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// Copyright (c) 2016, 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.
//
#include <GraphMol/RDKitBase.h>
#include <GraphMol/QueryOps.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/MonomerInfo.h>
#include <RDGeneral/types.h>
#include "RDFreeSASA.h"
#include "boost/format.hpp"
extern "C" {
#include "freesasa.h"
}
namespace RDKit {
namespace common_properties {
namespace Atom {
const std::string SASA = "SASA";
; // Solvent Accessible Surface Area for atom- double
const std::string SASAClass = "SASAClass"; // Class type, 0,1,2... etc
const std::string SASAClassName =
"SASAClassName"; // Class name, Polar, APolar etc...
} // namespace Atom
namespace Molecule {
const std::string SASA =
"SASA"; // Total Solvent Accessible Surface area for molecule;
}
} // namespace common_properties
} // namespace RDKit
namespace FreeSASA {
using namespace RDKit;
bool classifyAtoms(ROMol &mol, std::vector<double> &radii,
const SASAOpts &opts) {
radii.clear();
const freesasa_classifier *classifier = nullptr;
switch (opts.classifier) {
case SASAOpts::Protor:
classifier = &freesasa_protor_classifier;
break;
case SASAOpts::NACCESS:
classifier = &freesasa_naccess_classifier;
break;
case SASAOpts::OONS:
classifier = &freesasa_oons_classifier;
break;
default:
throw ValueErrorException("unknown FreeSASA classifier specified");
return false;
}
bool success = true;
for (ROMol::AtomIterator at = mol.beginAtoms(); at != mol.endAtoms(); ++at) {
Atom *atom = *at;
freesasa_atom_class cls = FREESASA_ATOM_UNKNOWN;
std::string classification = "Unclassified";
double radius = 0.0;
const AtomMonomerInfo *info = atom->getMonomerInfo();
if (info) {
const char *atom_name = info->getName().c_str();
const char *res_name = nullptr;
if (info->getMonomerType() == AtomMonomerInfo::PDBRESIDUE) {
res_name = ((AtomPDBResidueInfo *)info)->getResidueName().c_str();
radius = freesasa_classifier_radius(classifier, res_name, atom_name);
if (radius == 0.0) {
BOOST_LOG(rdWarningLog)
<< "Atom " << atom->getIdx() << " has zero radius" << std::endl;
}
cls = freesasa_classifier_class(classifier, res_name, atom_name);
if (cls == FREESASA_ATOM_UNKNOWN) {
BOOST_LOG(rdWarningLog) << "Atom " << atom->getIdx()
<< " could not be classified" << std::endl;
success = false;
} else {
classification = freesasa_classifier_class2str(cls);
}
}
}
radii.push_back(radius);
atom->setProp<int>(common_properties::Atom::SASAClass, (int)cls);
atom->setProp(common_properties::Atom::SASAClassName, classification);
}
return success;
}
namespace {
double internalCalcSASA(const ROMol &mol, const std::vector<double> &radii,
int confIdx, const SASAOpts &opts) {
PRECONDITION(mol.getNumConformers(), "No conformers in molecule");
PRECONDITION(mol.getNumAtoms(), "Empty molecule");
freesasa_parameters params = freesasa_default_parameters;
params.n_threads = 1;
switch (opts.algorithm) {
case SASAOpts::LeeRichards:
params.alg = FREESASA_LEE_RICHARDS;
break;
case SASAOpts::ShrakeRupley:
params.alg = FREESASA_SHRAKE_RUPLEY;
break;
default:
throw ValueErrorException("Unknown freesasa algorithm");
}
// sneaky, but legal :)
std::vector<double> coords(mol.getNumAtoms() * 3);
const RDGeom::POINT3D_VECT &vec = mol.getConformer(confIdx).getPositions();
for (size_t i = 0; i < mol.getNumAtoms(); ++i) {
coords[i * 3] = vec[i].x;
coords[i * 3 + 1] = vec[i].y;
coords[i * 3 + 2] = vec[i].z;
}
freesasa_result *res =
freesasa_calc_coord(&coords[0], &radii[0], mol.getNumAtoms(), ¶ms);
if (!res) return 0.0;
CHECK_INVARIANT(res->n_atoms == rdcast<int>(mol.getNumAtoms()),
"freesasa didn't return the correct number of atoms");
double sasa = res->total;
mol.setProp(common_properties::Molecule::SASA, sasa);
size_t i = 0;
for (ROMol::ConstAtomIterator at = mol.beginAtoms(); at != mol.endAtoms();
++at, ++i) {
(*at)->setProp(common_properties::Atom::SASA, res->sasa[i]);
}
freesasa_result_free(res);
return sasa;
}
} // namespace
double calcSASA(const RDKit::ROMol &mol, const std::vector<double> &radii,
int confIdx, const RDKit::QueryAtom *query,
const SASAOpts &opts) {
double result = internalCalcSASA(mol, radii, confIdx, opts);
if (query) {
result = 0.0f;
for (ROMol::ConstQueryAtomIterator at = mol.beginQueryAtoms(query);
at != mol.endQueryAtoms(); ++at) {
const Atom *atom = *at;
result += atom->getProp<double>("SASA");
}
}
return result;
}
const RDKit::QueryAtom *makeFreeSasaAPolarAtomQuery() {
auto *qa = new QueryAtom;
qa->setQuery(makePropQuery<Atom, std::string>("SASAClassName", "Apolar"));
return qa;
}
const RDKit::QueryAtom *makeFreeSasaPolarAtomQuery() {
auto *qa = new QueryAtom;
qa->setQuery(makePropQuery<Atom, std::string>("SASAClassName", "Polar"));
return qa;
}
} // namespace FreeSASA
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