Code provided on the exeResearch LLC website ( www.exeResearch.com ) http://www.exeResearch.com
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
SVLutilities
README.md

README.md

Code :: InformationIsPower

Code provided on the exeResearch LLC website ( www.exeResearch.com ).

The following functions/applications are commonly used in our research projects. A brief description of each function is provided below along with detailed instructions. The Scientific Vector Language (SVL) functions require the use of Chemical Computing Group, Inc's Molecular Operating Environment (MOE).

MACCS Key Counts (SVL)

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']]


Set Amide Bonds to 180 Degrees (SVL)

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:'']]


Notes:

  • SVL functions (code) are traditionally stored by the author in ~/code/svl. Unless otherwise noted, the provided SVL code is stored in ~/code/svl/utilities. The instructions for each function reflects where each file is stored.