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