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115 lines
4.5 KiB
OpenEdge ABL
115 lines
4.5 KiB
OpenEdge ABL
/*
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* $Id$
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*
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* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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%{
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#include <GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>
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#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
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#include <ForceField/ForceField.h>
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#include <ForceField/Contrib.h>
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#include <ForceField/UFF/AngleBend.h>
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#include <ForceField/UFF/BondStretch.h>
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#include <ForceField/UFF/Contribs.h>
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#include <ForceField/UFF/DistanceConstraint.h>
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#include <ForceField/UFF/Nonbonded.h>
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#include <ForceField/UFF/Params.h>
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#include <ForceField/UFF/TorsionAngle.h>
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#include <boost/tuple/tuple.hpp>
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#include <GraphMol/ROMol.h>
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%}
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// We have trouble with the definition as it is -- make it a Point3D_Vect instead
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%ignore ForceFields::ForceField::positions();
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%ignore ForceFields::ForceField::positions() const;
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%rename(get) ForceFields::UFF::ParamCollection::operator();
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%include <ForceField/ForceField.h>
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%include <ForceField/Contrib.h>
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%include <ForceField/UFF/AngleBend.h>
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%include <ForceField/UFF/BondStretch.h>
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%include <ForceField/UFF/Contribs.h>
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%include <ForceField/UFF/DistanceConstraint.h>
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%include <ForceField/UFF/Nonbonded.h>
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%include <ForceField/UFF/Params.h>
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%include <ForceField/UFF/TorsionAngle.h>
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%include <GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>
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%include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
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%template(FF_Contrib_Vect) std::vector<ForceFields::ContribPtr>;
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%extend ForceFields::ForceField {
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std::vector<RDGeom::Point3D *> &positions3D () {
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return ((std::vector<RDGeom::Point3D *> &) ($self)->positions());
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}
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static int UFFOptimizeMolecule(RDKit::ROMol &mol, int maxIters=200,
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double vdwThresh=10.0, int confId=-1,
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bool ignoreInterfragInteractions=true ) {
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ForceFields::ForceField *ff=RDKit::UFF::constructForceField(mol,vdwThresh, confId, ignoreInterfragInteractions);
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ff->initialize();
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int res=ff->minimize(maxIters);
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delete ff;
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return res;
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}
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static ForceFields::ForceField *UFFGetMoleculeForceField(RDKit::ROMol &mol,
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double vdwThresh=10.0,
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int confId=-1,
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bool ignoreInterfragInteractions=true ) {
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ForceFields::ForceField *ff=RDKit::UFF::constructForceField(mol,vdwThresh, confId, ignoreInterfragInteractions);
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ff->initialize();
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return ff;
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}
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static bool UFFHasAllMoleculeParams(const RDKit::ROMol &mol){
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RDKit::UFF::AtomicParamVect types;
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bool foundAll;
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boost::tie(types,foundAll)=RDKit::UFF::getAtomTypes(mol);
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return foundAll;
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}
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/* From GraphMol/ForceFieldHelpers/UFF/AtomTyper.h */
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static void UFFAddAtomChargeFlags(const RDKit::Atom *atom, std::string &atomKey, bool tolerateChargeMismatch=true) {
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RDKit::UFF::Tools::addAtomChargeFlags(atom, atomKey, tolerateChargeMismatch);
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}
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static std::string UFFGetAtomLabel(const RDKit::Atom *atom) {
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return RDKit::UFF::Tools::getAtomLabel(atom);
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}
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/* From GraphMol/ForceFieldHelpers/UFF/AtomTyper.h */
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static std::pair<RDKit::UFF::AtomicParamVect,bool> UFFGetAtomTypes(const RDKit::ROMol &mol, const std::string ¶mData="") {
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return RDKit::UFF::getAtomTypes(mol, paramData);
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}
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}
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