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/*
* $Id$
*
* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
%{
#include <ForceField/ForceField.h>
#include <GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/MMFF/Builder.h>
#include <ForceField/Contrib.h>
#include <ForceField/UFF/Params.h>
#include <ForceField/UFF/AngleBend.h>
#include <ForceField/UFF/BondStretch.h>
#include <ForceField/UFF/Contribs.h>
#include <ForceField/UFF/DistanceConstraint.h>
#include <ForceField/UFF/Nonbonded.h>
#include <ForceField/UFF/TorsionAngle.h>
#include <ForceField/UFF/Inversion.h>
#include <boost/tuple/tuple.hpp>
#include <GraphMol/ROMol.h>
%}
// We have trouble with the definition as it is -- make it a Point3D_Vect instead
%ignore ForceFields::ForceField::positions();
%ignore ForceFields::ForceField::positions() const;
%rename(get) ForceFields::UFF::ParamCollection::operator();
%include <ForceField/ForceField.h>
%include <ForceField/Contrib.h>
%include <ForceField/UFF/Params.h>
%include <ForceField/UFF/AngleBend.h>
%include <ForceField/UFF/BondStretch.h>
%include <ForceField/UFF/DistanceConstraint.h>
%include <ForceField/UFF/Nonbonded.h>
%include <ForceField/UFF/TorsionAngle.h>
%include <ForceField/UFF/Inversion.h>
%template(FF_Contrib_Vect) std::vector<ForceFields::ContribPtr>;
%extend ForceFields::ForceField {
std::vector<RDGeom::Point3D *> &positions3D () {
return ((std::vector<RDGeom::Point3D *> &) ($self)->positions());
}
static int UFFOptimizeMolecule(RDKit::ROMol &mol, int maxIters=200,
double vdwThresh=10.0, int confId=-1,
bool ignoreInterfragInteractions=true ) {
ForceFields::ForceField *ff=RDKit::UFF::constructForceField(mol,vdwThresh, confId, ignoreInterfragInteractions);
ff->initialize();
int res=ff->minimize(maxIters);
delete ff;
return res;
}
%newobject UFFGetMoleculeForceField;
static ForceFields::ForceField *UFFGetMoleculeForceField(RDKit::ROMol &mol,
double vdwThresh=10.0,
int confId=-1,
bool ignoreInterfragInteractions=true ) {
ForceFields::ForceField *ff=RDKit::UFF::constructForceField(mol,vdwThresh, confId, ignoreInterfragInteractions);
ff->initialize();
return ff;
}
static bool UFFHasAllMoleculeParams(const RDKit::ROMol &mol){
RDKit::UFF::AtomicParamVect types;
bool foundAll;
boost::tie(types,foundAll)=RDKit::UFF::getAtomTypes(mol);
return foundAll;
}
/* From GraphMol/ForceFieldHelpers/UFF/AtomTyper.h */
static void UFFAddAtomChargeFlags(const RDKit::Atom *atom, std::string &atomKey, bool tolerateChargeMismatch=true) {
RDKit::UFF::Tools::addAtomChargeFlags(atom, atomKey, tolerateChargeMismatch);
}
static std::string UFFGetAtomLabel(const RDKit::Atom *atom) {
return RDKit::UFF::Tools::getAtomLabel(atom);
}
/* From GraphMol/ForceFieldHelpers/UFF/AtomTyper.h */
static std::pair<std::vector<const ForceFields::UFF::AtomicParams *>,bool> UFFGetAtomTypes(const RDKit::ROMol &mol, const std::string ¶mData="") {
return RDKit::UFF::getAtomTypes(mol, paramData);
}
static int MMFFOptimizeMolecule(RDKit::ROMol &mol,
std::string mmffVariant="MMFF94",
int maxIters=200,
double nonBondedThresh=100.0, int confId=-1,
bool ignoreInterfragInteractions=true ) {
int res=1;
RDKit::MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
if (mmffMolProperties.isValid()) {
ForceFields::ForceField *ff = RDKit::MMFF::constructForceField(mol,
&mmffMolProperties, nonBondedThresh, confId, ignoreInterfragInteractions);
ff->initialize();
res = ff->minimize(maxIters);
delete ff;
} else {
BOOST_LOG(rdErrorLog) << "Could not construct MMFF force field"<<std::endl;
}
return res;
}
%newobject MMFFGetMoleculeForceField;
static ForceFields::ForceField *MMFFGetMoleculeForceField(RDKit::ROMol &mol,
std::string mmffVariant="MMFF94",
double nonBondedThresh=100.0,
int confId=-1,
bool ignoreInterfragInteractions=true ) {
ForceFields::ForceField *ff = 0;
RDKit::MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
if (mmffMolProperties.isValid()) {
ff = RDKit::MMFF::constructForceField(mol,
&mmffMolProperties, nonBondedThresh,
confId, ignoreInterfragInteractions);
ff->initialize();
} else {
BOOST_LOG(rdErrorLog) << "Could not construct MMFF force field"<<std::endl;
}
return ff;
}
static bool MMFFHasAllMoleculeParams(RDKit::ROMol &mol){
RDKit::MMFF::MMFFMolProperties mmffMolProperties(mol);
return mmffMolProperties.isValid();
}
}
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