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479 lines
18 KiB
C++
479 lines
18 KiB
C++
// $Id$
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//
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// Copyright (C) 2001-2010 Greg Landrum and Rational Discovery LLC
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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 <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include "SmilesParse.h"
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#include "SmilesParseOps.h"
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#include <list>
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#include <algorithm>
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#include <boost/dynamic_bitset.hpp>
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#include <boost/foreach.hpp>
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#include <RDGeneral/RDLog.h>
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namespace SmilesParseOps{
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using namespace RDKit;
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void ReportParseError(const char *message,bool throwIt){
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if(!throwIt) BOOST_LOG(rdErrorLog) <<"SMILES Parse Error: "<< message << std::endl;
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else throw SmilesParseException(message);
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}
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void CleanupAfterParseError(RWMol *mol){
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PRECONDITION(mol,"no molecule");
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// blow out any partial bonds:
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RWMol::BOND_BOOKMARK_MAP *marks = mol->getBondBookmarks();
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RWMol::BOND_BOOKMARK_MAP::iterator markI=marks->begin();
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while(markI != marks->end()){
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RWMol::BOND_PTR_LIST &bonds=markI->second;
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for(RWMol::BOND_PTR_LIST::iterator bondIt=bonds.begin();
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bondIt!=bonds.end();++bondIt){
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delete *bondIt;
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}
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++markI;
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}
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}
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//
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// set bondOrder to Bond::IONIC to skip the formation of a bond
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// between the fragment and the molecule
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//
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void AddFragToMol(RWMol *mol,RWMol *frag,Bond::BondType bondOrder,
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Bond::BondDir bondDir,bool closeRings,bool doingQuery ){
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PRECONDITION(mol,"no molecule");
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PRECONDITION(frag,"no fragment");
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PRECONDITION(mol->getActiveAtom(),"no active atom");
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Atom *lastAt = mol->getActiveAtom();
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int nOrigAtoms = mol->getNumAtoms();
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int nOrigBonds = mol->getNumBonds();
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//
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// close any rings we can in the fragment
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//
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if(closeRings){
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CloseMolRings(frag,true);
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}
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//
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// Add the fragment's atoms and bonds to the molecule:
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//
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mol->insertMol(*frag);
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//
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// update ring-closure order information on the added atoms:
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//
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for(RWMol::AtomIterator atomIt=frag->beginAtoms();
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atomIt!=frag->endAtoms();atomIt++){
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if((*atomIt)->hasProp("_RingClosures")){
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INT_VECT tmpVect;
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(*atomIt)->getProp("_RingClosures",tmpVect);
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BOOST_FOREACH(int &v, tmpVect){
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// if the ring closure is not already a bond, don't touch it:
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if(v>=0) v += nOrigBonds;
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}
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Atom *newAtom = mol->getAtomWithIdx(nOrigAtoms+(*atomIt)->getIdx());
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newAtom->setProp("_RingClosures",tmpVect);
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}
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}
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//
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// ses up the bond between the mol and the branch
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//
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if( bondOrder != Bond::IONIC ){
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// FIX: this is not so much with the elegance...
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Atom *firstAt = mol->getAtomWithIdx(nOrigAtoms);
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Bond::BondType bo;
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int atomIdx1,atomIdx2;
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atomIdx1 = firstAt->getIdx();
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atomIdx2 = lastAt->getIdx();
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if(frag->hasBondBookmark(ci_LEADING_BOND)){
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//std::cout << "found it" << std::endl;
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const ROMol::BOND_PTR_LIST &leadingBonds=frag->getAllBondsWithBookmark(ci_LEADING_BOND);
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BOOST_FOREACH(Bond *leadingBond,leadingBonds){
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// we've already got a bond, so just set its local info
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// and then add it to the molecule intact (no sense doing
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// any extra work).
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leadingBond->setOwningMol(mol);
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leadingBond->setEndAtomIdx(leadingBond->getBeginAtomIdx()+nOrigAtoms);
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leadingBond->setBeginAtomIdx(atomIdx2);
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mol->addBond(leadingBond,true);
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}
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mol->clearBondBookmark(ci_LEADING_BOND);
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} else {
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if(!doingQuery){
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if(bondOrder == Bond::UNSPECIFIED){
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// no bond order provided, figure it out ourselves
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if(lastAt->getIsAromatic() && firstAt->getIsAromatic() ){
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bo = Bond::AROMATIC;
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}
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else{
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bo = Bond::SINGLE;
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}
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}
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else{
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bo = bondOrder;
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}
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if(bo==Bond::DATIVEL){
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int tmp=atomIdx2;
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atomIdx2 = atomIdx1;
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atomIdx1 = tmp;
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bo = Bond::DATIVE;
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} else if(bo == Bond::DATIVER){
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bo = Bond::DATIVE;
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}
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int idx = mol->addBond(atomIdx2,atomIdx1,bo)-1;
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mol->getBondWithIdx(idx)->setBondDir(bondDir);
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} else {
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// semantics are different in SMARTS, unspecified bonds can be single or aromatic:
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if(bondOrder == Bond::UNSPECIFIED){
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QueryBond *newB=new QueryBond(Bond::SINGLE);
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newB->expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),
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Queries::COMPOSITE_OR,
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true);
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newB->setOwningMol(mol);
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newB->setBeginAtomIdx(atomIdx1);
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newB->setEndAtomIdx(atomIdx2);
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mol->addBond(newB);
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delete newB;
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}
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else{
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bo=bondOrder;
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if(bo==Bond::DATIVEL){
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int tmp=atomIdx2;
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atomIdx2 = atomIdx1;
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atomIdx1 = tmp;
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bo = Bond::DATIVE;
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} else if(bo == Bond::DATIVER){
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bo = Bond::DATIVE;
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}
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int idx = mol->addBond(atomIdx2,atomIdx1,bo)-1;
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mol->getBondWithIdx(idx)->setBondDir(bondDir);
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}
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}
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}
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}
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//
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// okay, the next thing we have to worry about is the possibility
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// that there might be ring opening/closing in the fragment we just
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// dealt with e.g. for things like C1C(C1) and C1C.C1
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// We deal with this by copying in the bookmarks and partial bonds
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// that exist in the fragment
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//
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RWMol::ATOM_BOOKMARK_MAP::iterator atIt;
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for(atIt=frag->getAtomBookmarks()->begin();
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atIt!=frag->getAtomBookmarks()->end();
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++atIt){
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// don't bother even considering bookmarks outside
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// the range used for loops
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if(atIt->first < 100 && atIt->first > 0){
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RWMol::ATOM_PTR_LIST::iterator otherAt;
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for(otherAt=atIt->second.begin();
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otherAt!=atIt->second.end();otherAt++){
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Atom *at2 = *otherAt;
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int newIdx = at2->getIdx()+nOrigAtoms;
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mol->setAtomBookmark(mol->getAtomWithIdx(newIdx),atIt->first);
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//frag->clearAtomBookmark(atIt->first,at2);
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while( frag->hasBondBookmark(atIt->first) ){
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Bond *b = frag->getBondWithBookmark(atIt->first);
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int atomIdx1 = b->getBeginAtomIdx()+nOrigAtoms;
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b->setOwningMol(mol);
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b->setBeginAtomIdx(atomIdx1);
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mol->setBondBookmark(b,atIt->first);
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frag->clearBondBookmark(atIt->first,b);
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}
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}
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}
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}
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frag->clearAllAtomBookmarks();
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frag->clearAllBondBookmarks();
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};
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void _invChiralRingAtomWithHs(Atom *atom) {
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PRECONDITION(atom,"bad atom");
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// we will assume that this function is called on a ring atom with a
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// ring closure bond
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if (atom->getNumExplicitHs() == 1) {
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atom->invertChirality();
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}
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}
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typedef std::pair<int,int> INT_PAIR;
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bool operator<(const INT_PAIR &p1,const INT_PAIR &p2){
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return p1.first<p2.first;
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}
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void AdjustAtomChiralityFlags(RWMol *mol){
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PRECONDITION(mol,"no molecule");
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for(RWMol::AtomIterator atomIt=mol->beginAtoms();
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atomIt != mol->endAtoms();
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++atomIt){
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Atom::ChiralType chiralType=(*atomIt)->getChiralTag();
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if(chiralType==Atom::CHI_TETRAHEDRAL_CW ||
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chiralType==Atom::CHI_TETRAHEDRAL_CCW ){
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//
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// The atom is marked as chiral, set the SMILES-order of the
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// atom's bonds. This is easy for non-ring-closure bonds,
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// because the SMILES order is determined solely by the atom
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// indices. Things are trickier for ring-closure bonds, which we
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// need to insert into the list in a particular order
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//
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INT_VECT ringClosures;
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if((*atomIt)->hasProp("_RingClosures"))
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(*atomIt)->getProp("_RingClosures",ringClosures);
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#if 0
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std::cout << "CLOSURES: ";
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std::copy(ringClosures.begin(),ringClosures.end(),
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std::ostream_iterator<int>(std::cout," "));
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std::cout << std::endl;
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#endif
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std::list<INT_PAIR> neighbors;
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// push this atom onto the list of neighbors (we'll use this
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// to find our place later):
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neighbors.push_back(std::make_pair((*atomIt)->getIdx(),-1));
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std::list<int> bondOrder;
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RWMol::ADJ_ITER nbrIdx,endNbrs;
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boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(*atomIt);
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while(nbrIdx != endNbrs){
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Bond *nbrBond=mol->getBondBetweenAtoms((*atomIt)->getIdx(),*nbrIdx);
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if(std::find(ringClosures.begin(),
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ringClosures.end(),
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static_cast<int>(nbrBond->getIdx()))== ringClosures.end()){
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neighbors.push_back(std::make_pair(*nbrIdx,nbrBond->getIdx()));
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}
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++nbrIdx;
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}
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// sort the list of non-ring-closure bonds:
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neighbors.sort();
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// find the location of this atom. it pretty much has to be
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// first in the list, e.g for smiles like [C@](F)(Cl)(Br)I, or
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// second (everything else).
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std::list<INT_PAIR>::iterator selfPos=neighbors.begin();
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if(selfPos->first != static_cast<int>((*atomIt)->getIdx())){
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++selfPos;
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}
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CHECK_INVARIANT(selfPos->first==static_cast<int>((*atomIt)->getIdx()),"weird atom ordering");
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// copy over the bond ids:
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INT_LIST bondOrdering;
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for(std::list<INT_PAIR>::iterator neighborIt=neighbors.begin();
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neighborIt != neighbors.end(); ++neighborIt){
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if(neighborIt != selfPos){
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bondOrdering.push_back(neighborIt->second);
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} else {
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// we are not going to add the atom itself, but we will push on
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// ring closure bonds at this point (if required):
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BOOST_FOREACH(int closure,ringClosures){
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bondOrdering.push_back(closure);
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}
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}
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}
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// ok, we now have the SMILES ordering of the bonds, figure out the
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// permutation order.
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//
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// This whole thing is necessary because the ring-closure bonds
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// in the SMILES come before the bonds to the other neighbors, but
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// they come after the neighbors in the molecule we build.
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// A crude example:
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// in F[C@](Cl)(Br)I the C-Cl bond is index 1 in both SMILES
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// and as built
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// in F[C@]1(Br)I.Cl1 the C-Cl bond is index 1 in the SMILES
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// and index 3 as built.
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//
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int nSwaps=(*atomIt)->getPerturbationOrder(bondOrdering);
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// FIX: explain this one:
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if((*atomIt)->getDegree()==3 && (*atomIt)->hasProp("_SmilesStart")) ++nSwaps;
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if(nSwaps%2){
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(*atomIt)->invertChirality();
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}
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}
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}
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}
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Bond::BondType GetUnspecifiedBondType(const RWMol *mol,const Atom *atom1,const Atom *atom2){
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PRECONDITION(mol,"no molecule");
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PRECONDITION(atom1,"no atom1");
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PRECONDITION(atom2,"no atom2");
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Bond::BondType res;
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if(atom1->getIsAromatic() && atom2->getIsAromatic()) {
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res = Bond::AROMATIC;
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} else {
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res = Bond::SINGLE;
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}
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return res;
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}
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void CloseMolRings(RWMol *mol,bool toleratePartials){
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// Here's what we want to do here:
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// loop through the molecule's atom bookmarks
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// for each bookmark:
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// connect pairs of atoms sharing that bookmark
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// left to right (in the order in which they were
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// inserted into the molecule).
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// whilst doing this, we have to be cognizant of the fact that
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// there may well be partial bonds in the molecule which need
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// to be tied in as well. WOO HOO! IT'S A BIG MESS!
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PRECONDITION(mol,"no molecule");
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RWMol::ATOM_BOOKMARK_MAP::iterator bookmarkIt;
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bookmarkIt=mol->getAtomBookmarks()->begin();
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while(bookmarkIt!=mol->getAtomBookmarks()->end()){
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// don't bother even considering bookmarks outside
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// the range used for loops
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if(bookmarkIt->first < 100 && bookmarkIt->first >= 0){
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RWMol::ATOM_PTR_LIST::iterator atomIt,atomsEnd;
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RWMol::ATOM_PTR_LIST bookmarkedAtomsToRemove;
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atomIt = bookmarkIt->second.begin();
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atomsEnd = bookmarkIt->second.end();
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while(atomIt != atomsEnd){
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Atom *atom1 = *atomIt;
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++atomIt;
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if(!toleratePartials && atomIt==atomsEnd){
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ReportParseError("unclosed ring");
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} else if(atomIt!=atomsEnd && *atomIt==atom1){
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// make sure we don't try to connect an atom to itself,
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// this was bug 3145697:
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++atomIt;
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} else if(atomIt!=atomsEnd) {
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// we actually found an atom, so connect it to the first
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Atom *atom2 = *atomIt;
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++atomIt;
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int bondIdx=-1;
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// We're guaranteed two partial bonds, one for each time
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// the ring index was used. We give the first specification
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// priority.
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CHECK_INVARIANT(mol->hasBondBookmark(bookmarkIt->first),"Missing bond bookmark");
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// now use the info from the partial bond:
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// The partial bond itself will have a proper order and directionality
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// (with a minor caveat documented below) and will have its beginning
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// atom set already:
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RWMol::BOND_PTR_LIST bonds=mol->getAllBondsWithBookmark(bookmarkIt->first);
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RWMol::BOND_PTR_LIST::iterator bondIt=bonds.begin();
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CHECK_INVARIANT(bonds.size()>=2,"Missing bond");
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// get pointers to the two bonds:
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Bond *bond1=*bondIt;
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++bondIt;
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Bond *bond2=*bondIt;
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// remove those bonds from the bookmarks:
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mol->clearBondBookmark(bookmarkIt->first,bond1);
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mol->clearBondBookmark(bookmarkIt->first,bond2);
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// Make sure the bonds have the correct starting atoms:
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CHECK_INVARIANT(bond1->getBeginAtomIdx()==atom1->getIdx(),"bad begin atom");
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CHECK_INVARIANT(bond2->getBeginAtomIdx()==atom2->getIdx(),"bad begin atom");
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Bond *matchedBond;
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// figure out which (if either) bond has a specified type, we'll
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// keep that one. We also need to update the end atom index to match
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// FIX: daylight barfs when you give it multiple specs for the closure
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// bond, we'll just take the first one and ignore others
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// NOTE: we used to do this the other way (take the last specification),
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// but that turned out to be troublesome in odd cases like C1CC11CC1.
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if(!bond1->hasProp("_unspecifiedOrder")){
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matchedBond = bond1;
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matchedBond->setEndAtomIdx(atom2->getIdx());
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delete bond2;
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} else {
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matchedBond = bond2;
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matchedBond->setEndAtomIdx(atom1->getIdx());
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delete bond1;
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}
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if(matchedBond->getBondType()==Bond::UNSPECIFIED){
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Bond::BondType bondT=GetUnspecifiedBondType(mol,atom1,atom2);
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matchedBond->setBondType(bondT);
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}
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matchedBond->setOwningMol(mol);
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if(matchedBond->getBondType()==Bond::AROMATIC){
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matchedBond->setIsAromatic(true);
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}
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#if 0
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//
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// In cases like this: Cl\C=C1.F/1, we need to
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// reverse the directionality on the added bond
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// (because the bond is added from C -> F, but the
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// directionality is for F->C. We recognize these
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// cases because the matched bond direction isn't
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// the same as the added bond direction (i.e. atom1
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// isn't the begin atom for the matched bond).
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//
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// This was Issue 175
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if(atom1->getIdx()!=matchedBond->getBeginAtomIdx()){
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switch(matchedBond->getBondDir()){
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case Bond::ENDUPRIGHT:
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matchedBond->setBondDir(Bond::ENDDOWNRIGHT);
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break;
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case Bond::ENDDOWNRIGHT:
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matchedBond->setBondDir(Bond::ENDUPRIGHT);
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break;
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default:
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break;
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}
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}
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#endif
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// add the bond:
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bondIdx=mol->addBond(matchedBond,true);
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// we found a bond, so update the atom's _RingClosures
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// property:
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if(bondIdx>-1){
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CHECK_INVARIANT(atom1->hasProp("_RingClosures") &&
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atom2->hasProp("_RingClosures"),
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"somehow atom doesn't have _RingClosures property.");
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INT_VECT closures;
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atom1->getProp("_RingClosures",closures);
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INT_VECT::iterator closurePos= std::find(closures.begin(),
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closures.end(),
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-(bookmarkIt->first+1));
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CHECK_INVARIANT(closurePos!=closures.end(),
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"could not find bookmark in atom _RingClosures");
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*closurePos = bondIdx-1;
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atom1->setProp("_RingClosures",closures);
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atom2->getProp("_RingClosures",closures);
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closurePos= std::find(closures.begin(),
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closures.end(),
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-(bookmarkIt->first+1));
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CHECK_INVARIANT(closurePos!=closures.end(),
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"could not find bookmark in atom _RingClosures");
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*closurePos = bondIdx-1;
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atom2->setProp("_RingClosures",closures);
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}
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bookmarkedAtomsToRemove.push_back(atom1);
|
|
bookmarkedAtomsToRemove.push_back(atom2);
|
|
}
|
|
}
|
|
//
|
|
// increment the bookmark before calling erase. Otherwise we
|
|
// get a seg fault under MSVC++
|
|
//
|
|
int mark=bookmarkIt->first;
|
|
bookmarkIt++;
|
|
RWMol::ATOM_PTR_LIST::const_iterator aplci;
|
|
BOOST_FOREACH(Atom *atom,bookmarkedAtomsToRemove){
|
|
mol->clearAtomBookmark(mark,atom);
|
|
}
|
|
} else {
|
|
++bookmarkIt;
|
|
}
|
|
}
|
|
};
|
|
|
|
} // end of namespace SmilesParseOps
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