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// $Id: rdDepictor.cpp 1625 2011-01-13 04:22:56Z glandrum $
//
// Copyright (C) 2003-2010 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <boost/python.hpp>
#define PY_ARRAY_UNIQUE_SYMBOL Depictor_array_API
#include "numpy/oldnumeric.h"
#include <RDBoost/Wrap.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/Depictor/EmbeddedFrag.h>
#include <GraphMol/Depictor/DepictUtils.h>
using namespace RDDepict;
namespace python = boost::python;
namespace RDDepict {
unsigned int Compute2DCoords(RDKit::ROMol &mol, bool canonOrient,
bool clearConfs, python::dict &coordMap,
unsigned int nFlipsPerSample=3,
unsigned int nSamples=100,
int sampleSeed=100,
bool permuteDeg4Nodes=false,
double bondLength=-1.0){
RDGeom::INT_POINT2D_MAP cMap;
cMap.clear();
python::list ks = coordMap.keys();
for(unsigned int i=0;
i<python::extract<unsigned int>(ks.attr("__len__")());
i++){
unsigned int id = python::extract<unsigned int>(ks[i]);
if(id>=mol.getNumAtoms()){
throw_value_error("atom index out of range");
}
cMap[id] = python::extract<RDGeom::Point2D>(coordMap[id]);
}
double oBondLen=RDDepict::BOND_LEN;
if(bondLength>0){
RDDepict::BOND_LEN=bondLength;
}
unsigned int res;
res=RDDepict::compute2DCoords(mol,&cMap,canonOrient, clearConfs,
nFlipsPerSample,nSamples,
sampleSeed, permuteDeg4Nodes);
if(bondLength>0){
RDDepict::BOND_LEN=oBondLen;
}
return res;
}
unsigned int Compute2DCoordsMimicDistmat(RDKit::ROMol &mol,
python::object distMat,
bool canonOrient,
bool clearConfs,
double weightDistMat,
unsigned int nFlipsPerSample,
unsigned int nSamples,
int sampleSeed,
bool permuteDeg4Nodes,
double bondLength=-1.0) {
PyObject *distMatPtr = distMat.ptr();
if(!PyArray_Check(distMatPtr)){
throw_value_error("Argument isn't an array");
}
PyArrayObject *dmatrix = reinterpret_cast<PyArrayObject *>(distMatPtr);
unsigned int nitems = dmatrix->dimensions[0];
unsigned int na = mol.getNumAtoms();
if (nitems != na*(na-1)/2) {
throw_value_error("The array size does not match the number of atoms in the molecule");
}
double *inData = reinterpret_cast<double *>(dmatrix->data);
double *cData = new double[nitems];
memcpy(static_cast<void *>(cData),
static_cast<const void *>(inData),
nitems*sizeof(double));
DOUBLE_SMART_PTR dmat(cData);
double oBondLen=RDDepict::BOND_LEN;
if(bondLength>0){
RDDepict::BOND_LEN=bondLength;
}
unsigned int res;
res=RDDepict::compute2DCoordsMimicDistMat(mol, &dmat,
canonOrient, clearConfs,
weightDistMat,
nFlipsPerSample, nSamples,
sampleSeed, permuteDeg4Nodes);
if(bondLength>0){
RDDepict::BOND_LEN=oBondLen;
}
return res;
}
}
BOOST_PYTHON_MODULE(rdDepictor)
{
python::register_exception_translator<IndexErrorException>(&translate_index_error);
python::register_exception_translator<ValueErrorException>(&translate_value_error);
python::scope().attr("__doc__") =
"Module containing the functionality to compute 2D coordinates for a molecule"
;
import_array();
std::string docString;
docString = "Compute 2D coordinates for a molecule. \n\
The resulting coordinates are stored on each atom of the molecule \n\n\
ARGUMENTS: \n\n\
mol - the molecule of interest\n\
canonOrient - orient the molecule in a canonical way\n\
clearConfs - if true, all existing conformations on the molecule\n\
will be cleared\n\
coordMap - a dictionary mapping atom Ids -> Point2D objects \n\
with starting coordinates for atoms that should\n\
have their positions locked.\n\
nFlipsPerSample - number of rotatable bonds that are\n\
flipped at random at a time.\n\
nSample - Number of random samplings of rotatable bonds.\n\
sampleSeed - seed for the random sampling process.\n\
permuteDeg4Nodes - allow permutation of bonds at a degree 4\n\
node during the sampling process \n\
bondLength - change the default bond length for depiction \n\n\
RETURNS: \n\n\
ID of the conformation added to the molecule\n";
python::def("Compute2DCoords", RDDepict::Compute2DCoords,
(python::arg("mol"),
python::arg("canonOrient")=true,
python::arg("clearConfs")=true,
python::arg("coordMap")=python::dict(),
python::arg("nFlipsPerSample")=0,
python::arg("nSample")=0,
python::arg("sampleSeed")=0,
python::arg("permuteDeg4Nodes")=false,
python::arg("bondLength")=-1.0),
docString.c_str());
docString = "Compute 2D coordinates for a molecule such \n\
that the inter-atom distances mimic those in a user-provided\n\
distance matrix. \n\
The resulting coordinates are stored on each atom of the molecule \n\n\
ARGUMENTS: \n\n\
mol - the molecule of interest\n\
distMat - distance matrix that we want the 2D structure to mimic\n\
canonOrient - orient the molecule in a canonical way\n\
clearConfs - if true, all existing conformations on the molecule\n\
will be cleared\n\
weightDistMat - weight assigned in the cost function to mimicing\n\
the distance matrix.\n\
This must be between (0.0,1.0). (1.0-weightDistMat)\n\
is then the weight assigned to improving \n\
the density of the 2D structure i.e. try to\n\
make it spread out\n\
nFlipsPerSample - number of rotatable bonds that are\n\
flipped at random at a time.\n\
nSample - Number of random samplings of rotatable bonds.\n\
sampleSeed - seed for the random sampling process.\n\
permuteDeg4Nodes - allow permutation of bonds at a degree 4\n\
node during the sampling process \n\
bondLength - change the default bond length for depiction \n\n\
RETURNS: \n\n\
ID of the conformation added to the molecule\n";
python::def("Compute2DCoordsMimicDistmat", RDDepict::Compute2DCoordsMimicDistmat,
(python::arg("mol"),
python::arg("distMat"),
python::arg("canonOrient")=false,
python::arg("clearConfs")=true,
python::arg("weightDistMat")=0.5,
python::arg("nFlipsPerSample")=3,
python::arg("nSample")=100,
python::arg("sampleSeed")=100,
python::arg("permuteDeg4Nodes")=true,
python::arg("bondLength")=-1.0),
docString.c_str());
}
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