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// $Id$
//
// 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 <RDBoost/python.h>
#define PY_ARRAY_UNIQUE_SYMBOL Depictor_array_API
#include <RDBoost/Wrap.h>
#include <RDBoost/import_array.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/Depictor/EmbeddedFrag.h>
#include <GraphMol/Depictor/DepictUtils.h>
using namespace RDDepict;
namespace python = boost::python;
void rdDepictExceptionTranslator(DepictException const &e) {
std::ostringstream oss;
oss << "Depict error: " << e.message();
PyErr_SetString(PyExc_ValueError, oss.str().c_str());
}
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,
bool forceRDKit = false) {
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, forceRDKit);
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, bool forceRDKit = false) {
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 = PyArray_DIM(dmatrix, 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 *>(PyArray_DATA(dmatrix));
auto *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, forceRDKit);
if (bondLength > 0) {
RDDepict::BOND_LEN = oBondLen;
}
return res;
}
void GenerateDepictionMatching2DStructure(RDKit::ROMol &mol,
RDKit::ROMol &reference, int confId,
python::object refPatt,
bool acceptFailure,
bool forceRDKit = false) {
RDKit::ROMol *referencePattern = nullptr;
if (refPatt != python::object()) {
referencePattern = python::extract<RDKit::ROMol *>(refPatt);
}
RDDepict::generateDepictionMatching2DStructure(
mol, reference, confId, referencePattern, acceptFailure, forceRDKit);
}
void GenerateDepictionMatching3DStructure(RDKit::ROMol &mol,
RDKit::ROMol &reference, int confId,
python::object refPatt,
bool acceptFailure,
bool forceRDKit = false) {
RDKit::ROMol *referencePattern = nullptr;
if (refPatt) {
referencePattern = python::extract<RDKit::ROMol *>(refPatt);
}
RDDepict::generateDepictionMatching3DStructure(
mol, reference, confId, referencePattern, acceptFailure, forceRDKit);
}
void setPreferCoordGen(bool value) {
#ifdef RDK_BUILD_COORDGEN_SUPPORT
RDDepict::preferCoordGen = value;
#endif
}
}
BOOST_PYTHON_MODULE(rdDepictor) {
python::scope().attr("__doc__") =
"Module containing the functionality to compute 2D coordinates for a "
"molecule";
python::register_exception_translator<RDDepict::DepictException>(
&rdDepictExceptionTranslator);
rdkit_import_array();
python::def("SetPreferCoordGen", setPreferCoordGen, python::arg("val"),
#ifdef RDK_BUILD_COORDGEN_SUPPORT
"Sets whether or not the CoordGen library should be prefered to "
"the RDKit depiction library."
#else
"Has no effect (CoordGen support not enabled)"
#endif
);
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, python::arg("forceRDKit") = false),
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,
python::arg("forceRDKit") = false),
docString.c_str());
docString =
"Generate a depiction for a molecule where a piece of the \n\
molecule is constrained to have the same coordinates as a reference. \n\n\
This is useful for, for example, generating depictions of SAR data \n\
sets so that the cores of the molecules are all oriented the same way. \n\
ARGUMENTS: \n\n\
mol - the molecule to be aligned, this will come back \n\
with a single conformer. \n\
reference - a molecule with the reference atoms to align to; \n\
this should have a depiction. \n\
confId - (optional) the id of the reference conformation to use \n\
referencePattern - (optional) a query molecule to be used to \n\
generate the atom mapping between the molecule \n\
and the reference. \n\
acceptFailure - (optional) if True, standard depictions will be generated \n\
for molecules that don't have a substructure match to the \n\
reference; if False, throws a DepictException.\n";
python::def(
"GenerateDepictionMatching2DStructure",
RDDepict::GenerateDepictionMatching2DStructure,
(python::arg("mol"), python::arg("reference"), python::arg("confId") = -1,
python::arg("refPatt") = python::object(),
python::arg("acceptFailure") = false, python::arg("forceRDKit") = false),
docString.c_str());
docString =
"Generate a depiction for a molecule where a piece of the molecule \n\
is constrained to have coordinates similar to those of a 3D reference \n\
structure.\n\
ARGUMENTS: \n\n\
mol - the molecule to be aligned, this will come back \n\
with a single conformer containing the 2D coordinates. \n\
reference - a molecule with the reference atoms to align to. \n\
By default this should be the same as mol, but with \n\
3D coordinates \n\
confId - (optional) the id of the reference conformation to use \n\
referencePattern - (optional) a query molecule to map a subset of \n\
the reference onto the mol, so that only some of the \n\
atoms are aligned. \n\
acceptFailure - (optional) if True, standard depictions will be generated \n\
for molecules that don't match the reference or the\n\
referencePattern; if False, throws a DepictException.\n";
python::def(
"GenerateDepictionMatching3DStructure",
RDDepict::GenerateDepictionMatching3DStructure,
(python::arg("mol"), python::arg("reference"), python::arg("confId") = -1,
python::arg("refPatt") = python::object(),
python::arg("acceptFailure") = false, python::arg("forceRDKit") = false),
docString.c_str());
}
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