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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 "Property.h"
#include <RDGeneral/types.h>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Atom.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/Descriptors/Crippen.h>
#include <GraphMol/Descriptors/MolSurf.h>
#ifdef RDK_THREADSAFE_SSS
#include <mutex>
#endif
namespace RDKit {
namespace Descriptors {
namespace {
void _registerDescriptors() {
REGISTER_DESCRIPTOR(exactmw, calcExactMW);
REGISTER_DESCRIPTOR(lipinskiHBA, calcLipinskiHBA);
REGISTER_DESCRIPTOR(lipinskiHBD, calcLipinskiHBD);
REGISTER_DESCRIPTOR(NumRotatableBonds, calcNumRotatableBonds);
REGISTER_DESCRIPTOR(NumHBD, calcNumHBD);
REGISTER_DESCRIPTOR(NumHBA, calcNumHBA);
REGISTER_DESCRIPTOR(NumHeteroatoms, calcNumHeteroatoms);
REGISTER_DESCRIPTOR(NumAmideBonds, calcNumAmideBonds);
REGISTER_DESCRIPTOR(FractionCSP3, calcFractionCSP3);
REGISTER_DESCRIPTOR(NumRings, calcNumRings);
REGISTER_DESCRIPTOR(NumAromaticRings, calcNumAromaticRings);
REGISTER_DESCRIPTOR(NumAliphaticRings, calcNumAliphaticRings);
REGISTER_DESCRIPTOR(NumSaturatedRings, calcNumSaturatedRings);
REGISTER_DESCRIPTOR(NumHeterocycles, calcNumHeterocycles);
REGISTER_DESCRIPTOR(NumAromaticHeterocycles, calcNumAromaticHeterocycles);
REGISTER_DESCRIPTOR(NumSaturatedHeterocycles, calcNumSaturatedHeterocycles);
REGISTER_DESCRIPTOR(NumAliphaticHeterocycles, calcNumAliphaticHeterocycles);
REGISTER_DESCRIPTOR(NumSpiroAtoms, calcNumSpiroAtoms);
REGISTER_DESCRIPTOR(NumBridgeheadAtoms, calcNumBridgeheadAtoms);
REGISTER_DESCRIPTOR(NumAtomStereoCenters, numAtomStereoCenters);
REGISTER_DESCRIPTOR(NumUnspecifiedAtomStereoCenters,
numUnspecifiedAtomStereoCenters);
REGISTER_DESCRIPTOR(labuteASA, calcLabuteASA);
REGISTER_DESCRIPTOR(tpsa, calcTPSA);
REGISTER_DESCRIPTOR(CrippenClogP, calcClogP);
REGISTER_DESCRIPTOR(CrippenMR, calcMR);
};
}
void registerDescriptors() {
#ifdef RDK_THREADSAFE_SSS
static std::once_flag once;
std::call_once(once, _registerDescriptors);
#else
static bool initialized = false;
if (!initialized) {
_registerDescriptors();
initialized = true;
}
#endif
}
std::vector<boost::shared_ptr<PropertyFunctor>> Properties::registry;
int Properties::registerProperty(PropertyFunctor *prop) {
for (size_t i = 0; i < Properties::registry.size(); ++i) {
if (registry[i]->getName() == prop->getName()) {
Properties::registry[i] = boost::shared_ptr<PropertyFunctor>(prop);
return i;
}
}
// XXX Add mutex?
Properties::registry.push_back(boost::shared_ptr<PropertyFunctor>(prop));
return Properties::registry.size();
}
std::vector<std::string> Properties::getAvailableProperties() {
registerDescriptors();
std::vector<std::string> names;
BOOST_FOREACH (boost::shared_ptr<PropertyFunctor> prop,
Properties::registry) {
names.push_back(prop->getName());
}
return names;
}
boost::shared_ptr<PropertyFunctor> Properties::getProperty(
const std::string &name) {
registerDescriptors();
BOOST_FOREACH (boost::shared_ptr<PropertyFunctor> prop,
Properties::registry) {
if (prop.get() && prop->getName() == name) {
return prop;
}
}
throw KeyErrorException(name);
}
Properties::Properties() : m_properties() {
registerDescriptors();
BOOST_FOREACH (boost::shared_ptr<PropertyFunctor> prop,
Properties::registry) {
m_properties.push_back(prop);
}
}
Properties::Properties(const std::vector<std::string> &propNames) {
registerDescriptors();
BOOST_FOREACH (const std::string &name, propNames) {
m_properties.push_back(Properties::getProperty(name));
}
}
std::vector<std::string> Properties::getPropertyNames() const {
std::vector<std::string> names;
BOOST_FOREACH (boost::shared_ptr<PropertyFunctor> prop, m_properties) {
names.push_back(prop->getName());
}
return names;
}
std::vector<double> Properties::computeProperties(const RDKit::ROMol &mol,
bool annotate) const {
std::vector<double> res;
res.reserve(m_properties.size());
BOOST_FOREACH (boost::shared_ptr<PropertyFunctor> prop, m_properties) {
res.push_back((*prop)(mol));
if (annotate) {
mol.setProp<double>(prop->getName(), (*prop)(mol));
}
}
return res;
}
void Properties::annotateProperties(RDKit::ROMol &mol) const {
BOOST_FOREACH (boost::shared_ptr<PropertyFunctor> prop, m_properties) {
mol.setProp<double>(prop->getName(), (*prop)(mol));
}
}
PROP_RANGE_QUERY *makePropertyRangeQuery(const std::string &name, double min,
double max) {
auto *filter = new PROP_RANGE_QUERY(min, max);
filter->setDataFunc(Properties::getProperty(name)->d_dataFunc);
return filter;
}
}
}
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