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//
// Copyright (C) 2015 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 PY_ARRAY_UNIQUE_SYMBOL rdmmpa_array_API
#include <boost/python.hpp>
#include <GraphMol/ROMol.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <RDBoost/Wrap.h>
#include <GraphMol/MMPA/MMPA.h>
namespace python = boost::python;
namespace {
python::tuple fragmentMolHelper(const RDKit::ROMol &mol, unsigned int maxCuts,
unsigned int maxCutBonds,
const std::string &pattern,
bool resultsAsMols) {
std::vector<std::pair<RDKit::ROMOL_SPTR, RDKit::ROMOL_SPTR>> tres;
bool ok = RDKit::MMPA::fragmentMol(mol, tres, maxCuts, maxCutBonds, pattern);
python::list pyres;
if (ok) {
for (std::vector<std::pair<RDKit::ROMOL_SPTR, RDKit::ROMOL_SPTR>>::
const_iterator pr = tres.begin();
pr != tres.end(); ++pr) {
python::list lres;
if (resultsAsMols) {
lres.append(pr->first);
lres.append(pr->second);
} else {
if (pr->first) {
lres.append(RDKit::MolToSmiles(*(pr->first), true));
} else {
lres.append("");
}
lres.append(RDKit::MolToSmiles(*(pr->second), true));
}
pyres.append(python::tuple(lres));
}
}
return python::tuple(pyres);
}
python::tuple fragmentMolHelper2(const RDKit::ROMol &mol, unsigned int minCuts,
unsigned int maxCuts, unsigned int maxCutBonds,
const std::string &pattern,
bool resultsAsMols) {
std::vector<std::pair<RDKit::ROMOL_SPTR, RDKit::ROMOL_SPTR>> tres;
bool ok = RDKit::MMPA::fragmentMol(mol, tres, minCuts, maxCuts, maxCutBonds,
pattern);
python::list pyres;
if (ok) {
for (std::vector<std::pair<RDKit::ROMOL_SPTR, RDKit::ROMOL_SPTR>>::
const_iterator pr = tres.begin();
pr != tres.end(); ++pr) {
python::list lres;
if (resultsAsMols) {
lres.append(pr->first);
lres.append(pr->second);
} else {
if (pr->first) {
lres.append(RDKit::MolToSmiles(*(pr->first), true));
} else {
lres.append("");
}
lres.append(RDKit::MolToSmiles(*(pr->second), true));
}
pyres.append(python::tuple(lres));
}
}
return python::tuple(pyres);
}
python::tuple fragmentMolHelper3(const RDKit::ROMol &mol, python::object ob,
unsigned int minCuts, unsigned int maxCuts,
bool resultsAsMols) {
std::vector<std::pair<RDKit::ROMOL_SPTR, RDKit::ROMOL_SPTR>> tres;
std::unique_ptr<std::vector<unsigned int>> v =
pythonObjectToVect<unsigned int>(ob);
if (!v) {
throw_value_error("bondsToCut must be non-empty");
}
bool ok = RDKit::MMPA::fragmentMol(mol, tres, *v, minCuts, maxCuts);
python::list pyres;
if (ok) {
for (std::vector<std::pair<RDKit::ROMOL_SPTR, RDKit::ROMOL_SPTR>>::
const_iterator pr = tres.begin();
pr != tres.end(); ++pr) {
python::list lres;
if (resultsAsMols) {
lres.append(pr->first);
lres.append(pr->second);
} else {
if (pr->first) {
lres.append(RDKit::MolToSmiles(*(pr->first), true));
} else {
lres.append("");
}
lres.append(RDKit::MolToSmiles(*(pr->second), true));
}
pyres.append(python::tuple(lres));
}
}
return python::tuple(pyres);
}
} // namespace
BOOST_PYTHON_MODULE(rdMMPA) {
python::scope().attr("__doc__") =
"Module containing a C++ implementation of code for doing MMPA";
std::string docString =
"Does the fragmentation necessary for an MMPA analysis";
python::def("FragmentMol", fragmentMolHelper,
(python::arg("mol"), python::arg("maxCuts") = 3,
python::arg("maxCutBonds") = 20,
python::arg("pattern") = "[#6+0;!$(*=,#[!#6])]!@!=!#[*]",
python::arg("resultsAsMols") = true),
docString.c_str());
python::def("FragmentMol", fragmentMolHelper2,
(python::arg("mol"), python::arg("minCuts"),
python::arg("maxCuts"), python::arg("maxCutBonds"),
python::arg("pattern") = "[#6+0;!$(*=,#[!#6])]!@!=!#[*]",
python::arg("resultsAsMols") = true),
docString.c_str());
python::def("FragmentMol", fragmentMolHelper3,
(python::arg("mol"), python::arg("bondsToCut"),
python::arg("minCuts") = 1, python::arg("maxCuts") = 3,
python::arg("resultsAsMols") = true),
docString.c_str());
}
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