mirror of
https://github.com/rdkit/rdkit.git
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0164ac7fae
* fixes * do not leak MolCatalogParams * do not leak points on align failures * give python ownership of pointers returned in getFingerprintsHelper * clean up ScaffoldNetwork ptr if createNetworkHelper fails * manage FF ptrs during construction * wire in ownsBondInvGenerator in getMorganGenerator * manage weights in rdMolAlign CalcRMS * fix ownership of matches list/tuple in generateRmsdTransMatchPyTuple * manage stream in createForwardSupplier during construction * drop redundant Point3D allocations in GetUSRDistributionsFromPoints * fix signed comparison mismatch
104 lines
4.2 KiB
C++
104 lines
4.2 KiB
C++
//
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// Copyright (C) 2015-2018 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef RD_MMFFCONVENIENCE_H
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#define RD_MMFFCONVENIENCE_H
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#include <ForceField/ForceField.h>
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#include <GraphMol/ForceFieldHelpers/FFConvenience.h>
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#include <RDGeneral/RDThreads.h>
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#include "AtomTyper.h"
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#include "Builder.h"
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namespace RDKit {
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class ROMol;
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namespace MMFF {
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//! Convenience function for optimizing a molecule using MMFF
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/*
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\param mol the molecule to use
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\param maxIters the maximum number of force-field iterations
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\param mmffVariant the MMFF variant to use, should be "MMFF94" or "MMFF94S"
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\param nonBondedThresh the threshold to be used in adding non-bonded terms
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to the force field. Any non-bonded contact whose
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current
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distance is greater than \c nonBondedThresh * the minimum
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value
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for that contact will not be included.
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\param confId the optional conformer id, if this isn't provided, the
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molecule's
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default confId will be used.
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\param ignoreInterfragInteractions if true, nonbonded terms will not be added
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between
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fragments
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\return a pair with:
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first: -1 if parameters were missing, 0 if the optimization converged, 1 if
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more iterations are required.
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second: the energy
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*/
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inline std::pair<int, double> MMFFOptimizeMolecule(
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ROMol &mol, int maxIters = 1000, std::string mmffVariant = "MMFF94",
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double nonBondedThresh = 10.0, int confId = -1,
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bool ignoreInterfragInteractions = true) {
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std::pair<int, double> res = std::make_pair(-1, -1);
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MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
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if (mmffMolProperties.isValid()) {
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std::unique_ptr<ForceFields::ForceField> ff(MMFF::constructForceField(
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mol, nonBondedThresh, confId, ignoreInterfragInteractions));
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res = ForceFieldsHelper::OptimizeMolecule(*ff, maxIters);
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}
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return res;
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}
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//! Convenience function for optimizing all of a molecule's conformations using
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/// MMFF
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/*
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\param mol the molecule to use
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\param res vector of (needsMore,energy) pairs
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\param numThreads the number of simultaneous threads to use (only has an
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effect if the RDKit is compiled with thread support).
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If set to zero, the max supported by the system will be
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used.
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\param maxIters the maximum number of force-field iterations
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\param mmffVariant the MMFF variant to use, should be "MMFF94" or "MMFF94S"
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\param nonBondedThresh the threshold to be used in adding non-bonded terms
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to the force field. Any non-bonded contact whose
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current
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distance is greater than \c nonBondedThresh * the minimum
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value
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for that contact will not be included.
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\param ignoreInterfragInteractions if true, nonbonded terms will not be added
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between
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fragments
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*/
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inline void MMFFOptimizeMoleculeConfs(ROMol &mol,
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std::vector<std::pair<int, double>> &res,
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int numThreads = 1, int maxIters = 1000,
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std::string mmffVariant = "MMFF94",
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double nonBondedThresh = 10.0,
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bool ignoreInterfragInteractions = true) {
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MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
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if (mmffMolProperties.isValid()) {
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std::unique_ptr<ForceFields::ForceField> ff(
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MMFF::constructForceField(mol, &mmffMolProperties, nonBondedThresh, -1,
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ignoreInterfragInteractions));
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ForceFieldsHelper::OptimizeMoleculeConfs(mol, *ff, res, numThreads,
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maxIters);
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} else {
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res.resize(mol.getNumConformers());
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for (unsigned int i = 0; i < mol.getNumConformers(); ++i) {
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res[i] = std::make_pair(static_cast<int>(-1), static_cast<double>(-1));
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}
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}
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}
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} // namespace MMFF
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} // end of namespace RDKit
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#endif
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