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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 <DistGeom/ChiralSet.h>
#include <DistGeom/BoundsMatrix.h>
#include <DistGeom/DistGeomUtils.h>
#include <GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h>
#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <DistGeom/TriangleSmooth.h>
#include <GraphMol/ROMol.h>
%}
// This prevents duplicate definitions in Java code (due to 2 C++ functions resolving to the same Java function)
%ignore RDKit::DGeomHelpers::initBoundsMat(DistGeom::BoundsMatPtr, double, double);
%ignore RDKit::DGeomHelpers::initBoundsMat(DistGeom::BoundsMatPtr,double);
%ignore RDKit::DGeomHelpers::initBoundsMat(DistGeom::BoundsMatPtr);
// This conflicts with definitions in UFF::, so ignore and make it a method on the bounds matrix
%ignore DistGeom::constructForceField;
%include <DistGeom/ChiralSet.h>
%include <DistGeom/BoundsMatrix.h>
%include <GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h>
%include <DistGeom/DistGeomUtils.h>
%include <DistGeom/TriangleSmooth.h>
%ignore RDKit::DGeomHelpers::EmbedMolecule;
%ignore RDKit::DGeomHelpers::EmbedMultipleConfs;
// make sure the struct has a copy constructor:
%copyctor RDKit::DGeomHelpers::EmbedParameters;
// we want to ignore the const global parameter objects because SWIG does a
// poor job of making them read-only when they are exposed to Java.
%ignore RDKit::DGeomHelpers::KDG;
%ignore RDKit::DGeomHelpers::ETDG;
%ignore RDKit::DGeomHelpers::ETKDG;
%ignore RDKit::DGeomHelpers::ETKDGv2;
%include <GraphMol/DistGeomHelpers/Embedder.h>
// create functions to return copies of the global parameter objects
%newobject RDKit::DGeomHelpers::getKDG;
%newobject RDKit::DGeomHelpers::getETDG;
%newobject RDKit::DGeomHelpers::getETKDG;
%newobject RDKit::DGeomHelpers::getETKDGv2;
%inline {
namespace RDKit{
namespace DGeomHelpers {
EmbedParameters *getKDG() {
return new EmbedParameters(KDG);
}
EmbedParameters *getETDG() {
return new EmbedParameters(ETDG);
}
EmbedParameters *getETKDG() {
return new EmbedParameters(ETKDG);
}
EmbedParameters *getETKDGv2() {
return new EmbedParameters(ETKDGv2);
}
}
}
}
// A class to hang special distance geometry methods on.
%inline {
namespace DistGeom {
class DistanceGeom {
public:
/* From Embedder.h */
static int EmbedMolecule(RDKit::ROMol &mol,
unsigned int maxIterations=0, int seed=-1,
bool clearConfs=true,
bool useRandomCoords=false,double boxSizeMult=2.0,
bool randNegEig=true,
unsigned int numZeroFail=1,
const std::map<int,RDGeom::Point3D> *coordMap=0,
double optimizerForceTol=1e-3,
bool ignoreSmoothingFailures=false,
bool enforceChirality=true,
bool useExpTorsionAnglePrefs=false,
bool useBasicKnowledge=false,
bool verbose=false,
double basinThresh=5.0) {
return RDKit::DGeomHelpers::EmbedMolecule(mol,
maxIterations, seed,
clearConfs,
useRandomCoords, boxSizeMult,
randNegEig,
numZeroFail,
coordMap,
optimizerForceTol,
ignoreSmoothingFailures,
enforceChirality,
useExpTorsionAnglePrefs,
useBasicKnowledge,
verbose,
basinThresh);
}
static int EmbedMolecule(RDKit::ROMol &mol,const RDKit::DGeomHelpers::EmbedParameters ¶ms) {
return RDKit::DGeomHelpers::EmbedMolecule(mol,params);
}
static RDKit::INT_VECT EmbedMultipleConfs(RDKit::ROMol &mol,
unsigned int numConfs=10,
unsigned int maxIterations=30,
int seed=-1, bool clearConfs=true,
bool useRandomCoords=false,double boxSizeMult=2.0,
bool randNegEig=true, unsigned int numZeroFail=1,
double pruneRmsThresh=-1.0,
const std::map<int,RDGeom::Point3D> *coordMap=0,
double optimizerForceTol=1e-3,
bool ignoreSmoothingFailures=false,
bool enforceChirality=true,
bool useExpTorsionAnglePrefs=false,
bool useBasicKnowledge=false,
bool verbose=false,
double basinThresh=5.0) {
return RDKit::DGeomHelpers::EmbedMultipleConfs(mol,
numConfs,
maxIterations,
seed, clearConfs,
useRandomCoords,boxSizeMult,
randNegEig, numZeroFail,
pruneRmsThresh,
coordMap,
optimizerForceTol,
ignoreSmoothingFailures,
enforceChirality,
useExpTorsionAnglePrefs,
useBasicKnowledge,
verbose,
basinThresh);
}
static RDKit::INT_VECT EmbedMultipleConfs(RDKit::ROMol &mol,
unsigned int numConfs,
const RDKit::DGeomHelpers::EmbedParameters ¶ms) {
return RDKit::DGeomHelpers::EmbedMultipleConfs(mol, numConfs, params);
}
static void SetTopolBounds(RDKit::ROMol &mol,
DistGeom::BoundsMatrix* mmat,
bool set15bounds=true, bool scaleVDW=false) {
DistGeom::BoundsMatPtr* mmatAsSmartPtr = new DistGeom::BoundsMatPtr(mmat);
RDKit::DGeomHelpers::setTopolBounds(mol, *mmatAsSmartPtr, set15bounds, scaleVDW);
}
static ForceFields::ForceField *ConstructForceField(DistGeom::BoundsMatrix& mmat,
RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets,
double weightChiral=1.0,
double weightFourthDim=0.1,
std::map< std::pair<int,int>,double> *extraWeights=0,
double basinSizeTol=5.0) {
return DistGeom::constructForceField(mmat, positions, csets,
weightChiral,
weightFourthDim,
extraWeights,
basinSizeTol);
}
// This is hard to override in Java, so do it here.
static bool ComputeInitialCoords(const RDNumeric::SymmMatrix<double> &distmat,
std::vector<RDGeom::Point3D *> &positions, bool randNegEig=false,
unsigned int numZeroFail=2) {
return DistGeom::computeInitialCoords(distmat, (RDGeom::PointPtrVect &) positions, randNegEig, numZeroFail);
}
};
}
}
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