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// $Id$
//
// Copyright (C) 2015 Paolo Tosco
//
// Copyright (C) 2003-2010 Greg Landrum and 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.
//
#define NO_IMPORT_ARRAY
#include <boost/python.hpp>
#include <string>
// ours
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Resonance.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDBoost/PySequenceHolder.h>
#include <RDBoost/iterator_next.h>
#include "MolSupplier.h"
#include "substructmethods.h"
namespace python = boost::python;
namespace RDKit {
PyObject *GetResonanceSubstructMatches(
ResonanceMolSupplier &suppl, const ROMol &query, bool uniquify = false,
bool useChirality = false, bool useQueryQueryMatches = false,
unsigned int maxMatches = 1000, int numThreads = 1) {
std::vector<MatchVectType> matches;
int matched =
SubstructMatch(suppl, query, matches, uniquify, true, useChirality,
useQueryQueryMatches, maxMatches, numThreads);
PyObject *res = PyTuple_New(matched);
for (int idx = 0; idx < matched; idx++) {
PyTuple_SetItem(res, idx, convertMatches(matches[idx]));
}
return res;
}
std::string resonanceMolSupplierClassDoc =
"A class which supplies resonance structures (as mols) from a mol.\n \
\n \
Usage examples:\n \
\n \
1) Lazy evaluation: the resonance structures are not constructed\n \
until we ask for them:\n \
>>> suppl = ResonanceMolSupplier(mol)\n \
>>> for resMol in suppl:\n \
... resMol.GetNumAtoms()\n \
\n \
2) Lazy evaluation 2:\n \
>>> suppl = ResonanceMolSupplier(mol)\n \
>>> resMol1 = suppl.next()\n \
>>> resMol2 = suppl.next()\n \
>>> suppl.reset()\n \
>>> resMol3 = suppl.next()\n \
# resMol3 and resMol1 are the same: \n \
>>> MolToSmiles(resMol3)==MolToSmiles(resMol1)\n \
\n \
3) Random Access:\n \
>>> suppl = ResonanceMolSupplier(mol)\n \
>>> resMol1 = suppl[0] \n \
>>> resMol2 = suppl[1] \n \
NOTE: this will generate an IndexError if the supplier doesn't have that many\n \
molecules.\n \
\n \
4) Random Access 2: looping over all resonance structures\n \
>>> suppl = ResonanceMolSupplier(mol)\n \
>>> nResMols = len(suppl)\n \
>>> for i in range(nResMols):\n \
... suppl[i].GetNumAtoms()\n \
\n";
struct resmolsup_wrap {
static void wrap() {
python::enum_<ResonanceMolSupplier::ResonanceFlags>("ResonanceFlags")
.value("ALLOW_INCOMPLETE_OCTETS",
ResonanceMolSupplier::ALLOW_INCOMPLETE_OCTETS)
.value("ALLOW_CHARGE_SEPARATION",
ResonanceMolSupplier::ALLOW_CHARGE_SEPARATION)
.value("KEKULE_ALL", ResonanceMolSupplier::KEKULE_ALL)
.value("UNCONSTRAINED_CATIONS",
ResonanceMolSupplier::UNCONSTRAINED_CATIONS)
.value("UNCONSTRAINED_ANIONS",
ResonanceMolSupplier::UNCONSTRAINED_ANIONS)
.export_values();
python::class_<ResonanceMolSupplier, boost::noncopyable>(
"ResonanceMolSupplier", resonanceMolSupplierClassDoc.c_str(),
python::init<ROMol &, unsigned int, unsigned int>(
(python::arg("mol"), python::arg("flags") = 0,
python::arg("maxStructs") = 1000)))
.def("__iter__", (ResonanceMolSupplier * (*)(ResonanceMolSupplier *)) &
MolSupplIter,
python::return_internal_reference<1>())
.def(NEXT_METHOD, (ROMol * (*)(ResonanceMolSupplier *)) &
MolSupplNextAcceptNullLastMolecule,
"Returns the next resonance structure in the supplier. Raises "
"_StopIteration_ on end.\n",
python::return_value_policy<python::manage_new_object>())
.def("__getitem__",
(ROMol * (*)(ResonanceMolSupplier *, int)) & MolSupplGetItem,
python::return_value_policy<python::manage_new_object>())
.def("reset", &ResonanceMolSupplier::reset,
"Resets our position in the resonance structure supplier to the "
"beginning.\n")
.def("__len__", &ResonanceMolSupplier::length)
.def("atEnd", &ResonanceMolSupplier::atEnd,
"Returns whether or not we have hit the end of the resonance "
"structure supplier.\n")
.def("GetNumConjGrps", &ResonanceMolSupplier::getNumConjGrps,
"Returns the number of individual conjugated groups in the "
"molecule\n")
.def("GetBondConjGrpIdx",
(unsigned int (ResonanceMolSupplier::*)(unsigned int)) &
ResonanceMolSupplier::getBondConjGrpIdx,
"Given a bond index, it returns the index of the conjugated group"
"the bond belongs to, or -1 if it is not conjugated\n")
.def("GetAtomConjGrpIdx",
(unsigned int (ResonanceMolSupplier::*)(unsigned int)) &
ResonanceMolSupplier::getAtomConjGrpIdx,
"Given an atom index, it returns the index of the conjugated group"
"the atom belongs to, or -1 if it is not conjugated\n")
.def("SetNumThreads", (void (ResonanceMolSupplier::*)(unsigned int)) &
ResonanceMolSupplier::setNumThreads,
"Sets the number of threads to be used to enumerate resonance\n"
"structures (defaults to 1; 0 selects the number of concurrent\n"
"threads supported by the hardware; negative values are added\n"
"to the number of concurrent threads supported by the hardware)\n")
.def("Enumerate", &ResonanceMolSupplier::enumerate,
"Ask ResonanceMolSupplier to enumerate resonance structures"
"(automatically done as soon as any attempt to access them is "
"made)\n")
.def("GetIsEnumerated", &ResonanceMolSupplier::getIsEnumerated,
"Returns true if resonance structure enumeration has already "
"happened\n")
.def("GetSubstructMatch",
(PyObject * (*)(ResonanceMolSupplier & m, const ROMol &query, bool,
bool))GetSubstructMatch,
(python::arg("self"), python::arg("query"),
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false),
"Returns the indices of the molecule's atoms that match a "
"substructure query,\n"
"taking into account all resonance structures in "
"ResonanceMolSupplier.\n\n"
" ARGUMENTS:\n"
" - query: a Molecule\n\n"
" - useChirality: enables the use of stereochemistry in the "
"matching\n\n"
" - useQueryQueryMatches: use query-query matching logic\n\n"
" RETURNS: a tuple of integers\n\n"
" NOTES:\n"
" - only a single match is returned\n"
" - the ordering of the indices corresponds to the atom "
"ordering\n"
" in the query. For example, the first index is for the "
"atom in\n"
" this molecule that matches the first atom in the "
"query.\n")
.def("GetSubstructMatches", GetResonanceSubstructMatches,
(python::arg("self"), python::arg("query"),
python::arg("uniquify") = false,
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false,
python::arg("maxMatches") = 1000, python::arg("numThreads") = 1),
"Returns tuples of the indices of the molecule's atoms that match "
"a substructure query,\n"
"taking into account all resonance structures in "
"ResonanceMolSupplier.\n\n"
" ARGUMENTS:\n"
" - query: a Molecule.\n"
" - uniquify: (optional) determines whether or not the matches "
"are uniquified.\n"
" Defaults to 1.\n\n"
" - useChirality: enables the use of stereochemistry in the "
"matching\n\n"
" - useQueryQueryMatches: use query-query matching logic\n\n"
" - maxMatches: The maximum number of matches that will be "
"returned.\n"
" In high-symmetry cases with medium-sized "
"molecules, it is\n"
" very easy to end up with a combinatorial "
"explosion in the\n"
" number of possible matches. This argument "
"prevents that from\n"
" having unintended consequences\n\n"
" - numThreads: The number of threads to be used (defaults to "
"1; 0 selects the\n"
" number of concurrent threads supported by the "
"hardware; negative\n"
" values are added to the number of concurrent "
"threads supported\n"
" by the hardware).\n\n"
" RETURNS: a tuple of tuples of integers\n\n"
" NOTE:\n"
" - the ordering of the indices corresponds to the atom "
"ordering\n"
" in the query. For example, the first index is for the "
"atom in\n"
" this molecule that matches the first atom in the "
"query.\n");
};
};
}
void wrap_resmolsupplier() { RDKit::resmolsup_wrap::wrap(); }
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