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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 "../SmilesParse/SmilesWrite.h"
#include "../SmilesParse/SmilesWrite.h"
#include "StructChecker.h"
#include "Pattern.h"
#include "Stereo.h"
#include "ReCharge.h"
#include "Tautomer.h"
#include "StripSmallFragments.h"
namespace RDKit {
namespace StructureCheck {
unsigned StructChecker::checkMolStructure(RWMol &mol) const {
unsigned flags = NO_CHANGE; // == 0. return value
if (0 != Options.MaxMolSize && (mol.getNumAtoms() > Options.MaxMolSize ||
mol.getNumBonds() > Options.MaxMolSize)) {
return SIZE_CHECK_FAILED;
}
if (mol.getNumAtoms() == 0) {
return SIZE_CHECK_FAILED;
}
if (!mol.getRingInfo()->isInitialized()) mol.getRingInfo()->initialize();
/* it uses SDL text
if (Options.ConvertAtomTexts)
{
if(!convertAtomAliases(mol))
flags |= ALIAS_CONVERSION_FAILED;
else
flags |= TRANSFORMED;
}
if (Options.ConvertSText)
;//new_data_list = ConvertSTEXTToData(mol, new_data_list);
*/
if (!Options.AugmentedAtomPairs.empty()) {
if (TransformAugmentedAtoms(mol, Options.AugmentedAtomPairs, Options.Verbose)) {
flags |= TRANSFORMED;
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << MolToSmiles(mol) << "\n";
}
}
unsigned stereo_result = DubiousStereochemistry(mol);
if (0 != (FixDubious3DMolecule(mol) & CONVERTED_TO_2D)) {
stereo_result = 1;
flags |= DUBIOUS_STEREO_REMOVED;
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << MolToSmiles(mol) << "\n";
}
if (Options.RemoveMinorFragments) {
AddMWMF(mol, true); // Add mol mass data field "MW_PRE"
if (StripSmallFragments(mol, Options.Verbose)) {
flags |= FRAGMENTS_FOUND;
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "Striped SmallFragments"
<< MolToSmiles(mol) << "\n";
}
AddMWMF(mol, false); // Add mol mass data field "MW_POST"
}
// do tautomer standardization
for (unsigned i = 0; i < Options.FromTautomer.size(); i++) {
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "tautomerizing with rule " << i << "\n";
// fprintf(stderr, "tautomerizing with rule %d\n", i);
for (unsigned j = 0; j < 3; j++) // limit to 3 run per rule
{
StructCheckTautomer sct(mol, Options);
if (!sct.applyTautomer(i)) break;
flags |= TAUTOMER_TRANSFORMED;
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "molecule: has been tautomerized with rule "
<< i << ":\n" << MolToSmiles(mol) << "\n";
// sprintf(msg_buffer,"%10s: has been tautomerized with
// rule '%s'", mp->name, from_tautomer[i]->name);
// AddMsgToList(msg_buffer);
}
}
/* if (!IsNULL(data_list) && !IsNULL(new_data_list))
{ // append new data list if any
for (dph = data_list; !IsNULL(dph->next); dph = dph->next)
;
dph->next = new_data_list;
}
*/
if (stereo_result == EITHER_BOND_FOUND) { // looks for EITHER bonds
flags |= EITHER_WARNING;
RemoveDubiousStereochemistry(mol);
flags |= DUBIOUS_STEREO_REMOVED;
} else if (stereo_result > EITHER_BOND_FOUND) { // more severe errors
flags |= STEREO_ERROR;
if (Options.CheckStereo) {
flags |= BAD_MOLECULE;
} else {
RemoveDubiousStereochemistry(mol);
flags |= DUBIOUS_STEREO_REMOVED;
}
}
// line 1612
if (TotalCharge(mol) != Options.DesiredCharge) {
unsigned ndeprot;
unsigned nrefine;
ChargeFix ch(Options, mol);
if (ch.rechargeMolecule(ndeprot, nrefine)) {
flags |= RECHARGED;
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "Recharged Molecule:" << MolToSmiles(mol) << "\n";
}
}
//
const double clashLimit = Options.CollisionLimitPercent/100.0;
if (Options.CheckCollisions && AtomClash(mol, clashLimit)) {
flags |= ATOM_CLASH;
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "AtomClash done:" << MolToSmiles(mol) << "\n";
}
if (!Options.GoodAtoms.empty())
if (!CheckAtoms(mol, Options.GoodAtoms, Options.Verbose))
flags |= ATOM_CHECK_FAILED;
if (Options.CheckStereo && !CheckStereo(mol)) flags |= STEREO_ERROR;
// if (Options.GroupsToSGroups)
// ConvertGroupsToSGroups(mol);
/*
//line 1630
stereo_bad = FALSE;
for (i = 0; i<nstereopat; i++)
{
ssp = stereo_patterns[i];
tmp = ForceStereoTemplate(mp, ssp);
if (tmp == (-1))
{
flags |= STEREO_FORCED_BAD; // problem enforcing
stereochemistry of 'ssp->name'
}
else if (tmp == 15) // "STEREO_FORCED"
{
flags |= STEREO_TRANSFORMED; // stereochemistry of
'ssp->name' enforced",
}
}
//line 1655
for (i = 0; i<npat; i++) // do template cleaning
{
ssp = patterns[i];
if (TemplateClean(mol, ssp))
{
result |= TEMPLATE_TRANSFORMED; // has been cleaned with
template 'ssp->name'
}
}
//line 1669
for (i = 0; i<nrpat; i++) // do template rotation
{
ssp = rotate_patterns[i];
if (TemplateRotate(mol, ssp))
{
result |= TEMPLATE_TRANSFORMED; // has been rotated by
template 'ssp->name'
}
}
}
*/
// the end:
if (0 != (flags & TRANSFORMED)) { // sanitaze molecule
// + ???? .............. ????
if (mol.getRingInfo()->isInitialized()) mol.getRingInfo()->reset();
mol.getRingInfo()->initialize();
}
return flags;
}
} // namespace StructureCheck
} // namespace RDKit
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