details
Applies automatic bond typing to all molecules in a database.
Re-types atoms for all molecules in a MOE database,
removes ring threading and fixes NO2 groups

Usage:
(1) Enter

svl>run 'autotype_db.svl'

at the SVL command line.
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3D --> 2D molecule conversion tool
New version generate more reasonable 2D structure for most of molecules. Also, revised 'Database Minimize' panel with '2D option' is now available in GUI mode.
Date 2007-06-07
Author junichi goto
Category Z- Obsolete Code
Downloads 237
Details
3D --> 2D molecule conversion tool

2D Clean Up based on CS4D.svl. Produces 2D structures from 3D structures
May be used on individual molecules or on a database of molecules.
Usage:
A: one molecule
(1) open a molecule (and fix any desired atoms)
(2) load (compile) this program
(3) Enter

svl> Clean2D []

at the SVL command line.

B: Database processing in command line
(1) Load this function
(2) Enter

svl> Clean2D_MDB mdb_filename
at the SVL command line.

(3) Alternately, open the database into a database viewer and enter
svl> Clean2D_MDB []
in the database CLI.

C: Database processing in GUI
(1)replace $MOE/lib/svl/db.svl/dbmin.svl with the revised version downloaded from this site.
(2)Load this 2d_clean.svl
(3)Select 'Database Viewer|Compute|Energy Minimize' to open Database Minimize panel
(4)Set 'Rebuild Structure From Scratch' = ON and click '2D' button
(5)click OK

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VAMP Plugin for SCF Framework
Date 2007-04-27
Author Guido Kirsten
Category Simulations
Downloads 16
Details
This svl file provides an interface to Tim Clark's semiempirical program VAMP http://www.accelrys.com/products/mstudio/modeling/quantumandcatalysis/vamp.html


Installation:

SetRC['vamp_dir','path_to_vamp']

"Load" this SVL file (eg by saving it to $HOME/svl/vamp.svl or $MOE/lib/svl/patch/vamp.svl

Then either launch a VAMP job from the MOE | Compute | Simulations | SCF Calculation panel or by typing

The command executed is:
$vamp_dir/vamprun 'inputfile'

Please submit suggestions for further modifications to support@chemcomp.com
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Implements the interface between external invocation of PC GAMESS (ab initio
quantum package) and the MOE SCF wavefunction framework.
Date 2007-03-30
Author Guido Kirsten
Category Simulations
Downloads 69
Details
Interface to the PC GAMESS package available from:
http://classic.chem.msu.su/gran/gamess/index.old.html

Installation:
Create subdirectory called 'work' in PC GAMESS
installation directory.

Start MOE and enter:
SetRC['pcgamess.exec','C:/pcgamess/pcgamess.exe']
SetRC['pcgamess.work','C:/pcgamess/work']
SetRC['pcgamess.engine', 'PC GAMESS']

load file

(
Please replace 'C:/pcgamess/pcgamess.exe' by the path to the PC GAMESS executable on your system.
Please note that the names of the rc variables have changed since the last revision!
)

Tested with PC GAMESS 7.0 on Windows
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Decomposes a database into a scaffold structure and
R-groups.
Date 2007-01-31
Author Chris Williams
Category Combinatorial Chemistry
Downloads 435
Details
Given a database of compounds and a SMILES/SMARTS match string (the scaffold), the function loops through the database and decomposes the compounds based on the scaffold match. The groups detached from the scaffold match are written out as R-groups to their own molecule fields.

Usage:
(1) Load this function
(2) Open the database of compounds you wish to decompose
(3) At the SVL command line in the Database Viewer enter

svl>combi_decompose[]

The Combi-Decompose panel should appear.

(4) The panel give you choices for the following:


A Wilson table, which reports of the occurance of each R-group at each position may also be
produced.

The following options are supported:
(1) The user may enter any desired SMILES or SMARTS string for matching the scaffold.

(2) SMILES matches may be extracted from molecules in the current MOE window using the 'Match Extract'button.

(3)Decomposition Options include
(a) Ignore R = -H substituents;

(b) Import all data fields to output database
if the output database <> source database

(c)produce a report file listing the number
of successful decompositions and the number
of unique R-group positions.
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A collection of enhanced fingerprints based on MACCS, TGT and MP61. The enhancements include the frequency of features (MACCSF and TGTF), the overlapping nature of hydrogen-bonding types (TGTO), and finer resolution of property bins (MP61q)
Date 2007-01-12
Author Todd Ewing
Category Pharmacophores and Fingerprints
Downloads 133
Details
This zip archive contains svl code for the following fingerprints:

MACCSF Standard 166 MACCS Keys + Frequencies
TGTF TGT + Frequency
TGTO TGT + Overlapping Types
TGTFO TGT + Freq + Overlap
TGTFOP TGT + Freq + Overlap + Planar (my favorite)
MP61q MP61 with quartile property bins

It also includes a pdf file of slides describing the enhancements. The svl contained in this submission is described in Ewing, et. al., J. Chem. Inf. Model. 2006, 46, 2423-2431. Feel free to contact me for an electronic copy of the JCIM manuscript.

Usage:

To use these fingerprints, download the unzip the file and "load" the SVL files. The fingerprints will then be available in the applications like the DBV | Compute | Cluster panel.

You can load the SVL files automatically when a MOE session starts by saving them into the $MOE/lib/svl/patch directory (where they will be available for all the users of a shared installation of MOE) or $HOME/svl (where they will only be available for that user).

Enjoy!
Todd
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Aligns protein chains according to their UID and INS codes.
Date 2006-12-12
Author Keith Ball
Category Protein Tools
Downloads 51
Details
For certain families of proteins (such as trypsin-like serine proteases, shown in the snapshot) there is a defined indexing using both the residue UID with INS codes indicating insertions into the overall template.

This function aligns such a group of related sequences, whose indexing (UID+INS code) refers to a multiple alignment template, by the special indexing so that each column in the Sequence Editor corresponds to a unique position in the alignment (see snapshot).

To run, either issue "run 'prot_index_align.svl'"
(having selected the sequences you wish to align) or load the SVL file and call the function:

prot_index_align chainlist

or

prot_index_align []

to align selected chains (or all chains, if none are selected).
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Graphical user interface to calculate RMSD of docking results
Date 2006-11-27
Author Guido Kirsten
Category Basic Molecular Tools
Downloads 377
Details
Calculates RMSD values for docking results. Crystal structure of ligand can be in MOE window or database. Docking results are expected to be in mdb format with mseq field.
For comparing two databases both need to have a mseq field.
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Bug fix for PPCH and PPCH_All pharmacophore schemes
Date 2006-11-20
Author CCG Support
Category Z- Obsolete Code
Downloads 64
Details
Description:
Contents of archive ph4_PPCH_patch.zip:

File: lib/svl/patch/ph4s_pch.svl
Contents: corrected PPCH and PPCH_All schemes
Copy to: $MOE/lib/svl/patch/

Files: html/tutorials/ph4_tut.html, html/tutorials/ph4_tut/*.png
Contents: corrected HTML tutorial
Copy to: $MOE/html/tutorials/

Files: sample/mol/serotonin_*.ph4
Contents: corrected ph4 query files for the tutorial
Copy to: $MOE/sample/mol/

Usage:

Copy each file in ph4_PPCH_patch.zip to its appropriate location in your MOE
2005.06 installation directory.

To check that the updated copy of ph4s_pch.svl has been loaded, open the SVL commands window and type the following command:

alltrue m_uniq (ph4_scheme_PCH 'PPCH').tcode

This should return a value of 1 if the fixed code is being used.
Cluster membership now independent of database order. This patch has only been tested with MOE 2005.06.
Date 2006-11-20
Author CCG Support, Chemical Computing Group (CCG), Inc.
Category Z- Obsolete Code
Downloads 83
Details
USAGE

1. Download this file (ph4clust.svl)
2. With MOE 2005.06 copy it to $MOE/lib/svl/patch/ph4clust.svl
3. Restart MOE

To use this script with an older version of MOE, rename the
existing $MOE/lib/svl/ph4.svl/ph4clust.svl to a filename that
does not end in .svl (eg $MOE/lib/svl/ph4.svl/ph4clust.txt),
and then save this file to $MOE/lib/svl/ph4.svl/ph4clust.svl
This descriptor computes Andrews Average dG and is an independent implementation of the original publication.
Date 2006-10-24
Author CCG Support
Category Molecular Descriptors and QSAR
Downloads 273
Details
Functional Group Contributions to Drug-Receptor Interactions P.R.Andrews, D.J.Craik, J.L.Martin J.Med.Chem., 27, 1984, 1648-1657

USAGE:
Load this file with the MOE File Open panel (click OK) and then compute the descriptor 'andrews' in the MOE Database Viewer.
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This tool can be used to derive and display structure-activity relationships in compound sets of medium size (up to 9,000 structures).
Date 2006-10-13
Author CCG Support
Category MOE Database Tools
Downloads 412
Details
// DESCRIPTION:
//
// This tool can be used to derive and display
// structure-activity relationships in compound sets
// of medium size (up to 9,000 structures).
//
// We disassemble all structures in the dataset using
// bond breaking rules and learn a large number of resulting
// molecular templates. Then, for each template, we find
// out how many times it occurs in the actives and how many
// times it occurs in inactives. The resulting two counts
// (active and inactive occurrences) are then used to rank
// various templates we found in the compound set.
// At the last step of the process, we can visually trace
// each of the top-ranking templates and their combinations
// to the original compounds via a point-and-click interface.
//
// If you want to explore an SAR around a particular scaffold,
// the combi_decompose script at http://svl.chemcomp.com
// can be used (downloaded separately).
//
// D.Bondarev.
//
// Note that the algorithm takes into account the chirality
// and cis/trans isomerism of molecular templates.
//
// USAGE:
//
// Run this code with the MOE File Open panel ("Run SVL").
// Then press the 'Tutorial' button in the panel.
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Finds duplicate molecules in a database
Date 2006-10-13
Author CCG Support
Category Informatics and File I/O
Downloads 403
Details
Select duplicate molecules in a database viewer, write entry numbers of the duplicates in a new field. So you can run this code in batch as well as interactive mode. Takes into account topology.

D.Bondarev

Please contact the author with comments.

revised 11 feb 2004:
more robust handling of chiral flags from SD source files,
progress message in the main MOE window.
A simple toolbox to prepare a molecular database : evaluate druglikeness, redundancy ...
Date 2006-10-13
Author eric arnoult
Category Molecular Descriptors and QSAR
Downloads 282
Details
This script have been used in 9th Electronic Computational Chemistry Conference (mar-2003)

Preparation of a molecular database from a set of 2 million compounds for virtual screening applications : gathering, structural analysis and filtering.

http://www.univ-orleans.fr/SCIENCES/ICOA/eposter/eccc9/ECCC9i.htm


SYNTAX : Load 'eval_drug_likeness.svl' then eval_drug_likeness []

or

Paste the file eval_drug_likeness.svl in the directory $MOE/lib/svl/run and paste this line $MOE/lib/moe-menus :
MENU "GizMOE"
...
--> "Drug Like" exec "run'eval_drug_likeness.svl'"
ENDMENU
You can now launch the windl menu just by cliking on the 'GizMOE | Drug Like' Button

Search for compounds from database B that are dis-similar to compounds in database A, then remove duplicate finds from the results. Similarity is based on fingerprint similarity/tanimoto, duplicates are by SMILES, cis/trans isomerism, chirality.
Date 2006-10-13
Author CCG Support
Category Informatics and File I/O
Downloads 229
Details
Search for compounds from database B that are dis-imilar to compounds in database A, copy these into a new file, then remove duplicate finds from the results. Similarity is based on fingerprint similarity, duplicates are by SMILES, cis/trans isomerism, chirality.

When it finishes, a new MOE database is created named "dissimilarity.mdb" containing those molecules from the MOE_database_1 (!!) that are dissimilar to all molecules from MOE_database_2.

USAGE:
1. load the program file: load 'db_dissimilarity.svl'
2. db_simsearch ['MOE_database_1', 'MOE_database_2']
where the larger library comes first!

You can easily change the defaults at the top of the program file. Currently it is set to MACCS, tanimoto=0.85.

Dimitri Bondarev
Assembles several SDF files into one .mdb file containing unique molecules / stereoisomers.
Date 2006-10-13
Author Chris Williams
Category MOE/batch
Downloads 103
Details
Assembles several SDF files into one .mdb file containing unique molecules / stereoisomers.
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Given a compound library, break structures in it into meaningful pieces and collect all resulting scaffolds and R-groups into two new libraries. Take into account scaffold chirality.

This is a bugfix. The db_unique function previous version would exclude some fragments which were not true duplicates.
Date 2006-10-13
Author CCG Support
Category MOE Database Tools
Downloads 862
Details
DESCRIPTION:
This program processes all structures in a database, fragments them and writes the fragments into two new databases. It then removes duplicate fragments.

You may want to also take a look at a related plugin at this website, 'SAR Elucidation and Visualization' which correlates scaffolds/substituents with experimental activity in HTS results.

D.Bondarev

USAGE:
Run this code with the MOE File Open panel ("Run SVL").

After the calculation finishes, two new library files will be created, scaffold_library.mdb and rgroup_library.mdb, containing all scaffolds and R-groups collected from the source library. The algorithm distinguishes scaffolds and r-groups by the number of attachment points.

For example, a phenyl would be classified as an r-group whereas a bridge benzene ring would be classified as a scaffold.

The rules used to fragment the structures have been taken from
'Drug-like Index: A New Approach To Measure Drug-like Compounds and Their Diversity', J. Chem. Inf. Comput. Sci. 2000, 40, 1177-1187 Jun Xu, James Stevenson
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Rainbow-colored backbone
Date 2006-09-07
Author Kinya Toda
Category Graphics and Rendering
Downloads 45
Details
1. Load 'rainbowcolorribbon.svl'.
2. run following command in the command line interface.
RainbowColorRibbon []
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Saves images using a defined set of rotations.
Date 2006-08-10
Author Randal R. Ketchem
Category Graphics and Rendering
Downloads 112
Details
This tool is very useful for saving a set of images to be made into a movie or for viewing multiple angles of a system. It saves JPEG files and can also write POVRAY if Andrew Henry's write_pov.svl function is loaded. For POVRAY you will have to edit this file to uncomment the Write_POV lines.

Running this function as rot_save[] will rotate 360 degrees about the Y axis in 5 degree steps, saving an image for each step. You can be much more creative, though.

Rotate 30 degrees about Y in 5 degree steps, and 60 degrees about Z in 10 degree steps (steps need to get to desired angles at same time), then 60 degrees about Y in 5 degree steps, and 120 degrees about Z in 10 degree steps:
rot_save[[
[startAngle:[0,0,0],
maxAngle:[0,30,60],
stepAngle:[0,5,10]],
[startAngle:[0,5,10],
maxAngle:[0,60,120],
stepAngle:[0,5,10]]
]]
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Shows only protein backbones, without oxygens, and cysteine sidechains.
Date 2006-08-04
Author Randal R. Ketchem
Category Graphics and Rendering
Downloads 32
Details
This is a simple tool that produces a protein view that has quickly become my default view. It shows and hides atoms so that just the protein backbone is shown, without oxygens, and also shows cysteine sidechains. This view removes the clutter and lets me quickly see the general structure.

Make it a button by adding the following to your .moe-menus file:
MENU APPEND "RightButtonBar"
SEPARATOR
"Show Cys..." exec 'showcys[]'
active atoms
ENDMENU
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A new Color sub-option is added to the Atoms option in popup menus in the Sequence Editor which allows the coloring of atoms without first selecting them.
Date 2006-07-13
Author Keith Ball
Category Graphics and Rendering
Downloads 24
Details
In each of the popup menus in the Sequence Editor (Chain, Selected Chains,
Residue, Selected Residues, Residue Column), a "Color" sub-option has been
added to the "Atoms" option. This allows the direct coloring of atoms in
residue(s), chain(s), or selected residues or chains without having to first
select the atoms. It's a mega time saver, if you're lazy like me!

How to install:

This is how I've done it:

1.) Create a $MOE.local/lib directory (for instance, /opt/moe.local/lib on
Linux) and place the downloaded "menu-se-color" there.


2.) Edit your $HOME/.moe-menus file so that the line which by default reads

include "$MOE/lib/menu-se"

instead reads:

include "$MOE.local/lib/menu-se-color"


3.) Restart MOE, or load the $MOE.local/lib/menu-se menu file.
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Rapidly convert a 2D molecular library into a 3D library honoring chirality information.
Date 2006-06-14
Author CCG Support
Category Z- Obsolete Code
Downloads 189
Details
This program rapidly converts 2D structures in an MOE database, for example, freshly imported from an SD file, into 3D structures, honoring chirality information.

USAGE:
Run this program with the MOE File Open panel ("Run SVL"). The 3D strctures will be written back into the database file, replacing the original 2D structures.

D. Bondarev

Note.
If you need to enumerate all possible stereoisomers for a compound library, use the Chiral Enumeration plugin instead.
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Implementation of
Deng, Zhan; Chuaqui, Claudio; Singh, Juswinder; Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions;
J. Med. Chem. 2004, 47, 337-344
Date 2006-06-13
Author Guido Kirsten
Category Pharmacophores and Fingerprints
Downloads 310
Details
Load the SVL file into MOE. Open the protein in the main window and calculate the fingerprint of docked poses of the ligands as usual. To execute a similarity search protein and reference ligand must be in the MOE main window. If the ligands in the database are docked in different pockets the fingerprints will have different length because the number of residues near the ligand is different. In these cases similarity will be zero or NaN.
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Calculates public 166 bit MACCS keys from www.mdli.com.

If you "run" this file, then a GUI panel opens below the
menu bar in the main MOE window with a list of the MACCS
keys that are hit by the atoms in the main MOE window.

If you "load" this file, then a descriptor is added to
the list in the DBV | Compute | Descriptors panel for each
of the 166 keys.
Date 2006-05-30
Author Chris Williams
Category Pharmacophores and Fingerprints
Downloads 369
Details
USAGE

To Highlight MACCS keys in the main MOE window:

1. Save this file to your hard disk.

For it to be available for use by all of the users of MOE,
create a directory called $MOE/lib/svl/patch/run and save this
file to that directory. eg on Windows and Linux, this might be:
c:\moe\lib\svl\patch\run\ph4maccs_x.svl
/usr/local/moe/lib/svl/patch/run/ph4maccs_x.svl

For the script to be available for use by a single user, then it
is best to create a directory in your home directory called svl,
and create a directory called run in that directory. Save this
file into that directory. eg on Windows and Linux, this might be:

c:\Documents and Settings\user_name\svl\run\ph4maccs_x.svl
/usr/people/user_name/svl/run/ph4maccs_x.svl

2. Run this file.
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.

(b) At the SVL command line, type:
run 'ph4maccs_x.svl'

=======================

To Calculate MACCS keys as Descriptors

1. Save this file to your hard disk.

For it to be available for use by all of the users of MOE, save
it to $MOE/lib/svl/patch/ph4maccs_x.svl eg on Windows and Linux,
this might be:
c:\moe\lib\svl\patch\ph4maccs_x.svl
/usr/local/moe/lib/svl/patch/ph4maccs_x.svl

For the script to be available for use by a single user, then it
is best to create a directory in your home directory called svl,

c:\Documents and Settings\user_name\svl\ph4maccs_x.svl
/usr/people/user_name/svl/ph4maccs_x.svl

2. In the Database Viewer select the Compute | Descriptors menu.
The new descriptors will be added to the list. If you type
MACCS in the "Filter" box at the bottom of the panel, then just
these descriptors will be shown. Select the descriptors the you
want to calculate and click the OK button.
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Implementation of:
Kazius, Jeroen; McGuire, Ross; Bursi, Roberta
Derivation and Validation of Toxicophores for Mutagenicity Prediction
J. Med. Chem. 2005, 48, 312-320
Date 2006-03-31
Author Guido Kirsten
Category Molecular Descriptors and QSAR
Downloads 244
Details
Load the attached file into MOE and a new descriptor named "TOX" will be avaiable. This descriptors counts the number of approved toxicophore features in a molecule.
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MOE fingerprints with more Similarity metrices
Date 2006-03-29
Author Guido Kirsten
Category Pharmacophores and Fingerprints
Downloads 117
Details
This zip archive contains a couple of svl files. After loading these files in MOE new fingerprints appear in the Fingerprint list. These Fingerprint start with X... They are identical to the fingerprints defined in the release code of MOE, but offer more similarity metrices.
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3D fingerprint
Date 2006-03-29
Author Chris Williams
Category Pharmacophores and Fingerprints
Downloads 221
Details
ph4_tri3d modified to output 'unencoded' fingerprint of form 'ABC{D1 D2 D3}' where 'A,B,C' are the pharmacophore types.
D1 = A-B distance
D2 = C-C distance
D3 = B-C distance

db_ph4_tri3d.svl includes a function that calculates these fingerprint for a database of compounds and writes them to a field called Ph4_tri3D. It is now the "main" function, so if you "run" this file, it will prompt you to pick a database and calculate the values for the first molecule field in it.

Usage:

1. Run this file.
(a) From the MOE | File | Open panel, select this file and click the "Run" button.
2. Load this file:
(a) From the MOE | File | Open panel, select this file and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points to a subdirectory such as $MOE/local_svl and then save this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL command line, type a command like

db_ph4_tri3d []
db_ph4_tri3d [mdb_key, input_mol_field]
mdb = db_Open 'in.mdb';db_ph4_tri3d [mdb, 'mol']

Normally a fingerprint function like this would be accessible through the DBV | Compute | Fingerprints panel, but this function is missing a function to measure the similarity of the fingerprint.
Calculates descriptors for a database of compounds for C2 symmetry as described at http://en.wikipedia.org/wiki/Rotational_symmetry
Date 2006-03-27
Author gkirsten
Category Molecular Descriptors and QSAR
Downloads 50
Details
USAGE: load 'q_symmetry.svl'

1. Save this file to your hard disk.

For it to be available for use by all of the users of MOE, save
it to $MOE/lib/svl/patch/q_symmetry.svl eg on Windows
and Linux, this might be:
c:\moe\lib\svl\patch\q_symmetry.svl
/usr/local/moe/lib/svl/patch/q_symmetry.svl

For the script to be available for use by a single user, then it
is best to create a directory in your home directory called svl,

c:\Documents and Settings\user_name\svl\q_symmetry.svl
/usr/people/user_name/svl/q_symmetry.svl

2. In the Database Viewer select the Compute | Descriptors menu.
The new descriptors will be added to the list. If you type
sym in the "Filter" box at the bottom of the panel, then just
these descriptors will be shown. Select the descriptors the you
want to calculate and click the OK button.
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Clustering by K-Means algorithm
Date 2006-01-30
Author Kinya Toda
Category MOE Database Tools
Downloads 177
Details
This is the tool for clustering the data in a MDB file by K-Means algorithm. As the results of the calculation, the cluster number and the center flag of each clusters are saved in the MDB file.

<Usage>
1. Load 'kmean.svl'
2. Type the "KMean[]" command in CLI of the target MDB file.
3. Set the parameters and click "OK"

<Settings>
Cluster Field: Field name for saving the cluster number. The same number means the same cluster.

Center Field: Field name for saving the cluster center flag. "1" is saved at cluster center entries, and others are "0".

N of Cluster: The number of clusters.

Initial Center: The method to select the initial cluster centeres in K-Means algorithm. "Random": Random sample of N entries. "First N": First N entries of MDB file.

Options: List of all the numeric fields in the MDB file. Loaded QuaSAR descriptors are selected automatically. The selected fields will be used in the calculation and the unselected fields will be ignored.

----------
The screenshot is the 3D plot of the result of K-Mean Cluster created by [DBV | compute | Analysis | 3D Plot].
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Generates a GIF file for each snapshot in an MDB output database from a molecular dynamics simulation
Date 2005-11-28
Author Niall English
Category Graphics and Rendering
Downloads 81
Details
Plots all of the configurations of an MD output database to the MOE Window and also writes out a GIF file for each configuration. If you would like to write the configurations to JPG, BMP or PNG, then change the command to fwrite_JPG or fwrite_BMP etc at line 23 of the code, and similarly for lines 60 and 63.
The files are written to the current working directory as 'md_00001.gif', 'md_00002.gif' etc.
You may then use a third party program to convert the graphics files into an AVI or MPEG film.
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Converts all Isis Draw sketch file in a directory into a MOE database file
Date 2005-11-16
Author Guido Kirsten
Category Informatics and File I/O
Downloads 91
Details
run 'skc2mdb.svl' in GUI mode or
load 'skc2mdb.svl' and say:
skc2mdb ['directory','mdb-filename',options]
options convert_3D:1 means convert to 3D,
open_dbv:1 open mdb in DBV after import
one_molecule:1 split multi molecule skc's

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This is an enhanced MOE FlexAlign 2005. You can select the atoms which will be important in an alignment, and the UNselected atoms will be ignored in the alignment. For example, you can superpose ligands only on certain donors/acceptors.

This version has been updated to include changes to the FlexAlign code in MOE 2005.06.
Date 2005-09-28
Author CCG Support
Category Simulations
Downloads 347
Details
DESCRIPTION:
This is an enhanced MOE FlexAlign 2005. You can select the atoms which will be important in an alignment, and the UNselected atoms will be ignored in the alignment.

For example, you can ignore unimportant donors/acceptors.

D.Bondarev

USAGE:
Save this program file flexalgn.svl and double-click on it in the MOE File Open panel. Select important atoms in the main MOE window and press OK to run the alignment.


keywords: flexalign, flexible alignment, superposition, pharmacophore.
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This code generates all stereoisomers for a compound library in MOE format, honoring the existing chiral center definitions.
Date 2005-09-26
Author D. Bondarev
Category Chirality Tools
Downloads 231
Details
Chiral N and P atoms are ignored in the enumeration and are set to the "S" configuration whenever possible (i.e. if that doesn't interfere with a complete enumeration on other chiral centers). They are denoted with lower-case letters in the output. All possible stereoisomers could be provided, even if the compound has constriants, by ignoring these constraints.

If the compounds came from an SDF file with chirality info, they will appear flat in the source MOE database. After you've run this plugin, a new database will be created, called chiral_isomers.mdb, containing the proper stereo-configurations of the defined chiral centers, all possible stereoisomers of the un-defined chiral centers and the number of chirality centers. Additionally non-chiral structures are listed in the new database.
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This is a directional pharmacophore scheme with conformation-dependent projected donor and acceptor features. The donor, acceptor, projected donor and projected acceptor features take into account tautomerism (e.g. in carboxyl groups). In those conformations where a projected don/acc feature is obscured, it is eliminated.
Date 2005-09-07
Author CCG Support
Category Pharmacophores and Fingerprints
Downloads 153
Details
This pharmacophore scheme is compatible with MOE 2003.02, 2004.03 and 2005.06.

Please read the tutorial contained in the attached .zip file.

The scheme is different from the default ones in MOE and contains the following features:

1. Aromatic ring center,
2. Symmetric aromatic axial features (3.5 Angstroms away from the ring plane),
3. Hydrophobic moiety (at a geometric center of a hydrophobic atom group),
4. Charged species (at a protonated or deprotonated atom),
5. Hydrogen bond donor,
6. Symmetric peer acceptor feature (2.8 Angstroms away from an h-bond donor, oriented depending on the chemical type of the donor),
7. Hydrogen bond acceptor,
8. Symmetric projected peer donor feature (2.8 Angstroms away from an h-bond acceptor, oriented depending on the chemical type of the acceptor).

The donor, acceptor, peer donor (DonPeer) and peer acceptor (AccPeer) features take into account tautomerism (e.g. in carboxyl groups). The DonPeer and AccPeer features are conformation-dependent. In those conformations where a projected don/acc feature is obscured, it is eliminated.
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This is a standard MOE molecular builder with an add-on: buttons to set and remove chiral constraints.
Date 2005-08-24
Author CCG Support
Category Z- Obsolete Code
Downloads 39
Details
DESCRIPTION:

This builder is a standard one with an addition of a button bar (see picture) to set and remove chiral constraints and a button to invert the molecule.

USAGE:

Run this code with the MOE File Open panel ("Run SVL"). Once you've set the desired chiral constraints, subsequent conformational searches will honour these. Also, when you copy the molecular structure into an MOE database, the constraints will be copied along with it (and saved for future usage).

D.Bondarev
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Search and display SVL source file from SVL commadns, QuaSAR descriptors and run SVL files. Launch Function Help File from the SVL Command.
Date 2005-08-20
Author Kinya Toda
Category SVL Utilities
Downloads 52
Details
INTRODUCTION>
MOE's SVL is a excellent tool for computational chemistry. One of the reasons for it is that we can use SVL source code created by developers. Thus we often need to refer to the specified SVL source file. Combining 'ted_Open' and 'sym_file' commands, we can open SVL source file. But that is often bother.
Using this program (source_file.svl), SVL source files are searched and opened easily. There is another 'help' function is already submitted at http://svl.chemcomp.com/filedetails.php?lid=397&cid=37

<USAGE>
1. Load this file:
(a) From the [MOE|File|Open] panel, select this file and click the "Load SVL File" button.
(b) Save this file under '$MOE/lib/svl/'. And start MOE.

2. At the SVL command line interpreter, type commands like:
source_file 'global_function'
==> Open source file and set cursor if it exist

source_file 'QuaSAR_descriptor'
==> Open source file and set cursor

souce_file 'run-time_svl'
==> Open source file

source_file 'a_part_of_global_function'
==> Print candidate lists

help 'global_function'
==> Open help file by web browser

For example:
svl> source_file 'FlexAlign'

svl> source_file 'add'
'add' is SVL built-in function.

svl> source_file 'SlogP_VSA0'
Global Function: 'QuaSAR_calc_SLogP'

svl> source_file 'builder.svl'
Open run-time SVL: 'c:/ccg/moe/lib/svl/run/builder.svl'

svl> source_file 'Flex'
'Flex' is not found. Other global SVL functions related to 'Flex' :
'FlexAlign'
'FlexAlignPanel'
'FlexAlignSimilarityScore'
..........

svl> help 'db_Read'
Displaying '$MOE/html/moe/fcnref/db_read.htm'

<NOTE>
Typing "sou" + TAB key, the "source_file" command is entered automatically.
In MOE 2003, R-group clip for alkyl groups only clips Met, and not anything longer. This code is a fix for that.
Date 2005-08-12
Author CCG Support
Category Z- Obsolete Code
Downloads 46
Details
This is the modified version of r-group clipping tool which clips off anything that is attached to the leaving group, along with the leaving group.

In MOE 2003, R-group clip for alkyl groups only clips Met, and not anything longer. To correct this oversight of ours, please use the attached code, dbvclip.svl. Run it with the MOE File Open panel ("Run SVL").
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This (modified) rmsd and superposition tool takes into account molecular symmetry.
Date 2005-08-12
Author CCG Support
Category Z- Obsolete Code
Downloads 122
Details
DESCRIPTION:
When computing RMSD, it is important to take into account molecular symmetry, for example in the case of benzene rings. If a ring flips, rmsd should still be the same. This code for Conformation Geometry tool has been modified to include molecular symmetry.

USAGE:
With the MOE File Open panel, "Run SVL".
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Evaluates and displays hydrogen bonds between two sets of atoms, along with the h bond angle, score and length
Date 2005-07-21
Author Niall English
Category Graphics and Rendering
Downloads 156
Details
Two sets of atoms, A and B, are passed to the function, which evaluates the hydrogen bond contact 'strengths', lengths and bond angles. The hydrogen bonds are shown in the main MOE window, based on their strengths (a value between 0 and 1). H bonds with scores greater than a specified threshold are shown in the desired colour, along with the h bond lengths, angles and strengths. The h bonds are rendered D-H....A, unlike the MOE default D.....A
The algorithm for scoring the strength of a hydrogen bond is taken from Dimitri Bondarev's script scoring.svl at the SVL exchange.

USAGE

Load this file:

From the MOE | File | Open panel, select this file and click the "Load" button.

Ensure that hydrogens have been added to the system, and define the sets of atoms A and B. The colour of the hydrogen bonds may be specified in the options vector, in addition to the minimum score necessary for display purposes:

e.g.

Add_H Atoms []
A = cat cAtoms first Chains []
B = cat cAtoms second Chains []
opts = [colors: 'blue', threshold: 0.6]
hbond_analysis [A, B, opts]
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This guide is meant as a recommendation, to help you write easily readable/maintainable MOE programs and plugins.
Date 2005-04-18
Author CCG
Category Practical Questions Answered
Downloads 432
Details
This guide is meant as a recommendation, to help you write easily readable/maintainable MOE programs and plugins.
This is an exampleof a web oriented use of a Moebatch utility (batch_sd_to_ascii.svl).
Date 2004-08-27
Author Matteo Floris
Category Miscellaneous
Downloads 65
Details
The main file is a simple PHP script: it can be used for web applications. The script give the possibility to draw a molecule for obtaining ca. 60 descriptors. The calculation in based on a SVL file from the SVL exchange (batch_sd_to_ascii.svl).
Append the "append_file" to the "old_file"
Date 2004-08-25
Author Chris Williams
Category Informatics and File I/O
Downloads 118
Details
USAGE

1. Run this file.
(a) From the MOE | File | Open panel, select this file
and click the "Run" button.
2. Load this file:
(a) From the MOE | File | Open panel, select this file
and click the "Load" button.
(b) Create an environment variable MOE_SVL_LOAD that points
to a subdirectory such as $MOE/local_svl and then save
this file into that subdirectory.

(c) In an SVL function, in a MOE menu file or at the SVL
command line, type commands like

file_reader []
file_reader [old_file, append_file]
file_reader ['old.txt, 'update.txt']
run 'file_reader.svl'
run ['file_reader.svl', ['old.txt, 'update.txt']]
Typed Graph Distance Fingerprints with bit counts
Date 2004-08-18
Author Original file edited by Chris Williams
Category Pharmacophores and Fingerprints
Downloads 127
Details
.
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To Change the tube thickness and color by temperature factor, Residue Hydrophobicity or Residue Volume.
Date 2004-06-01
Author Kinya Toda
Category Graphics and Rendering
Downloads 46
Details
(1) Load this function
(2) Enter
svl> RibbonThickness []
at the SVL command line.

After selecting 'Thickness' and 'Color', click 'Apply'. If 'Color' checkbox is turned off, the color of backbone is not changed.
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This is a descriptor that determines the pattern of existing aromatic substitution in a ring system: ortho, meta, para.
Date 2004-04-23
Author CCG Support
Category Molecular Descriptors and QSAR
Downloads 97
Details
The descriptor is called aro_subst and it returns: 1: ortho, 2: meta, 3: para, 0: none or many.

Please double-click on the attached program file q_substitution.svl on the list in the MOE File Open panel.

You can then compute the aro_subst descriptor in MOE.
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An implementation of drug-like index descriptors
Date 2004-04-13
Author CCG Support
Category Molecular Descriptors and QSAR
Downloads 318
Details
Drug-like Index: A New Approach To Measure Drug-like Compounds and Their Diversity', J. Chem. Inf. Comput. Sci. 2000, 40, 1177-1187 Jun Xu, James Stevenson

Some descriptors here may differ because of MOE definitions for SSSR, donors, acceptors, n_of_aromatic_systems, n_nonH_polar_bonds

NEW:
Three more descriptors added:
'DLI(26)', 'total number of 3-8 membered rings'
'DLI(27)', 'total number of 3to8 saturated rings'
'DLI(28)', 'total number of 3to8 unsaturated rings'

I assumed we were interested in a total count of 3-8 rings (together). Also, I assumed that we were interested only in 3-8 membered saturated and unsaturated rings, and a ring was considered unsaturated when it contained at least one double bond or was fused with an aromatic ring.

D.Bondarev
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This tool can be used for protein loop modeling in situations where MOE Homology does not work, for example in non-standard residues and covalently bound ligands.
Date 2004-04-02
Author CCG Support
Category Protein Tools
Downloads 219
Details
DESCRIPTION:

This algorithm relies on distance geometry with subsequent forcefield refinement and backbone angle checks, stereochemistry checks, followed by knowledge potential scoring (adopted from MOE Homology).

D.Bondarev
bondarev@chemcomp.com

USAGE:

Select atoms of interest and run the program.

Run this program with the MOE File Open panel. In MOE 2004, just double-click on the program file in the panel. In MOE 2003, press "Run SVL".


keywords:
loop modeling modelling gpcr gpcrs homology covalent
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Fuzzy clustering is a method that can account for
compounds that belong to several chemical classes
at the same time. In this way, all amides in your
dataset will be clustered together, and all imidazoles
will be in another cluster. A compound that has both
functional groups will simultaneously belong to two
clusters. In many situations, this would be the
preferred way to look at compound sets.
Date 2004-03-17
Author CCG Support
Category Basic Molecular Tools
Downloads 141
Details
This tool can be used to derive and display fuzzy
clusters in compound sets. For example, if you have an HTS dataset and want to salvage false negatives. In that case, you can spot false negatives when they occur in the same clusters with multiple positives.

D.Bondarev
bondarev@chemcomp.com

Please read the tutorial (press the Tutorial button in the clustering panel).

Start the clustering plugin by using MOE File Open (press the "Run SVL" button).

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Automaticaly rotate, draw BB, wave Z-Clip, etc...
Date 2004-01-15
Author Kinya Toda
Category Graphics and Rendering
Downloads 121
Details
(1) Load this function
(2) Enter
svl> Exhibition []
at the SVL command line.

Turn on the check boxes which you prefer and click 'OK' or 'Apply'. If you clicked 'OK' button, the window would be closed.

Rotation:
Rotation: XYZ - rotation axis
Step: - the angle for 1 step of the rotation
Wait time: - wating time/sec until next step

Back Bone:
Simultaneous: - If some chains were exist, all chains were drawn simultaneousely. In the case of dimers or superposed homologues.

Slice:
- It is good for using with Molecular Surfase Objects.
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Removes chiral constraints from all structures in an MOE database.
Date 2003-12-22
Author CCG Support
Category Chirality Tools
Downloads 66
Details
USAGE:

Run this code with the MOE File Open ("Run SVL"). You can also run it as a function, see inside the file for details.

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This code is based on the standard MOE SiteFinder and automatically creates dummy atoms defining the larges binding pocket on a protein, with no need for a GUI panel.
Date 2003-12-11
Author CCG Support
Category Protein Tools
Downloads 160
Details
This code is based on the standard MOE SiteFinder and automatically creates dummy atoms defining the larges binding pocket on a protein, with no need for a GUI panel.

USAGE:
MOE | File | Open, highlight this program file on the list and click "Run SVL".

keywords: binding pocket, alphasite points, dummy atoms, sitefinder, site finder, batch.
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Read and display molecules from an Oracle database.
Date 2003-10-03
Author Scott Burlington & CCG Support
Category Informatics and File I/O
Downloads 79
Details
host:port:database

It assumes structures are kept as MDL mol files, either as CLOB or VARCHAR, the script should be able to determine that automatically. It is of course possible to modify it to read SMILES strings.

When you run it, the structure(s) returned from Oracle should be written into an MOE database file named oracle_compounds.mdb.

Please email or phone me if you think this might be a basis for something you could use. Dimitri Bondarev

// USAGE:
//
// 1. Install Java Run-Time Environment 1.2 or later on your computer:
// you can download it from http://java.sun.com for example.
// Note that it may already be on your computer! To check, type
// java -version at the command prompt of your computer.
//
// 2. Install Oracle Java Database Drivers on your computer:
// These can be found on the Oracle Installation CDs or downloaded
// from http://www.oracle.com
// The drivers are contained in a single file, classes12.zip.
//
// 3. In your operating system, set the environment variable CLASSPATH
// to point to this classes12.zip file, for example:
// set CLASSPATH = c:\jdbc\classes12.zip
// Note that in Windows XP you can set environment variables using
// Control Panel | System | Advanced | Environment Variables but you
// need to have logged on as Administrator.
//
// 4. Make sure you can see the Oracle database server on your network
// and that you have a user name and password to access data in it.
//
// 5. Run this program!
// Use the MOE File Open panel to highlight this program on the list
// and then click on the "Run SVL" button in the File Open panel.
//
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A descriptor which applies a decision tree to specified molecular properties and outputs the class (pass or fail, for example, or one of several classes: 1,2,3).
Date 2003-09-22
Author CCG Support
Category Molecular Descriptors and QSAR
Downloads 72
Details
DESCRIPTION:
After having built a decision tree in MOE-Classify, write down the split points and the properties by which the splitting is made. Then, edit this code to change the decision tree example given in it. This descriptor then becomes your decision tree in an easily computed format!

USAGE:
Load this code (OK in the MOE File Open panel) and compute the descriptor 'classifier' for an MOE database.
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This script shift residue UID's by a user-specified number.
Date 2003-09-18
Author CCG Support
Category Protein Tools
Downloads 125
Details
Use the MOE File Open panel (click OK) to load the code. Then in the MOE Command Line type

renumber 10 to shift the residue ID's by 10,
renumber -10 to shift the residue ID's by 10 back,
renumber 50 by 50, etcetera.

Then (if you want to display the labels in the 3D rendering window) type label[] or unlabel[].
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This script brings up an interface panel which allows you to rotate the molecule in the main MOE window by a predefined angle (see the picture).
Date 2003-09-18
Author CCG Support
Category Basic Molecular Tools
Downloads 78
Details
USAGE:

Run this code with the MOE File Open panel ("Run SVL").
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A checklist for the setup of MOE in distributed mode.
Date 2003-09-18
Author CCG Support
Category Practical Questions Answered
Downloads 63
Details
1. Make sure you have enough tokens to run the desired parallel setup. For example, it's necessary to have 3 tokens to run 3 moebatches, or 4 tokens to run one moe and one moebatch.

2. Make sure you can start MOE on all the machines by hand.

3. Make sure you are running an IP network (each machine has an IP address). If it's just one machine, don't worry about this.

4. Make sure rexecd is running on all machines. In UNIX, your sysadmin can enable it. In Windows NT/2K/XP, set it up as a service using the file $MOE/bin-i4w9/rexecd (rexecd -install). You will need to decide whether to start this service automatically whenever the computer is restarted or not to. In Windows 95/98/Me, run rexecd -start each time before moe on each computer.

5. In regular MOE, type
mpu_password 'your_network_password_here'
and keep the response handy.

6. Create a machine.txt file on the master computer ONLY, as follows:
$mpu-user your_network_user_name_here
$mpu-password ogocddhiig_and_so_on <---- NO QUOTES
$mpu-rexec complete_path_here/moebatch -mpu -
localhost moe -mpu - <----- could be moebatch -mpu -
hostname2 <---- this can be a name or an IP address
hostname3
hostname4

The complete_path_here should be the command to start MOE, for example C:\moe\bin-i4w9\moebatch.exe or /usr/local/moe/bin/moe. If MOE is installed elsewhere on some machines, type the appropriate path after their names, for example
biology3 /net/moe/bin-i4w9/moebatch -mpu -
starco /bldg5/apps/moe/bin-i4w9/moebatch -mpu -
so that the command above is executed instead of the default in the $mpu-rexec line.

7. On the master computer, type
moe -mpu machine.txt or moebatch -mpu machine.txt.

8. The computers can be on the same local network or connected long-distance, they can run different operating systems. If you want to run on multiprocessor machines, include their hostname several times in the file.(!!!!)

9. In MOE 2002.03, the following are parallel: Conformation Import, Homology Search, stochastic search in $MOE/sample/smics.svl.

10. Conformational Import will take advantage of parallel MOE when it sees it is running.

TROUBLESHOOTING:
not enough tokens, the $mpu-rexec command is incorrect on at least one machine, rexecd is not running or is hungup on at least one machine, username/password is incorrect or not the same for at least one machine.


I'm attaching a code example, dbloop.svl. Load the file on the master machine in a parallel setup (or just load it if running on one machine).

In the MOE Commands Line, type dbloop 'databasename.mdb' to run the code, which will count heavy atoms in each molecule in the first molecular field in the database.
MOE sometimes wouldn't let me type anything in the Commands Line or in dialog boxes.
Date 2003-09-18
Author CCG Support
Category Practical Questions Answered
Downloads 22
Details
The mysterious keyboard behavior in MOE on computers with Windows **and multiple languages** is caused by a conflict between Windows and MOE as to who gets to respond to Alt-Shift (molecule movement in MOE) first. Windows wins, and MOE doesn\'t show typed text anymore.

To stop this, please set the keyboard shortcut to None in the Microsoft Windows | Start | Control Panel | Keyboard | Language and press OK.

You will still be able to use the multiple keyboard languages you have on your system by clicking on the language icon at the botton right of your Windows desktop.
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This sample code displays a 'please wait' message in the main MOE window.
Date 2003-09-18
Author CCG Support
Category SVL Utilities
Downloads 51
Details
Run this code with the MOE File Open panel ("Run SVL").
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This is a plugin which allows you to draw distance meters of varying colors and line types.
Date 2003-09-17
Author CCG Support
Category Graphics and Rendering
Downloads 81
Details
The picture says it all.

USAGE:
Run this plugin with the MOE File Open panel ("Run SVL"). Select the line type and other attributes, then click on two atoms, and a meter will be drawn. You can hide/show/delete the meters you have drawn from MOE | Window | Graphics Objects menu option. To exit the 'cross-hair' cursor mode, press Escape on the keyboard.
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A "tutorial" for creating a database looping
function using SVL.
Date 2003-09-16
Author Raelene Lawrence
Category SVL Utilities
Downloads 281
Details
This svl function is a database looper which
calculates the molar mass and # carbons for each
entry in a database.

As a tutorial, the file contains plenty of
description and explanation to help a new SVLer
get up and running.

Usage:
1. Save and load the function.
2. At the SVL Command line, enter:

svl> database_tutor 'filename.mdb'

where filename.mdb is the name of the database
which you will perform the calculation upon.
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This is an enhanced version of the MOE Database Browser. It displays the ligands in stick, etc. mode and shows their associated data in the browser panel.
Date 2003-09-16
Author CCG Support
Category Graphics and Rendering
Downloads 108
Details
USAGE:
Run this plugin with the MOE File Open panel ("Run SVL").
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Draws rings in aromatic cycles
Date 2003-09-16
Author CCG Support
Category Graphics and Rendering
Downloads 46
Details
Draws graphic object rings in aromatic cycles.

To properly view the rings, the useer may need to turn on a
second white light gun (MOE|Render|Setup) in the +1 Z direction

Usage:
(1) Load this function.
(2) Enter

svl> draw_aromatic_rings[]

at the SVL command line.
(3) Rings should be drawn in all ring ayatems detected as aromatic

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This file contains three descriptors, total, polar and hydrophobic water-accessible surface areas. The values are computed using the logic from MOE Rotamer Explorer and (the same) from surface coloring panel.
Date 2003-09-16
Author D. Bondarev
Category Molecular Descriptors and QSAR
Downloads 155
Details
USAGE:
Using MOE File Open panel, click OK and then in the Database Viewer compute three descriptors: 'wat_acc_surf', 'directional_pol_sa', 'directional_hyd_sa'.

Colors atoms by scalar
Date 2003-09-16
Author Chris Williams
Category Graphics and Rendering
Downloads 60
Details
Function colors selected atoms by a give scalar; If no atoms
are selected all atoms are colored by the scalar

Usage:
(1) Load this function
(2) At the SVL command line enter

svl> color_by_scalar X

where X is a scalar between 0 and 1 (0 = violet, 1 = red)
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Keep track of atom selection sets in an MOE session.
Date 2003-09-16
Author D. Bondarev
Category Graphics and Rendering
Downloads 75
Details
Each selection set has a name, and it is possible to combine selection sets. The sets are not saved into a file.

USAGE:
Run this file with the MOE File Open panel ("Run SVL").
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The Hodgkin and Carbo fingerprint similarity indices.
Date 2003-09-15
Author D. Bondarev
Category Pharmacophores and Fingerprints
Downloads 108
Details
Two fingerprints with bits A,B. Common bits: C.

Tanimoto: C/(A+B-C)
Hodgkin index: 2C/(A+B)
Carbo index: C/sqrt(A*B)

The submission contains a .zip archive file with several .svl program files which should be saved where MOE can automatically load them. Once loaded, the similarity indices will appear everywhere in MOE alongside with the Tanimoto coefficient.

USAGE:
Open the .zip archive and save its contents (several .svl files) into a directory where MOE will load them on start-up. For example, create a new directory 'toload' and create a system environment variable MOE_SVL_LOAD = 'path/path/toload'. After restarting MOE, any .svl files from 'toload' should be loaded by MOE automatically.
Forcefield parameters descriptors
Date 2003-08-20
Author Dimitri Bondarev
Category Molecular Descriptors and QSAR
Downloads 86
Details
Descriptors for confirming correct MM atom typing throughout a database.

Usage:
(1) This is a QuaSAR-Descriptor enabled function.
(2) Load this function.
(3) Open a descriptor calculator as usual

(DBV | Compute | Descriptors )

(4) The following new descriptors will appear. Each will have valuse
of 0 or 1 depending on whether or not all the types and parameters
can be found for each molecule in the database

[ 'FFType_all', 'Forcefield Parameters Descriptor all_ok', '2D', []]
[ 'FFType_oop', 'Forcefield Parameters Descriptor oop', '2D', []]
[ 'FFType_tor', 'Forcefield Parameters Descriptor tor', '2D', []]
[ 'FFType_ang', 'Forcefield Parameters Descriptor angle', '2D', []]
[ 'FFType_bond', 'Forcefield Parameters Descriptor bond', '2D', []]
[ 'FFType_atom', 'Forcefield Parameters Descriptor atom', '2D', []]

Finds compounds from multiple MOE databases containing any of the substructures given as smarts patterns.
Date 2003-08-19
Author Dimitri Bondarev
Category Informatics and File I/O
Downloads 249
Details
Finds compounds from multiple MOE databases containing any of the substructures given as smarts patterns. Tracks the file source of matching compounds and the smarts pattern that matched.

USAGE:
1. Load this file (OK in the MOE File Open panel)
2. In the MOE Commands Line, type
db_substr_smiles [['C','ccc'], ['file1.mdb','file2.mdb','file3.mdb']]
3. A new MOE database will be created, output.mdb containing all matching compounds.
This function returns a list of tokens. All files in a given directory and its subdirectories are listed, with the full path prepended to each filename.
Date 2003-08-19
Author Dimitri Bondarev
Category SVL Utilities
Downloads 73
Details
This function returns a list of tokens. All files in a given directory and its subdirectories are listed, with the full path prepended to each filename.

Load this file and type
filelist 'directoryname'

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Computes root mean square deviation between a structure in the Main MOE window and its conformations in an MOE database.
Date 2003-08-15
Author Dimitri Bondarev
Category Basic Molecular Tools
Downloads 365
Details
Computes root mean square deviation between a structure in the Main MOE window and its conformations in an MOE database. The molecules are automatically superimposed. Molecular symmetry is taken into account.

To run the code, bring the structure into the main MOE Window and bring up the MOE File Open panel. Highlight the program file on the list and click "Run SVL".
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Allows the user to load a BLAST alignment.
Date 2003-05-28
Author Raelene Lawrence
Category Protein Tools
Downloads 59
Details
This function allows the user to load a BLAST
generated alignment into MOE. A fasta file
containing the alignment is also written since to
open the BLAST alignment into MOE, it is first
converted into fasta format.

There are a couple of preparation steps and notes
before you can use this svl function.

1. This function is designed to deal with an
alignment of only 2 chains; a query and a subject.
It will not work for any more than 2 chains.

2. This function does not load any structure that
may be affiliated with the alignment. It loads
the sequence alignment ONLY. Once the BLAST
sequence alignment is loaded into MOE, it is up
to the user to load any structure file and set
its residue positions to the residue positions
from the alignment.

3. To set up the \"blastfile\", cut and paste the
alignment from the BLAST website into a text
editor and save it. - there is more formatting
description in the svl file.


USAGE:

1. Save and load the svl file.

2. At the SVL command line, enter:

svl> blast_2_fasta [\'blastfile\', \'fastafile\']

where blastfile is the filename of the text file
containing the BLAST alignment and fastafile is
the name of the fasta file that is written.
Creates a text file suitable for input to Barton's
Alscript program.
Date 2003-05-28
Author Raelene Lawrence
Category Protein Tools
Downloads 40
Details
Description:
Function writes a text file for an alignment that
is suitable for submission to alscript (Barton).

Barton, G. J. (1993a),
"ALSCRIPT - A Tool to Format Multiple Sequence
Alignments", Prot. Eng., 6, 37-40.

http://www.compbio.dundee.ac.uk/Software/software.html

Function writes a text report of the chain
sequence information such that:
ch(1)res(1) ch(2)res(1) ch(3)res(1) ch(4)res(1)
ch(1)res(2) ch(2)res(2) ch(3)res(2) ch(4)res(2)
ch(1)res(3) ch(2)res(3) ch(2)res(3) ch(2)res(3)

with gaps preserved as spaces.

Usage:

1. Save and load the function.

2. Load the aligned system into MOE.

3. At the SVL Command line, enter

svl> make_alscript_input 'filename'

where filename is the name of the text file to be
created.
Export a set of fields from entries listed in a file to an ASCII file.
Date 2003-04-17
Author Pierre-Jean L'Heureux
Category Informatics and File I/O
Downloads 125
Details
This function preprocesses several lists in order to make a valid call to db_ExportASCII. For example, when doing QSAR, one would want to export a specific set of features in a specific order corresponding to a given set of compounds listed in a file.
/////
Note: I use a personal version of db_ExportASCII that is able to export a complete vector field. See the appendice of this file for a hint.
/////
function db_ExportASCIIList [
dbFileName, // Name or key of database to export
dstFileName, // Output filename fieldsFileName, // Filename for the list of
// fields to output. The order in
// which they appear will be
// enforced
entriesFileName,// Filename for the list of
// entries to export
IndexField] // Token of the field choosen as
// the unique identifier
// of each entry.
i3D Polar Surface Area descriptor
Date 2003-03-31
Author junichi goto
Category Molecular Descriptors and QSAR
Downloads 198
Details
Ref:

J. Med. Chem., 1998, 41, 5382 - 5392
Pharmaceutical Research, vol. 16, No. 10, 1999, p. 1520-1526.
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Graphic Object Manager' like tool for molecules
Date 2003-03-31
Author junichi goto
Category Graphics and Rendering
Downloads 136
Details
Usage:

(1)Load this file
(2)Open files
for example, read
$MOE/sample/moe/biotin.moe and biotin_rec.moe
(3)Enter
svl> MolObjectManager []
in command line

You can toggle Hide/Show, Selected/Unselected,
Active/Inactive in single click chain by chain
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Revised 'Dihedral Contour Plot'
Date 2003-03-31
Author junichi goto
Category Basic Molecular Tools
Downloads 98
Details
Most of users who run 'Dihedral Contour Plot' should be
interested in the region of energy local minima.

Original version of dihcont.svl use threashold value 50
and it doed not always give reasonable plot.
So, we add 'Slider' to change this parameter after
the calculation.
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For a double nested vector, this function will perform a db_Write[], using a construct as fieldname.
Date 2003-03-24
Author Pierre-Jean L'Heureux
Category Informatics and File I/O
Downloads 49
Details
Because db_Write[] cannot handle double nested
vector, this function will create new fields for writing them.
The name of the new fields will be a cat[fieldname,index].

Input
mdb: a key to an already opened database
entrie: a single database entry key
fieldname: a vector of n field names
fieldtype: a vector of n field types
value:a vector of n values or a matrix of n
vectors of values
Output
entrie: the entry key as returned by db_Write[]
Prepares a sequence alignment for adding to pdb.fam
Date 2003-03-23
Author Dimitri Bondarev
Category Protein Tools
Downloads 50
Details
Given an aligned MOE system, this function writes a sequence alignment file suitable for inclusion in a *.fam file. The chain tag is taken as the chain name.

Sequence only data is given the default 'XXX' header. Structured sequences get the 'PDB' header.

Usage:
Run this file using the MOE File Open panel. It will create the file named seqfamily.fam.
Computes ligand-protein contacts
Date 2003-03-23
Author Chris Williams
Category Protein Tools
Downloads 367
Details
1. User gives the evaluation script a multi-mol2 file with the protein (let's assume correctly charged and protonated) as molecule 1, and the ligand (let's again assume correctly charged and protonated) as molecule 2.

2. Minimize the ligand (MMFF, GBSA solvation) with protein atoms fixed.

3. Evaluate the ligand: ClogP, SlogP, Mol. Weight, # Rotatable Bonds, #chiral centers, solvation/desolvation E, internal strain energy (delta E from ground state; as per your scsearch svl), and predicted permeability usingan in-house model (we already have an svl script for this).

4. Evaluate the protein-ligand interaction: # H-bonds made, # hydrophobic contacts (as per your protein contact function), and non-bonded interaction energy (coulombic and van der Waals).

5. Write out all values to a text file ("multi-mol2_MOE.data").

6. Write out separate mol2 files for input into other software (protein in one ligand in the other; multi-mol2_PROTEIN.mol2 and multi-mol2_LIGAND.mol2)
Builds a homology model
Date 2003-03-23
Author Raelene Lawrence
Category Protein Tools
Downloads 131
Details
Builds a homology model for an unknown sequence, using a prealigned set of proteins that are in moe format. The .pir files are stored in a query directory that is designated in the function call.

This function assumes that the aligned sequences are saved as a .moe file.

The program sequentially builds models for all files in the query directory and saves them as promodel_X.moe/mdb.

X = the number associated with the query file
Utilities to add hydrogens or delete hydrogens from all or selected molecule fields in a database.
Date 2003-03-23
Author Chris Williams
Category MOE/batch
Downloads 184
Details
Utilities to add hydrogens or delete hydrogens from all or selected molecule fields in a database.
Performs batch homology modeling.
Date 2003-03-23
Author Dimitri Bondarev
Category MOE/batch
Downloads 160
Details
1. Prepare the options file for batch homology modeling:

a) Load this file (SVL | Save and Load) or
svl> load 'bh.svl'
b) Bring a sample query-template file into MOE
c) MOE | Window | Potential Control, set to Engh-Huber and turn on the solvation term.
d) Sequence Editor | Homology | Homology Model, set the options, also set Ignore Outgaps, then click OK. A batch options file is written, named homology.task. This file will be used to build all homology models. You can re-use this file for subsequent runs.

2. Prepare the input files:

a) Query-template alignments in the PIR format (multiple files, each containing exactly two aligned protein sequences). Query sequence is the first, template is the second!
b) Template structures in the PDB format (multiple files, non-protein chains will be treated as environment, each file containing at least one protein chain). Only the chain matching the template sequence from the .pir file will be used as a template.
c) A list of templates and alignments named filelist.txt, as follows:
file.pdb file.pir modelfilename.pdb
file.pdb file.pir modelfilename.pdb
file.pdb file.pir modelfilename.pdb
file.pdb file.pir modelfilename.pdb

3. Run the batch job:

sys_prompt> $MOE/bin/moebatch -exec "run ['bh.svl', ['homology.task','filelist.txt']]" -exit

4. The code generates homology models in PDB format and a logfile.
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Displays iterations of Conway's Game of Life.
Date 2003-03-19
Author Martin Santavy
Category Miscellaneous
Downloads 192
Details
Displays iterations of Conway's Game of Life. Each iteration updates and displays a binary matrix according to the "Rules of Life". Action buttons either reset the matrix or present a screen more acceptable to your boss. Selection by mouse inverts a rectangular portion of the matrix. (See the top of the file for more details on the rules and usage.) Note: This program is meant to amuse you. However, it also demonstrates how to use SVL vector indices to replace nested loops of traditional programming languages.
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SD file to Patty-typed SD file
Date 2003-03-18
Author CCG Support
Category Informatics and File I/O
Downloads 135
Details
This function sequentially reads records of an SD file, assigns patty
types to the atoms,

B.L.Bush, R.P.Sheridan PATTY: A Programmable Atom Typer and Language for
Automatic Classification of Atoms in Molecular Databases.
J.Chem.Info.Comp.Sci, 33, pp756-762, 1993

and writes out as a string the comma separated
types to an output SD file. Note that the code $MOE/sample/patty.svl
must be loaded before loading this function.
Note that an intermediate MOE database is NOT created in this code.

Usage:
(1) Load the sample file $MOE/sample/patty.svl
(2) Load this function
(3) Enter

svl> sd_PATTY_Type_sd 'filename.sdf'

at the SVL command line.
(4) A new SDF file

'filename_PATTYprocessed.sdf'

will be created.
Find ligand atoms in a protein system
Date 2003-03-18
Author Chris Williams
Category Protein Tools
Downloads 66
Details
This file contains two functions:

(A) select_non_peptide[]

Returns the atom keys of all atoms in non-water, non-aa and
non-aa bound structures. The function also selects those atoms

Usage:
(1) Load this function
(2) Given a structure in the MOE window, enter

svl> select_non_peptide[]

(3) The non-water, non-aa and non-aa bound atoms will
be selected in the MOE window and their keys will be returned.


(B) contains_non_peptide []

Returns a 1 if the structure contains residues other than amino acids
and water molecules.

Usage:
(1) Load this function
(2) Given a structure in the MOE window, enter

svl>contains_non_peptide []

(3) The function will return 1 if there is a non-water/non-amino
residue in the system, and 0 if the system contains a non-water
non-amino residue
Forcefield Charge descriptors
Date 2003-03-17
Author Paul Labute
Category Molecular Descriptors and QSAR
Downloads 77
Details
Binned VDW surface area descriptors based on forcefield charges. The
partial charges of the currently loaded forcefield are employed.

Usage:
(1) Load this funtion
(2) Open a descriptor calculation panel ( DBV | Compute | Descriptor)
(3) A new set of 'FF_' descriptors will appear in the panel

....
....
[ 'FF_VSA+6', 'Total positive 6 vdw surface area', '2D', [] ],
[ 'FF_VSA+5', 'Total positive 5 vdw surface area', '2D', [] ],
....
....
Calculates the maximum number of contiguous rotatable bonds as a descriptor
Date 2003-03-17
Author CCG Support
Category Molecular Descriptors and QSAR
Downloads 99
Details
Computes as a decriptor the number of contiguous rotatable bonds in
a molecule. The rotatable bonds are defined as non-ring single bonds.

Non-ring single bonds to be excluded from the rotatable bonds list
are defined in the constant NON_ROTATABLE. To be considered
non-rotatable by the current code, SMARTS match for the A and B
atoms in the non-ring single bond shoudol be entered in the
NON_ROTATABLE constant.

name A atom B atom
['amide', '[#6](=O)[#7]', '[#7]-[#6](=O)' ],
['amidinium', '[#7]([#6](=[#7])[#7])', '[#6](=[#7])([#7])[#7]' ],
['halogens', '[#G7]-[#Q]', '[#Q]-[#G7]' ],
['terminals', '[#QQ1]-[#Q]', '[#Q]-[#QQ1]' ],


Usage:
(1) Load this function
(2) A new descriptor

b_Cont_Rot # of contiguous rotatable bonds 2D

will appear in the descriptor list
(3) the descriptor uses smiles matching to find the longest
continuous chain of rotatable bond
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Geometry optimization in torsional space
Date 2003-03-16
Author Dimitri Bondarev
Category Basic Molecular Tools
Downloads 117
Details
Finds a (global) minimum-energy structure in torsional space.

Usage:
(1) Load the structure you wish to minimize.
(2) This is a run file. Enter

svl> run 'torsional_drive.svl'

at the SVL command line.
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The function decomposes database entries based on reactions specified by SMILES/SMARTS matches.
Date 2003-03-16
Author Dimitri Bondarev
Category Combinatorial Chemistry
Downloads 151
Details
-function decomposes database entries based on reaction
chemistries. The reactions are specified in a BONDS constant
which has the following format:

Rnx: # name AB A env. B env
['1', 'amide', 'C-N', 'C=O', 'NC(=O)'],
['2', 'ester', 'C-O', 'C=O', 'OC(=O)'],
...

where

Rxn:# -# of reaction in list
name: -name of reaction
AB -list of smiles matches for AB bonds
A env. -list of smiles matches for A environments
B env. -list of smiles matches for B environment


The reactants are written out with terminal H attachment points.
The H points are labeled

AX
where X = Rxn. # (from BONDS list)

(Alternately, Axxy where xx = Rxn. # and y is the instanced of that
reaction. Useful for testing and reconstruction)

The root heavy atom at the connection point is renamed

ElementX
Element = element symbol; X = # of reaction in reactant list

Thus, each run is currently limited to 9 detachments
points per reaction

Decomposed products are written to reactant fields named
'Reactant_Y' where Y = 1-n for the n different fragments generated
from the source molecule. If there is no reactive decomposition,
the original molecule is written to a field 'Reactant_0'

Usage:
(1) Load this function
(2) Open the database you wish to decompose
(3) Enter

svl> BondDecompose[]

at the SVL command line at the top of the database
you wish to decompose.

(4) When the panel appears, select the reaction(s) you
wish to consider in the decomposition run.
(5) Press 'Apply' to star the decomposition

Reference:
RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New
Technique for Identifying Privileged Molecular Fragments with Useful
Applications in Combinatorial Chemistry , Lewell, X. Q.; Judd, D. B.;
Watson, S. P.; Hann, M. M.;
J. Chem. Inf. Comput. Sci.; 1998; 38(3); 511-522.
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Builds a hexagonal Au surface X atoms by Y atoms
Date 2003-03-16
Author Chris Williams
Category Basic Molecular Tools
Downloads 62
Details
13-nov-00 (cw) created

Makes a hexagonal gold surface X atoms by Y atoms

Usage:
(1) Load this function
(2) At the SVL command line, enter

svl>make_gold_surface[X,Y]

where X = # of gold atoms in a row, Y = # of gold atoms rows

The AU_AU distance is set by the const AU_AU ( default 2.88 angstroms)
Entire surface is reparented to 1 chain, 1 residue


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Forces E or Z isomerism on all double bonds in a database of compounds.
Date 2003-03-16
Author Dimitri Bondarev
Category Basic Molecular Tools
Downloads 39
Details
Forces either E or Z isomerism on all double bonds a database

Usage:
Open the database in the Database Viewer and (optionally)
select some compounds. If you don't select any, everything
will be processed. If there are several molecular fields in
the database, the script will process the first one or the
first selected one.

Load this file and type

svl> db_force_ez 'E'

or

svl> db_force_ez 'Z'

then see the report in the Commands Window
Auto-connect closely positioned atoms in the presence of other molecules
Date 2003-03-16
Author Chris Williams
Category Basic Molecular Tools
Downloads 72
Details
Given chain keys, function loop through the residues
in each chain and connects and types the atoms of that
residue. Use in lieu of the generig autotypa and connect
when fragments are in a proximity such that the autotyper
will confuse atoms from different fragments as being in the same
molecule

Usage:
(1) Load this function

svl>load 'connect_mfss_fragments.svl'

(2) Open the file of interest.
(3) Select the chains with the fragments whose bonding you wish to fix.
(4) Enter

svl>connect_mfss_fragments[]

at the SVL command line. The bonding patterns of the
chosen fragment chains should be fixed
For a database, computes brutto formulas for all compounds
Date 2003-03-16
Author Dimitri Bondarev
Category Molecular Descriptors and QSAR
Downloads 120
Details
Write the molecular formula for all compounds in a MOE database

USAGE:
(1)Open the database in the Database Viewer and (optionally)
select some compounds. If you don't select any, everything
will be processed.
(2)If there are several molecular fields in
the database, the script will process the first one or the
first selected one.
(3) This is a run file. Enter

svl>run'db_formula.svl'

at the SVL command line
Builds a combinatorial library from a specified chemical reaction.
Date 2003-03-16
Author Elizabeth Sourial
Category Combinatorial Chemistry
Downloads 123
Details
This script will generate a combinatorial library from a specific reaction.
The input parameters are defined by COMBI_DEFAULTS. For example, the default
scaffold file is scaff.mol2 and the substition position on the scaffold is
set to atom number 1.

The substitution reaction is defined by R_rxn. The default is for a
substitution addition of a primary amine.
liglibrary.sdf contains the r groups.

By default the combichem products will be minimized using the MMFF94 force
field and in solvent before being written to the output database, 'combi_out.mdb'.
The molecule's name will correspond to scaffname.rgroupname
In order to generate the R group names the liglibrary.sd file must contain a
character field called MOLNAME which contains the fragment's name.

USAGE:
INTERACTIVELY
1) Load the function
2) At the CLI enter

svl> combi_batch options

where options is a tagged vector specifying the combichem default parameters
(see COMBI_DEFAULTS constant).

If you would like to use the default parameters enter:

svl> combi_batch []

MOEBATCH
1)Open moebatch
2)Load the function by entering:
load 'combi_batch.svl' (you may need to specify the full path to the file)
3)Enter:
combi_batch options (as described above)

EXAMPLE:
To run the script with the following options:
substitution on scaffold atom number 14
scaffold file = scaff.mol2
primary amine substition

Enter:
svl> combi_batch [rxn_point:14, scaffold:'scaff.mol2', R_rxn: '[NH2X3]']
Computes descriptors for an SD file and outputs an ASCII file (molecules are converted to SMILES strings)
Date 2003-03-16
Author Chris Williams
Category Molecular Descriptors and QSAR
Downloads 139
Details
Given an SD file token and a list of descriptors, the function
imports the SD file, calculates the descriptors and exports the
results back to an ASCII file

Usage:
(1) Load thus function;
(2) At the SVL command line, enter

svl> batch_sd_to_ascii[ 'sd_filename','ascii_file', ['d1,'d2',d3',..'d']]


where 'd1' - 'd' are descriptor name tokens

(3) Alternately, the file can be run from batch mode


moebatch -exec "run ['batch_sd_to_ascii.svl',['sdfile.sdf','ascii_file',['d1,'d2]]"

Returns nearby atoms given atom keys and a distance
Date 2003-03-16
Author Chris Williams
Category Basic Molecular Tools
Downloads 127
Details
Lifted from the installation code $MOE/lib/svl/aselect.svl.
Given a set of atom keys 'atoms' and a distance 'r', the function
returns the atom keys of all atom within r angstroms of the 'atoms'
set.

Usage:
(1) Load the function
(2) Enter

svl> atom_proximity[r, atoms]

where r is the distance
atoms is the atom subset (default to selected atoms if [])
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Panel with buttons that copy symbols to the clipboard.
Date 2003-03-07
Author Martin Santavy
Category Miscellaneous
Downloads 59
Details
Run the SVL file. A panel is created with buttons
labeled with different symbols. Pressing a button
will copy the corresponding symbol to the
system clipboard. The user can then copy the
symbol anywhere in MOE by pressing Shift-Insert.
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Checks a protein structure for missing bonds and atoms
Date 2003-02-20
Author Dimitri Bondarev
Category Protein Tools
Downloads 238
Details
Checks a protein structure and prints a report of missing bonds and atoms
Import a directory of pdb files into an MOE database
Date 2003-02-20
Author Dimitri Bondarev
Category Informatics and File I/O
Downloads 377
Details
Import everything or just the ligands
Lists residues close to the ligands in an MOE database of complexes
Date 2003-02-20
Author Dimitri Bondarev
Category Protein Tools
Downloads 204
Details
Lists residues close to the ligands in an MOE database of complexes
Generic template for a database loop code
Date 2003-02-20
Author Dimitri Bondarev
Category SVL Utilities
Downloads 215
Details
Loops over a database and runs a function on all entries
The database filter tool enables the user to filter a database based on float values in the database.
Date 2003-02-20
Author Chris Williams
Category SVL Utilities
Downloads 101
Details
The database filter tool enables the user to filter a database based on float values in the database. The current range of a given value is displayed.
Computes the distance between centroids of sets of atoms.
Date 2003-02-20
Author Chris Williams
Category SVL Utilities
Downloads 90
Details
Prompts the user to sequentially select two sets of atoms defining centroid 1 and centroid 2; the centroid distance is then calculated throughout the database.
Adds counterions to a database of molecules.
Date 2003-02-20
Author Dongqing Wei
Category SVL Utilities
Downloads 56
Details
The input.sdf is a sd data base, and the output.sdf is the output sd database contains compounds with salt added.
created based on ph4ttri.svl
Date 2003-02-19
Author Junichi Goto (Ryoka Systems)
Category Pharmacophores and Fingerprints
Downloads 64
Details
This fingerprint uses aromatic center 'R' instead of 'H' in ph4ttri.svl
Other algorithm is all the same as original code
Converts all MDL files in a directory with extension to Tripos files with extension 'MOL2'.
Date 2003-02-19
Author Chris Williams
Category Informatics and File I/O
Downloads 98
Details
Converts all MDL files in a directory with extension to Tripos files with extension 'MOL2'.
The base filename is retained
batch ligand-receptor contact calculation
Date 2003-02-19
Author Chris Williams
Category Protein Tools
Downloads 405
Details
given a databse of protein/ligand complexes, the function loops through the database and calculates the protein/ligand contacts for each complex.
selects residues without complete backbones
Date 2003-02-19
Author Chris Williams
Category Protein Tools
Downloads 80
Details
selects residues without complete backbones
Converts float database fields to integer
Date 2003-02-19
Author Chris Williams
Category SVL Utilities
Downloads 55
Details
Function loops through a database, and converts either all the float fields (if no fields are selected) or just the selected float fields to integer. The program must create temporary int fields that are renamed after the databse has been scanned
Converts database float fields to char-int fields
Date 2003-02-19
Author Chris Williams
Category SVL Utilities
Downloads 77
Details
Converts database float fields to char-int fields
Loops through a database and exports each structure to a separate PDB file
Date 2003-02-19
Author Chris Williams
Category Informatics and File I/O
Downloads 350
Details
Loops through a database and exports each structure to a separate PDB file
Runs MOE SiteFinder in batch, outputs dummy atoms
Date 2003-02-19
Author Dimitri Bondarev
Category MOE/batch
Downloads 135
Details
Runs SiteFinder and outputs the dummy atoms of the active sites into a pdb file.