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//
// Copyright (C) 2017 Greg Landrum
//
// @@ 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/MolBundle.h>
#include <RDBoost/PySequenceHolder.h>
#include <RDBoost/iterator_next.h>
#include "substructmethods.h"
namespace python = boost::python;
namespace RDKit {
std::string molBundleClassDoc =
"A class for storing gropus of related molecules.\n\
Here related means that the molecules have to have the same number of atoms.\n\
\n";
struct molbundle_wrap {
static void wrap() {
python::class_<MolBundle, boost::noncopyable>(
"MolBundle", molBundleClassDoc.c_str(), python::init<>())
.def("__getitem__", &MolBundle::getMol)
.def("__len__", &MolBundle::size)
.def("AddMol", &MolBundle::addMol)
.def("GetMol", &MolBundle::getMol)
.def("Size", &MolBundle::size)
// substructures
.def("HasSubstructMatch",
(bool (*)(const MolBundle &m, const ROMol &query, bool, bool,
bool))HasSubstructMatch,
(python::arg("self"), python::arg("query"),
python::arg("recursionPossible") = true,
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false),
"Queries whether or not any molecule in the bundle contains a "
"particular substructure.\n\n"
" ARGUMENTS:\n"
" - query: a Molecule\n\n"
" - recursionPossible: (optional)\n\n"
" - useChirality: enables the use of stereochemistry in the "
"matching\n\n"
" - useQueryQueryMatches: use query-query matching logic\n\n"
" RETURNS: True or False\n")
.def("GetSubstructMatch",
(PyObject * (*)(const MolBundle &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 atoms from the first molecule in a "
"bundle that matches a substructure query.\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",
(PyObject * (*)(const MolBundle &m, const ROMol &query, bool, bool,
bool, unsigned int))GetSubstructMatches,
(python::arg("self"), python::arg("query"),
python::arg("uniquify") = true,
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false,
python::arg("maxMatches") = 1000),
"Returns tuple of all indices of the atoms from the first "
"molecule in a bundle that matches a substructure query.\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"
" 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")
.def("HasSubstructMatch",
(bool (*)(const MolBundle &m, const MolBundle &query, bool, bool,
bool))HasSubstructMatch,
(python::arg("self"), python::arg("query"),
python::arg("recursionPossible") = true,
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false),
"Queries whether or not any molecule in the first bundle matches "
"any molecule in the second bundle.\n\n"
" ARGUMENTS:\n"
" - query: a MolBundle\n\n"
" - recursionPossible: (optional)\n\n"
" - useChirality: enables the use of stereochemistry in the "
"matching\n\n"
" - useQueryQueryMatches: use query-query matching logic\n\n"
" RETURNS: True or False\n")
.def("GetSubstructMatch",
(PyObject * (*)(const MolBundle &m, const MolBundle &query, bool,
bool))GetSubstructMatch,
(python::arg("self"), python::arg("query"),
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false),
"Returns the indices of the atoms from the first molecule in a "
"bundle that matches a substructure query from a bundle.\n\n"
" ARGUMENTS:\n"
" - query: a MolBundle\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",
(PyObject * (*)(const MolBundle &m, const MolBundle &query, bool,
bool, bool, unsigned int))GetSubstructMatches,
(python::arg("self"), python::arg("query"),
python::arg("uniquify") = true,
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false,
python::arg("maxMatches") = 1000),
"Returns tuple of all indices of the atoms from the first "
"molecule in a bundle that matches a substructure query from the "
"second bundle.\n\n"
" ARGUMENTS:\n"
" - query: a MolBundle.\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"
" 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_molbundle() { RDKit::molbundle_wrap::wrap(); }
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