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
81 lines
3.3 KiB
C++
81 lines
3.3 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_UFFCONVENIENCE_H
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#define RD_UFFCONVENIENCE_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 "Builder.h"
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namespace RDKit {
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class ROMol;
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namespace UFF {
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//! Convenience function for optimizing a molecule using UFF
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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 vdwThresh the threshold to be used in adding van der Waals terms
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to the force field. Any non-bonded contact whose current
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distance is greater than \c vdwThresh * the minimum 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: 0 if the optimization converged, 1 if more iterations are required.
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second: the energy
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*/
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inline std::pair<int, double> UFFOptimizeMolecule(
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ROMol &mol, int maxIters = 1000, double vdwThresh = 10.0, int confId = -1,
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bool ignoreInterfragInteractions = true) {
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std::unique_ptr<ForceFields::ForceField> ff(UFF::constructForceField(
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mol, vdwThresh, confId, ignoreInterfragInteractions));
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std::pair<int, double> res =
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ForceFieldsHelper::OptimizeMolecule(*ff, maxIters);
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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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/// UFF
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/*
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\param mol the molecule to use
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\param res vector of (needsMore,energy)
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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 vdwThresh the threshold to be used in adding van der Waals terms
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to the force field. Any non-bonded contact whose current
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distance is greater than \c vdwThresh * the minimum 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 UFFOptimizeMoleculeConfs(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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double vdwThresh = 10.0,
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bool ignoreInterfragInteractions = true) {
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std::unique_ptr<ForceFields::ForceField> ff(UFF::constructForceField(
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mol, vdwThresh, -1, ignoreInterfragInteractions));
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ForceFieldsHelper::OptimizeMoleculeConfs(mol, *ff, res, numThreads, maxIters);
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}
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} // end of namespace UFF
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} // end of namespace RDKit
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#endif
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