rdkit/Code/GraphMol/Descriptors/Property.cpp

//
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#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 <RDGeneral/BoostStartInclude.h>
#include <boost/thread/once.hpp>
#include <RDGeneral/BoostEndInclude.h>
#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 boost::once_flag once = BOOST_ONCE_INIT;
  boost::call_once(&_registerDescriptors, once);
#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) {
  PROP_RANGE_QUERY *filter = new PROP_RANGE_QUERY(min, max);
  filter->setDataFunc( Properties::getProperty(name)->d_dataFunc );
  return filter;
}

}
}