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RDKitPerformTorsionScan.py - Perform torsion scan
RDKitPerformTorsionScan.py [--addHydrogens <yes or no>] [--conformerGenerator <SDG, KDG, ETDG, ETKDG, ETKDGv2>] [--forceField <UFF, or MMFF>] [--forceFieldMMFFVariant <MMFF94 or MMFF94s>] [--enforceChirality <yes or no>] [--infile3D <yes or no>] [--infileParams <Name,Value,...>] [--modeMols <First or All>] [--modeTorsions <First or All> ] [--maxConfs <number>] [--maxConfsTorsion <number>] [--maxIters <number>] [--mp <yes or no>] [--mpLevel <Molecules or TorsionAngles>] [--mpParams <Name,Value,...>] [--outfileMolName <yes or no>] [--outfileParams <Name,Value,...>] [--outPlotParams <Name,Value,...>] [--outPlotRelativeEnergy <yes or no>] [--outPlotTitleTorsionSpec <yes or no>] [--overwrite] [--quiet <yes or no>] [--removeHydrogens <yes or no>] [--randomSeed <number>] [--torsionsFilterbyAtomIndices <Index1, Index2, ...>] [--torsionMaxMatches <number>] [--torsionMinimize <yes or no>] [--torsionRangeMode <Range or Angles>] [--torsionRange <Start,Stop,Step or Angle1,Angle2,...>] [--useChirality <yes or no>] [--useTethers <yes or no>] [-w <dir>] -t <torsions> -i <infile> -o <outfile>
RDKitPerformTorsionScan.py -h | --help | -e | --examples
Perform torsion scan for molecules around torsion angles specified using SMILES/SMARTS patterns. A molecule is optionally minimized before performing a torsion scan. A set of initial 3D structures are generated for a molecule by scanning the torsion angle across the specified range and updating the 3D coordinates of the molecule. A conformation ensemble is optionally generated for each 3D structure representing a specific torsion angle. The conformation with the lowest energy is selected to represent the torsion angle. An option is available to skip the generation of the conformation ensemble and simply calculate the energy for the initial 3D structure for a specific torsion angle.
The torsions are specified using SMILES or SMARTS patterns. A substructure match is performed to select torsion atoms in a molecule. The SMILES pattern match must correspond to four torsion atoms. The SMARTS patterns containing atom map numbers may match more than four atoms. The atom map numbers, however, must match exactly four torsion atoms. For example: [s:1][c:2]([aX2,cH1])!@[CX3:3](O)=[O:4] for thiophene esters and carboxylates as specified in Torsion Library (TorLib) [Ref 146].
A set of four output files is generated for each torsion match in each molecule. The names of the output files are generated using the root of the specified output file. They may either contain sequential molecule numbers or molecule names as shown below:
The supported input file formats are: Mol (.mol), SD (.sdf, .sd), SMILES (.smi, .csv, .tsv, .txt)
The supported output file formats are: SD (.sdf, .sd)
Add hydrogens before minimization.
Conformation generation methodology for generating initial 3D structure of a molecule and conformation ensemble representing a specific torsion angle. No conformation ensemble is generated for 'No' value of '--torsionMinimize' option.
The possible values along with a brief description are shown below:
Forcefield method to use for energy minimization of initial 3D structure of a molecule and conformation ensemble representing a specific torsion. No conformation ensemble is generated during for 'No' value of '--torsionMinimze' option and constrained energy minimization is not performed. Possible values: Universal Force Field (UFF) [ Ref 81 ] or Merck Molecular Mechanics Force Field [ Ref 83-87 ] .
Variant of MMFF forcefield to use for energy minimization.
Enforce chirality for defined chiral centers during generation of conformers.
Print examples.
Print this help message.
Input file name.
Skip generation and minimization of initial 3D structures for molecules in input file containing 3D coordinates.
A comma delimited list of parameter name and value pairs for reading molecules from files. The supported parameter names for different file formats, along with their default values, are shown below:
Possible values for smilesDelimiter: space, comma or tab.
Perform torsion scan for the first molecule or all molecules in input file.
Perform torsion scan for the first or all specified torsion pattern in molecules up to a maximum number of matches for each torsion specification as indicated by '--torsionMaxMatches' option.
Maximum number of conformations to generate for initial 3D structure of a molecule. The lowest energy conformation is written to the output file.
Maximum number of conformations to generate for conformation ensemble representing a specific torsion. A constrained minimization is performed using the coordinates of the specified torsion and the lowest energy conformation is written to the output file.
Maximum number of iterations to perform for a molecule during minimization to generation initial 3D structures. This option is ignored during 'yes' value of '--infile3D' option.
Use multiprocessing.
By default, input data is retrieved in a lazy manner via mp.Pool.imap() function employing lazy RDKit data iterable. This allows processing of arbitrary large data sets without any additional requirements memory.
All input data may be optionally loaded into memory by mp.Pool.map() before starting worker processes in a process pool by setting the value of 'inputDataMode' to 'InMemory' in '--mpParams' option.
A word to the wise: The default 'chunkSize' value of 1 during 'Lazy' input data mode may adversely impact the performance. The '--mpParams' section provides additional information to tune the value of 'chunkSize'.
Perform multiprocessing at molecules or torsion angles level. Possible values: Molecules or TorsionAngles. The 'Molecules' value starts a process pool at the molecules level. All torsion angles of a molecule are processed in a single process. The 'TorsionAngles' value, however, starts a process pool at the torsion angles level. Each torsion angle in a torsion match for a molecule is processed in an individual process in the process pool.
A comma delimited list of parameter name and value pairs to configure multiprocessing.
The supported parameter names along with their default and possible values are shown below:
These parameters are used by the following functions to configure and control the behavior of multiprocessing: mp.Pool(), mp.Pool.map(), and mp.Pool.imap().
The chunkSize determines chunks of input data passed to each worker process in a process pool by mp.Pool.map() and mp.Pool.imap() functions. The default value of chunkSize is dependent on the value of 'inputDataMode'.
The mp.Pool.map() function, invoked during 'InMemory' input data mode, automatically converts RDKit data iterable into a list, loads all data into memory, and calculates the default chunkSize using the following method as shown in its code:
For example, the default chunkSize will be 7 for a pool of 4 worker processes and 100 data items.
The mp.Pool.imap() function, invoked during 'Lazy' input data mode, employs 'lazy' RDKit data iterable to retrieve data as needed, without loading all the data into memory. Consequently, the size of input data is not known a priori. It's not possible to estimate an optimal value for the chunkSize. The default chunkSize is set to 1.
The default value for the chunkSize during 'Lazy' data mode may adversely impact the performance due to the overhead associated with exchanging small chunks of data. It is generally a good idea to explicitly set chunkSize to a larger value during 'Lazy' input data mode, based on the size of your input data and number of processes in the process pool.
The mp.Pool.map() function waits for all worker processes to process all the data and return the results. The mp.Pool.imap() function, however, returns the the results obtained from worker processes as soon as the results become available for specified chunks of data.
The order of data in the results returned by both mp.Pool.map() and mp.Pool.imap() functions always corresponds to the input data.
Output file name. The output file root is used for generating the names of the output files corresponding to structures, energies, and plots during the torsion scan.
Append molecule name to output file root during the generation of the names for output files. The default is to use <MolNum>. The non alphabetical characters in molecule names are replaced by underscores.
A comma delimited list of parameter name and value pairs for writing molecules to files. The supported parameter names for different file formats, along with their default values, are shown below:
A comma delimited list of parameter name and value pairs for generating plots using Seaborn module. The supported parameter names along with their default values are shown below:
Possible values:
Plot relative energies in the torsion plot. The minimum energy value is subtracted from energy values to calculate relative energies.
Append torsion specification to the title of the torsion plot.
Overwrite existing files.
Use quiet mode. The warning and information messages will not be printed.
Seed for the random number generator for generating initial 3D coordinates. Default is to use a random seed.
Remove hydrogens after minimization.
SMILES/SMARTS patterns corresponding to torsion specifications. It's a comma delimited list of valid SMILES/SMART patterns.
A substructure match is performed to select torsion atoms in a molecule. The SMILES pattern match must correspond to four torsion atoms. The SMARTS patterns containing atom map numbers may match more than four atoms. The atom map numbers, however, must match exactly four torsion atoms. For example: [s:1][c:2]([aX2,cH1])!@[CX3:3](O)=[O:4] for thiophene esters and carboxylates as specified in Torsion Library (TorLib) [Ref 146].
Comma delimited list of atom indices for filtering torsion matches corresponding to torsion specifications "-t, --torsions". The atom indices must be valid. No explicit validation is performed. The list must contain at least 4 atom indices.
The torsion atom indices, matched by "-t, --torsions" specifications, must be present in the list. Otherwise, the torsion matches are ignored.
Maximum number of torsions to match for each torsion specification in a molecule.
Perform constrained energy minimization on a conformation ensemble for a specific torsion angle and select the lowest energy conformation representing the torsion angle.
Perform torsion scan using torsion angles corresponding to a torsion range or an explicit list of torsion angles. Possible values: Range or Angles. You may use '--torsionRange' option to specify values for torsion angle or torsion angles.
Start, stop, and step size angles or a comma delimited list of angles in degrees for a torsion scan.
This value is '--torsionRangeMode' specific. It must be a triplet corresponding to 'start,Stop,Step' for 'Range' value of '--torsionRange' option. Otherwise, it is comma delimited list of one or more torsion angles for 'Angles' value of '--torsionRange' option.
The default values, based on '--torsionRangeMode' option, are shown below:
You must explicitly provide a list of torsion angle(s) for 'Angles' of '--torsionRangeMode' option.
Use chirrality during substructure matches for identification of torsions. --useTethers <yes or no> [default: yes] Use tethers to optimize the final conformation by applying a series of extra forces to align matching atoms to the positions of the core atoms. Otherwise, use simple distance constraints during the optimization.
Location of working directory which defaults to the current directory.
To perform a torsion scan from 0 to 360 degrees with a stepsize of 5 on the first molecule in a SMILES file using a minimum energy structure of the molecule selected from an ensemble of conformations, skipping generation of conformation ensembles for specific torsion angles and constrained energy minimization of the ensemble, generate output files corresponding to structure, energy and torsion plot, type:
To run the previous example for performing a torsion scan using a specific list of torsion angles, type:
To run the previous example on all molecules in a SD file, type:
To perform a torsion scan on the first molecule in a SMILES file using a minimum energy structure of the molecule selected from an ensemble of conformations, generation of conformation ensembles for specific torsion angles and constrained energy minimization of the ensemble, generate output files corresponding to structure, energy and torsion plot, type:
To run the previous example on all molecules in a SD file, type:
To run the previous example in multiprocessing mode at molecules level on all available CPUs without loading all data into memory and write out a SD file, type:
To run the previous example in multiprocessing mode at torsion angles level on all available CPUs without loading all data into memory and write out a SD file, type:
To run the previous example in multiprocessing mode on all available CPUs by loading all data into memory and write out a SD file, type:
To run the previous example in multiprocessing mode on specific number of CPUs and chunk size without loading all data into memory and write out a SD file, type:
To perform a torsion scan on first molecule in a SD file containing 3D coordinates, skipping generation of conformation ensembles for specific torsion angles and constrained energy minimization of the ensemble, generate output files corresponding to structure, energy and torsion plot, type:
To perform a torsion scan using multiple torsion specifications on all molecules in a SD file containing 3D coordinates, generation of conformation ensembles for specific torsion angles and constrained energy minimization of the ensemble, generate output files corresponding to structure, energy and torsion plot, type:
To run the previous example using a specific torsion scan range, type:
RDKitCalculateRMSD.py, RDKitCalculateMolecularDescriptors.py, RDKitCompareMoleculeShapes.py, RDKitConvertFileFormat.py, RDKitPerformConstrainedMinimization.py
Copyright (C) 2024 Manish Sud. All rights reserved.
The functionality available in this script is implemented using RDKit, an open source toolkit for cheminformatics developed by Greg Landrum.
This file is part of MayaChemTools.
MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
