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// Copyright (c) 2017, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
#include <boost/python/list.hpp>
//#include <boost/python/suite/indexing/map_indexing_suite.hpp>
//#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
//#include <string>
#include <math.h>
#include <RDGeneral/Exceptions.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/QueryAtom.h>
#include <RDFreeSASA.h>
#include <RDBoost/Wrap.h>
namespace python = boost::python;
namespace RDKit {
namespace {
python::object classifyAtomsHelper(RDKit::ROMol &mol,
const FreeSASA::SASAOpts &opts) {
std::vector<double> radii;
python::list l;
if (FreeSASA::classifyAtoms(mol, radii, opts)) {
for (double &i : radii) l.append(i);
return l;
}
return l;
}
double calcSASAHelper(const RDKit::ROMol &mol, python::object radii,
int confIdx, const RDKit::Atom *query,
const FreeSASA::SASAOpts &opts) {
const RDKit::QueryAtom *atom = nullptr;
if (query) {
atom = dynamic_cast<const RDKit::QueryAtom *>(query);
if (!atom) {
throw ValueErrorException("Query is not a query atom!");
}
}
std::vector<double> vradii;
unsigned int sz = python::extract<unsigned int>(radii.attr("__len__")());
for (unsigned int i = 0; i < sz; ++i) {
vradii.push_back(python::extract<double>(radii[i])());
}
return FreeSASA::calcSASA(mol, vradii, confIdx, atom, opts);
}
}
struct freesasa_wrapper {
static void wrap() {
std::string docString = "";
python::enum_<FreeSASA::SASAOpts::Algorithm>("SASAAlgorithm")
.value("LeeRichards", FreeSASA::SASAOpts::LeeRichards)
.value("ShrakeRupley", FreeSASA::SASAOpts::ShrakeRupley)
.export_values();
python::enum_<FreeSASA::SASAOpts::Classifier>("SASAClassifier")
.value("Protor", FreeSASA::SASAOpts::Protor)
.value("NACCESS", FreeSASA::SASAOpts::NACCESS)
.value("OONS", FreeSASA::SASAOpts::OONS)
.export_values();
python::enum_<FreeSASA::SASAOpts::Classes>("SASAClass")
.value("Unclassified", FreeSASA::SASAOpts::Unclassified)
.value("APolar", FreeSASA::SASAOpts::APolar)
.value("Polar", FreeSASA::SASAOpts::Polar)
.export_values();
python::class_<FreeSASA::SASAOpts>(
"SASAOpts", docString.c_str(),
python::init<>("Constructor takes no arguments"))
.def(python::init<FreeSASA::SASAOpts::Algorithm,
FreeSASA::SASAOpts::Classifier>())
.def_readwrite("algorithm", &FreeSASA::SASAOpts::algorithm)
.def_readwrite("classifier", &FreeSASA::SASAOpts::classifier);
docString =
"Classify the atoms in the molecule returning their radii if "
"possible.\n"
"ARGUMENTS:\n"
" - mol: molecule to classify\n"
" - options: FreeSASA options class specifying the classsification "
"method.\n"
" Current classifiers are Protor, NACCESS and OONS\n"
" classification is stored as atom property 'SASAClass' "
"for the integer value\n"
" and 'SASAClassName' for the string name of the class, "
"Polar, APolar...\n"
"\n"
"RETURNS:\n"
" list of radii where radii[atom.GetIdx()] is the radii of the atom.\n"
" If classification fails, NONE is returned\n";
python::def(
"classifyAtoms", classifyAtomsHelper,
(python::arg("mol"), python::arg("options") = FreeSASA::SASAOpts()),
docString.c_str());
docString =
"Compute the Solvent Accessible Surface Area using the FreeSASA "
"library\n"
"ARGUMENTS:\n"
" - mol: The molecule to compute.\n"
" - radii: A list of atom raddii where radii[atom.GetIdx()] is the "
"radius of the atom\n"
" These can be passed in or calculated with classifyAtoms "
"for some proteins\n"
" - confIdx: Specify the conformer to use for the 3D geometry "
"[default -1]\n"
" - query: Pass along a query atom to compute the SASA for a subset "
"of atoms.\n"
" precanned query atoms can be made with "
"MakeFreeSasaPolarAtomQuery and\n"
" MakeFreeSasaAPolarAtomQuery for classified polar and "
"apolar atoms respectively.\n"
" - opts: a SASAOpts class specifying the algorithm to use\n"
"\n"
"RETURNS:\n"
"The computed solvent accessible surface area.\n";
python::def(
"CalcSASA", calcSASAHelper,
(python::arg("mol"), python::arg("radii"), python::arg("confIdx") = -1,
python::arg("query") = python::object(),
python::arg("opts") = FreeSASA::SASAOpts()),
docString.c_str());
python::def(
"MakeFreeSasaAPolarAtomQuery", FreeSASA::makeFreeSasaAPolarAtomQuery,
python::return_value_policy<python::manage_new_object>(),
"Returns an APolar atom query for use with CalcSASA. An apolar atom "
"has the SASAClass\n"
"and SASAClassName set to the APOLAR class. (see classifyAtoms)");
python::def(
"MakeFreeSasaPolarAtomQuery", FreeSASA::makeFreeSasaPolarAtomQuery,
python::return_value_policy<python::manage_new_object>(),
"Returns a polar atom query for use with CalcSASA. An polar atom has "
"the SASAClass\n"
"and SASAClassName set to the POLAR class. (see classifyAtoms)");
}
};
}
BOOST_PYTHON_MODULE(rdFreeSASA) {
python::scope().attr("__doc__") =
"Module containing rdFreeSASA classes and functions.";
RDKit::freesasa_wrapper::wrap();
}
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