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//
// Copyright (C) 2016 Novartis Institutes for BioMedical Research
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <map>
#include "../MolOps.h"
#include "../Descriptors/MolDescriptors.h"
#include "StripSmallFragments.h"
#include "../SmilesParse/SmilesWrite.h"
#include "../FileParsers/MolFileStereochem.h"
// define snprintf for msvc
#if _MSC_VER
#if _MSC_VER < 1900
#define snprintf _snprintf
#endif
#endif
namespace RDKit {
namespace StructureCheck {
static inline std::string getMolecularFormula(const ROMol &mol) {
return RDKit::Descriptors::calcMolFormula(mol);
}
void AddMWMF(RWMol &mol,
bool pre) { // set formula & mass properties "MW_PRE" "MW_POST"
double mass = 0.0;
mass = RDKit::Descriptors::calcExactMW(mol);
/*
for (unsigned i = 0; i < mol.getNumAtoms(); i++) {
const Atom& atom = *mol.getAtomWithIdx(i);
mass += atom.getMass();
mass += atom.getNumImplicitHs() * 1.0080; // and add implicit
Hydrogens mass
}
*/
std::string formula = getMolecularFormula(mol);
if (!formula.empty()) mol.setProp((pre ? "MF_PRE" : "MF_POST"), formula);
char propertyValue[64];
snprintf(propertyValue, sizeof(propertyValue), "%g", mass);
mol.setProp((pre ? "MW_PRE" : "MW_POST"), mass);
}
bool StripSmallFragments(RWMol &mol, bool verbose) {
const bool sanitize = false;
std::vector<boost::shared_ptr<ROMol>> frags =
MolOps::getMolFrags(mol, sanitize);
if (frags.size() <= 1) return false;
size_t maxFragSize = 0;
size_t maxFragIdx = 0;
for (size_t i = 0; i < frags.size(); ++i) {
const unsigned int fragSize = frags[i].get()->getNumAtoms();
if (fragSize >= maxFragSize) {
maxFragSize = fragSize;
maxFragIdx = i;
}
}
if (verbose) {
std::string name = "<no name>";
mol.getPropIfPresent(common_properties::_Name, name);
for (size_t i = 0; i < frags.size(); ++i) {
if (i != maxFragIdx) {
BOOST_LOG(rdWarningLog) << name << " removed fragment i=" << i
<< " with " << frags[i].get()->getNumAtoms()
<< " atoms" << std::endl;
}
}
}
// we need to save chirality for checking later
bool checkChiral = false;
if (mol.hasProp(RDKit::common_properties::_MolFileChiralFlag)) {
unsigned int chiralflag =
mol.getProp<unsigned int>(RDKit::common_properties::_MolFileChiralFlag);
frags[maxFragIdx].get()->setProp<unsigned int>(
RDKit::common_properties::_MolFileChiralFlag, chiralflag);
checkChiral = chiralflag != 0;
}
mol = *frags[maxFragIdx].get();
// We need to see if the mol file's chirality possibly came from this
// fragment.
if (checkChiral) {
bool ischiral = false;
RWMol copy(mol);
try {
MolOps::sanitizeMol(copy);
ClearSingleBondDirFlags(copy);
MolOps::detectBondStereochemistry(copy);
MolOps::assignStereochemistry(copy, true, true, true);
for (ROMol::AtomIterator atIt = copy.beginAtoms();
atIt != copy.endAtoms(); ++atIt) {
if ((*atIt)->hasProp(common_properties::_ChiralityPossible)) {
ischiral = true;
checkChiral = false;
break;
}
}
} catch (...) {
}
// are chiral tags set
if (checkChiral) {
for (ROMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms();
++atIt) {
if ((*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW ||
(*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW) {
ischiral = true;
break;
}
}
for (ROMol::BondIterator bondIt = mol.beginBonds();
bondIt != mol.endBonds(); ++bondIt) {
if ((*bondIt)->getBondDir() == Bond::BEGINDASH ||
(*bondIt)->getBondDir() == Bond::BEGINWEDGE) {
ischiral = true;
break;
}
}
}
if (!ischiral) {
mol.setProp<unsigned int>(RDKit::common_properties::_MolFileChiralFlag,
0);
}
}
return true;
}
} // namespace StructureCheck
} // namespace RDKit
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