mirror of
https://github.com/rdkit/rdkit.git
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db93262a3e
* add safeSetattr to varios params objects * added safeSetattr to further params / options
190 lines
7.5 KiB
C++
190 lines
7.5 KiB
C++
// Copyright (c) 2017, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#define NO_IMPORT_ARRAY
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#include <RDBoost/python.h>
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#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
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#include <numpy/arrayobject.h>
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#include <boost/python/list.hpp>
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#include <cmath>
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#include <RDGeneral/Exceptions.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/QueryAtom.h>
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#include <RDFreeSASA.h>
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#include <RDBoost/Wrap.h>
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namespace python = boost::python;
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namespace RDKit {
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namespace {
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python::object classifyAtomsHelper(RDKit::ROMol &mol,
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const FreeSASA::SASAOpts &opts) {
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std::vector<double> radii;
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python::list l;
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if (FreeSASA::classifyAtoms(mol, radii, opts)) {
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for (double &i : radii) {
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l.append(i);
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}
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return l;
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}
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return l;
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}
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double calcSASAHelper(const RDKit::ROMol &mol, python::object radii,
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int confIdx, const RDKit::Atom *query,
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const FreeSASA::SASAOpts &opts) {
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const RDKit::QueryAtom *atom = nullptr;
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if (query) {
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atom = dynamic_cast<const RDKit::QueryAtom *>(query);
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if (!atom) {
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throw ValueErrorException("Query is not a query atom!");
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}
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}
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std::vector<double> vradii;
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unsigned int sz = boost::python::len(radii);
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for (unsigned int i = 0; i < sz; ++i) {
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vradii.push_back(python::extract<double>(radii[i])());
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}
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return FreeSASA::calcSASA(mol, vradii, confIdx, atom, opts);
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}
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} // namespace
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struct freesasa_wrapper {
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static void wrap() {
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std::string docString = "";
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python::enum_<FreeSASA::SASAOpts::Algorithm>("SASAAlgorithm")
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.value("LeeRichards", FreeSASA::SASAOpts::LeeRichards)
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.value("ShrakeRupley", FreeSASA::SASAOpts::ShrakeRupley)
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.export_values();
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python::enum_<FreeSASA::SASAOpts::Classifier>("SASAClassifier")
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.value("Protor", FreeSASA::SASAOpts::Protor)
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.value("NACCESS", FreeSASA::SASAOpts::NACCESS)
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.value("OONS", FreeSASA::SASAOpts::OONS)
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.export_values();
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python::enum_<FreeSASA::SASAOpts::Classes>("SASAClass")
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.value("Unclassified", FreeSASA::SASAOpts::Unclassified)
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.value("APolar", FreeSASA::SASAOpts::APolar)
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.value("Polar", FreeSASA::SASAOpts::Polar)
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.export_values();
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python::class_<FreeSASA::SASAOpts>(
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"SASAOpts", docString.c_str(),
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python::init<>(python::args("self"), "Constructor takes no arguments"))
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.def(python::init<FreeSASA::SASAOpts::Algorithm,
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FreeSASA::SASAOpts::Classifier>(
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python::args("self", "alg", "cls")))
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.def(python::init<FreeSASA::SASAOpts::Algorithm,
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FreeSASA::SASAOpts::Classifier, double>(
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python::args("self", "alg", "cls", "pr")))
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.def_readwrite("algorithm", &FreeSASA::SASAOpts::algorithm)
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.def_readwrite("classifier", &FreeSASA::SASAOpts::classifier)
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.def_readwrite("probeRadius", &FreeSASA::SASAOpts::probeRadius)
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.def("__setattr__", &safeSetattr);
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docString =
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"Classify the atoms in the molecule returning their radii if "
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"possible.\n"
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"ARGUMENTS:\n"
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" - mol: molecule to classify\n"
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" - options: FreeSASA options class specifying the classification "
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"method.\n"
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" Current classifiers are Protor, NACCESS and OONS\n"
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" classification is stored as atom property 'SASAClass' "
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"for the integer value\n"
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" and 'SASAClassName' for the string name of the class, "
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"Polar, APolar...\n"
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"\n"
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"RETURNS:\n"
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" list of radii where radii[atom.GetIdx()] is the radii of the atom.\n"
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" If classification fails, NONE is returned\n";
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python::def(
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"classifyAtoms", classifyAtomsHelper,
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(python::arg("mol"), python::arg("options") = FreeSASA::SASAOpts()),
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docString.c_str());
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docString =
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"Compute the Solvent Accessible Surface Area using the FreeSASA "
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"library\n"
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"ARGUMENTS:\n"
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" - mol: The molecule to compute.\n"
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" - radii: A list of atom raddii where radii[atom.GetIdx()] is the "
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"radius of the atom\n"
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" These can be passed in or calculated with classifyAtoms "
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"for some proteins\n"
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" - confIdx: Specify the conformer to use for the 3D geometry "
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"[default -1]\n"
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" - query: Pass along a query atom to compute the SASA for a subset "
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"of atoms.\n"
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" precanned query atoms can be made with "
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"MakeFreeSasaPolarAtomQuery and\n"
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" MakeFreeSasaAPolarAtomQuery for classified polar and "
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"apolar atoms respectively.\n"
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" - opts: a SASAOpts class specifying the algorithm to use\n"
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"\n"
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"RETURNS:\n"
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"The computed solvent accessible surface area.\n";
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python::def(
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"CalcSASA", calcSASAHelper,
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(python::arg("mol"), python::arg("radii"), python::arg("confIdx") = -1,
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python::arg("query") = python::object(),
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python::arg("opts") = FreeSASA::SASAOpts()),
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docString.c_str());
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python::def(
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"MakeFreeSasaAPolarAtomQuery", FreeSASA::makeFreeSasaAPolarAtomQuery,
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python::return_value_policy<python::manage_new_object>(),
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"Returns an APolar atom query for use with CalcSASA. An apolar atom "
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"has the SASAClass\n"
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"and SASAClassName set to the APOLAR class. (see classifyAtoms)");
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python::def(
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"MakeFreeSasaPolarAtomQuery", FreeSASA::makeFreeSasaPolarAtomQuery,
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python::return_value_policy<python::manage_new_object>(),
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"Returns a polar atom query for use with CalcSASA. An polar atom has "
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"the SASAClass\n"
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"and SASAClassName set to the POLAR class. (see classifyAtoms)");
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}
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};
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} // namespace RDKit
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BOOST_PYTHON_MODULE(rdFreeSASA) {
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python::scope().attr("__doc__") =
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"Module containing rdFreeSASA classes and functions.";
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RDKit::freesasa_wrapper::wrap();
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}
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