mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
551 lines
22 KiB
C++
Executable File
551 lines
22 KiB
C++
Executable File
// $Id$
|
|
//
|
|
// Copyright (C) 2003-2006 Rational Discovery LLC
|
|
//
|
|
// @@ All Rights Reserved @@
|
|
//
|
|
#include "RDKitBase.h"
|
|
#include <list>
|
|
#include "QueryAtom.h"
|
|
#include "QueryOps.h"
|
|
#include <Geometry/Transform3D.h>
|
|
#include <Geometry/point.h>
|
|
|
|
namespace RDKit{
|
|
|
|
// Local utility functionality:
|
|
namespace {
|
|
Atom *getAtomNeighborNot(ROMol *mol,const Atom *atom,const Atom *other){
|
|
PRECONDITION(mol,"bad molecule");
|
|
PRECONDITION(atom,"bad atom");
|
|
PRECONDITION(atom->getDegree()>1,"bad degree");
|
|
PRECONDITION(other,"bad atom");
|
|
Atom *res=0;
|
|
|
|
ROMol::ADJ_ITER nbrIdx,endNbrs;
|
|
boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(atom);
|
|
while(nbrIdx!=endNbrs){
|
|
if(*nbrIdx != other->getIdx()){
|
|
res = mol->getAtomWithIdx(*nbrIdx);
|
|
break;
|
|
}
|
|
nbrIdx++;
|
|
}
|
|
|
|
POSTCONDITION(res,"no neighbor found");
|
|
return res;
|
|
}
|
|
|
|
void setHydrogenCoords(ROMol *mol,unsigned int hydIdx,unsigned int heavyIdx){
|
|
// we will loop over all the coordinates
|
|
PRECONDITION(mol,"bad molecule");
|
|
PRECONDITION(heavyIdx!=hydIdx,"degenerate atoms");
|
|
Atom *hydAtom = mol->getAtomWithIdx(hydIdx);
|
|
PRECONDITION(mol->getAtomDegree(hydAtom)==1,"bad atom degree");
|
|
const Bond *bond=mol->getBondBetweenAtoms(heavyIdx,hydIdx);
|
|
PRECONDITION(bond,"no bond between atoms");
|
|
|
|
const Atom *heavyAtom = mol->getAtomWithIdx(heavyIdx);
|
|
double bondLength = PeriodicTable::getTable()->getRb0(1) +
|
|
PeriodicTable::getTable()->getRb0(heavyAtom->getAtomicNum());
|
|
|
|
RDGeom::Point3D dirVect(0,0,0);
|
|
|
|
RDGeom::Point3D perpVect,rotnAxis,nbrPerp;
|
|
RDGeom::Point3D nbr1Vect,nbr2Vect,nbr3Vect;
|
|
RDGeom::Transform3D tform;
|
|
RDGeom::Point3D heavyPos, hydPos;
|
|
|
|
const Atom *nbr1=0,*nbr2=0,*nbr3=0;
|
|
const Bond *nbrBond;
|
|
ROMol::ADJ_ITER nbrIdx,endNbrs;
|
|
|
|
switch(heavyAtom->getDegree()){
|
|
case 1:
|
|
// --------------------------------------------------------------------------
|
|
// No other atoms present:
|
|
// --------------------------------------------------------------------------
|
|
dirVect.z = 1;
|
|
// loop over the conformations and set the coordinates
|
|
for (ROMol::ConformerIterator cfi = mol->beginConformers();
|
|
cfi != mol->endConformers(); cfi++) {
|
|
heavyPos = (*cfi)->getAtomPos(heavyIdx);
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
}
|
|
break;
|
|
|
|
case 2:
|
|
// --------------------------------------------------------------------------
|
|
// One other neighbor:
|
|
// --------------------------------------------------------------------------
|
|
nbr1=getAtomNeighborNot(mol,heavyAtom,hydAtom);
|
|
for (ROMol::ConformerIterator cfi = mol->beginConformers();
|
|
cfi != mol->endConformers(); cfi++) {
|
|
heavyPos = (*cfi)->getAtomPos(heavyIdx);
|
|
RDGeom::Point3D nbr1Pos = (*cfi)->getAtomPos(nbr1->getIdx());
|
|
// get a normalized vector pointing away from the neighbor:
|
|
nbr1Vect = heavyPos.directionVector(nbr1Pos);
|
|
nbr1Vect *= -1;
|
|
|
|
// ok, nbr1Vect points away from the other atom, figure out where
|
|
// this H goes:
|
|
switch(heavyAtom->getHybridization()){
|
|
case Atom::SP3:
|
|
// get a perpendicular to nbr1Vect:
|
|
perpVect=nbr1Vect.getPerpendicular();
|
|
// and move off it:
|
|
tform.SetRotation((180-109.471)*M_PI/180.,perpVect);
|
|
dirVect = tform*nbr1Vect;
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
break;
|
|
case Atom::SP2:
|
|
// default position is to just take an arbitrary perpendicular:
|
|
perpVect = nbr1Vect.getPerpendicular();
|
|
|
|
if(nbr1->getDegree()>1){
|
|
// can we use the neighboring atom to establish a perpendicular?
|
|
nbrBond=mol->getBondBetweenAtoms(heavyIdx,nbr1->getIdx());
|
|
if(nbrBond->getIsAromatic() || nbrBond->getBondType()==Bond::DOUBLE){
|
|
nbr2=getAtomNeighborNot(mol,nbr1,heavyAtom);
|
|
nbr2Vect=nbr1Pos.directionVector((*cfi)->getAtomPos(nbr2->getIdx()));
|
|
perpVect = nbr2Vect.crossProduct(nbr1Vect);
|
|
}
|
|
}
|
|
perpVect.normalize();
|
|
// rotate the nbr1Vect 60 degrees about perpVect and we're done:
|
|
tform.SetRotation(60.*M_PI/180.,perpVect);
|
|
dirVect = tform*nbr1Vect;
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
break;
|
|
case Atom::SP:
|
|
// just lay the H along the vector:
|
|
dirVect=nbr1Vect;
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
break;
|
|
default:
|
|
// FIX: handle other hybridizations
|
|
// for now, just lay the H along the vector:
|
|
dirVect=nbr1Vect;
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
}
|
|
}
|
|
break;
|
|
case 3:
|
|
// --------------------------------------------------------------------------
|
|
// Two other neighbors:
|
|
// --------------------------------------------------------------------------
|
|
boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(heavyAtom);
|
|
while(nbrIdx!=endNbrs){
|
|
if(*nbrIdx != hydIdx){
|
|
if(!nbr1) nbr1 = mol->getAtomWithIdx(*nbrIdx);
|
|
else nbr2 = mol->getAtomWithIdx(*nbrIdx);
|
|
}
|
|
nbrIdx++;
|
|
}
|
|
TEST_ASSERT(nbr1);
|
|
TEST_ASSERT(nbr2);
|
|
for (ROMol::ConformerIterator cfi = mol->beginConformers();
|
|
cfi != mol->endConformers(); cfi++) {
|
|
// start along the average of the two vectors:
|
|
heavyPos = (*cfi)->getAtomPos(heavyIdx);
|
|
nbr1Vect = (*cfi)->getAtomPos(nbr1->getIdx()).directionVector(heavyPos);
|
|
nbr2Vect = (*cfi)->getAtomPos(nbr2->getIdx()).directionVector(heavyPos);
|
|
dirVect = nbr1Vect+nbr2Vect;
|
|
dirVect.normalize();
|
|
|
|
switch(heavyAtom->getHybridization()){
|
|
case Atom::SP3:
|
|
// get the perpendicular to the neighbors:
|
|
nbrPerp = nbr1Vect.crossProduct(nbr2Vect);
|
|
// and the perpendicular to that:
|
|
rotnAxis = nbrPerp.crossProduct(dirVect);
|
|
// and then rotate about that:
|
|
rotnAxis.normalize();
|
|
tform.SetRotation((109.471/2)*M_PI/180.,rotnAxis);
|
|
dirVect = tform*dirVect;
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
break;
|
|
case Atom::SP2:
|
|
// don't need to do anything here, the H atom goes right on the
|
|
// direction vector
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
break;
|
|
default:
|
|
// FIX: handle other hybridizations
|
|
// for now, just lay the H along the neighbor vector;
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
break;
|
|
}
|
|
}
|
|
break;
|
|
case 4:
|
|
// --------------------------------------------------------------------------
|
|
// Three other neighbors:
|
|
// --------------------------------------------------------------------------
|
|
boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(heavyAtom);
|
|
while(nbrIdx!=endNbrs){
|
|
if(*nbrIdx != hydIdx){
|
|
if(!nbr1) nbr1 = mol->getAtomWithIdx(*nbrIdx);
|
|
else if(!nbr2) nbr2 = mol->getAtomWithIdx(*nbrIdx);
|
|
else nbr3 = mol->getAtomWithIdx(*nbrIdx);
|
|
}
|
|
nbrIdx++;
|
|
}
|
|
TEST_ASSERT(nbr1);
|
|
TEST_ASSERT(nbr2);
|
|
TEST_ASSERT(nbr3);
|
|
for (ROMol::ConformerIterator cfi = mol->beginConformers();
|
|
cfi != mol->endConformers(); cfi++) {
|
|
// use the average of the three vectors:
|
|
heavyPos = (*cfi)->getAtomPos(heavyIdx);
|
|
nbr1Vect = (*cfi)->getAtomPos(nbr1->getIdx()).directionVector(heavyPos);
|
|
nbr2Vect = (*cfi)->getAtomPos(nbr2->getIdx()).directionVector(heavyPos);
|
|
nbr3Vect = (*cfi)->getAtomPos(nbr3->getIdx()).directionVector(heavyPos);
|
|
dirVect = nbr1Vect+nbr2Vect+nbr3Vect;
|
|
dirVect.normalize();
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
}
|
|
break;
|
|
default:
|
|
// --------------------------------------------------------------------------
|
|
// FIX: figure out what to do here
|
|
// --------------------------------------------------------------------------
|
|
hydPos = heavyPos + dirVect*bondLength;
|
|
for (ROMol::ConformerIterator cfi = mol->beginConformers();
|
|
cfi != mol->endConformers(); cfi++) {
|
|
(*cfi)->setAtomPos(hydIdx, hydPos);
|
|
}
|
|
break;
|
|
}
|
|
}
|
|
} // end of unnamed namespace
|
|
|
|
|
|
namespace MolOps {
|
|
// NOTE that we do not need to check for chiral atoms when adding Hs
|
|
// because the bond order goes from hydrogen implicitly first to
|
|
// hydrogen explicitly last. This is a cyclic permutation, so it
|
|
// doesn't affect the chirality. (Of course there can only be one H
|
|
// on the atom... otherwise it wouldn't be chiral!)
|
|
ROMol *addHs(const ROMol &mol,bool explicitOnly,bool addCoords){
|
|
RWMol *res = new RWMol(mol);
|
|
|
|
// when we hit each atom, clear its computed properties
|
|
// NOTE: it is essential that we not clear the ring info in the
|
|
// molecule's computed properties. We don't want to have to
|
|
// regenerate that. This caused Issue210 and Issue212:
|
|
res->clearComputedProps(false);
|
|
|
|
// precompute the number of hydrogens we are going to add so that we can
|
|
// pre-allocate the necessary space on the conformations of the molecule
|
|
// for their coordinates
|
|
unsigned int numAddHyds = 0;
|
|
for(ROMol::ConstAtomIterator at=mol.beginAtoms();at!=mol.endAtoms();++at){
|
|
numAddHyds += (*at)->getNumExplicitHs();
|
|
if (!explicitOnly) {
|
|
numAddHyds += (*at)->getNumImplicitHs();
|
|
}
|
|
}
|
|
unsigned int nSize = mol.getNumAtoms() + numAddHyds;
|
|
// now if we want to add coordinates to the hydrogens;
|
|
// loop over the conformations of the molecule and allocate new space
|
|
// for their locations
|
|
for (ROMol::ConformerIterator cfi = res->beginConformers();
|
|
cfi != res->endConformers(); ++cfi) {
|
|
(*cfi)->reserve(nSize);
|
|
}
|
|
|
|
for(ROMol::ConstAtomIterator at=mol.beginAtoms();at!=mol.endAtoms();++at){
|
|
unsigned int oldIdx,newIdx;
|
|
oldIdx = (*at)->getIdx();
|
|
Atom *newAt = res->getAtomWithIdx(oldIdx);
|
|
newAt->clearComputedProps();
|
|
// always convert explicit Hs
|
|
for(unsigned int i=0;i<(*at)->getNumExplicitHs();i++){
|
|
newIdx=res->addAtom(new Atom(1),false,true);
|
|
res->addBond(oldIdx,newIdx,Bond::SINGLE);
|
|
res->getAtomWithIdx(newIdx)->updatePropertyCache();
|
|
if(addCoords) setHydrogenCoords(res,newIdx,newAt->getIdx());
|
|
}
|
|
// clear the local property
|
|
newAt->setNumExplicitHs(0);
|
|
|
|
if(!explicitOnly){
|
|
// take care of implicits
|
|
for(unsigned int i=0;i<(*at)->getNumImplicitHs();i++){
|
|
newIdx=res->addAtom(new Atom(1),false,true);
|
|
res->addBond(oldIdx,newIdx,Bond::SINGLE);
|
|
// set the isImplicit label so that we can strip these back
|
|
// off later if need be.
|
|
res->getAtomWithIdx(newIdx)->setProp("isImplicit",1, true);
|
|
res->getAtomWithIdx(newIdx)->updatePropertyCache();
|
|
if(addCoords) setHydrogenCoords(res,newIdx,newAt->getIdx());
|
|
}
|
|
// be very clear about implicits not being allowed in this representation
|
|
newAt->setProp("origNoImplicit",newAt->getNoImplicit(), true);
|
|
newAt->setNoImplicit(true);
|
|
}
|
|
// update the atom's derived properties (valence count, etc.)
|
|
newAt->updatePropertyCache();
|
|
}
|
|
return static_cast<ROMol *>(res);
|
|
};
|
|
|
|
|
|
//
|
|
// This routine removes hydrogens (and bonds to them) from the molecular graph.
|
|
// Other Atom and bond indices may be affected by the removal.
|
|
//
|
|
// NOTES:
|
|
// - Hydrogens which aren't connected to a heavy atom will not be
|
|
// removed. This prevents molecules like "[H][H]" from having
|
|
// all atoms removed.
|
|
// - Labelled hydrogen (e.g. atoms with atomic number=1, but mass > 1),
|
|
// will not be removed.
|
|
//
|
|
ROMol *removeHs(const ROMol &mol,bool implicitOnly,bool updateExplicitCount,bool sanitize){
|
|
Atom *atom;
|
|
unsigned int currIdx=0,origIdx=0;
|
|
std::map<unsigned int,unsigned int> idxMap;
|
|
RWMol *res = new RWMol(mol);
|
|
while(currIdx < res->getNumAtoms()){
|
|
atom = res->getAtomWithIdx(currIdx);
|
|
idxMap[origIdx]=currIdx;
|
|
origIdx++;
|
|
if(atom->getAtomicNum()==1){
|
|
bool removeIt=false;
|
|
|
|
if(atom->hasProp("isImplicit")){
|
|
removeIt=true;
|
|
} else if(!implicitOnly && atom->getMass()<1.1){
|
|
ROMol::ADJ_ITER begin,end;
|
|
boost::tie(begin,end) = res->getAtomNeighbors(atom);
|
|
while(begin!=end){
|
|
if(res->getAtomWithIdx(*begin)->getAtomicNum() != 1){
|
|
removeIt=true;
|
|
break;
|
|
}
|
|
begin++;
|
|
}
|
|
}
|
|
|
|
if(removeIt){
|
|
ROMol::OEDGE_ITER beg,end;
|
|
boost::tie(beg,end) = res->getAtomBonds(atom);
|
|
ROMol::GRAPH_MOL_BOND_PMAP::type pMap = res->getBondPMap();
|
|
// note the assumption that the H only has one neighbor... I
|
|
// feel no need to handle the case of hypervalent hydrogen!
|
|
// :-)
|
|
Bond const *bond = pMap[*beg];
|
|
Atom *heavyAtom =bond->getOtherAtom(atom);
|
|
|
|
// we'll update the atom's explicit H count if we were told to
|
|
// *or* if the atom is chiral, in which case the H is needed
|
|
// in order to complete the coordination
|
|
// *or* if the atom has the noImplicit flag set:
|
|
if( updateExplicitCount || heavyAtom->getNoImplicit() ||
|
|
heavyAtom->getChiralTag()!=Atom::CHI_UNSPECIFIED ){
|
|
heavyAtom->setNumExplicitHs(heavyAtom->getNumExplicitHs()+1);
|
|
} else {
|
|
// this is a special case related to Issue 228 and the
|
|
// "disappearing Hydrogen" problem discussed in MolOps::adjustHs
|
|
//
|
|
// If we remove a hydrogen from an aromatic N, we need to
|
|
// be *sure* to increment the explicit count, even if the
|
|
// H itself isn't marked as explicit
|
|
if(heavyAtom->getAtomicNum()==7 && heavyAtom->getIsAromatic()
|
|
&& heavyAtom->getFormalCharge()==0){
|
|
heavyAtom->setNumExplicitHs(heavyAtom->getNumExplicitHs()+1);
|
|
}
|
|
}
|
|
|
|
// One other consequence of removing the H from the graph is
|
|
// that we may change the ordering of the bonds about a
|
|
// chiral center. This may change the chiral label at that
|
|
// atom. We deal with that by explicitly checking here:
|
|
if(heavyAtom->getChiralTag()!=Atom::CHI_UNSPECIFIED){
|
|
INT_LIST neighborIndices;
|
|
unsigned int atomsBeforeHeavy=0;
|
|
|
|
boost::tie(beg,end) = res->getAtomBonds(heavyAtom);
|
|
while(beg!=end){
|
|
if(pMap[*beg]->getIdx()!=bond->getIdx()){
|
|
neighborIndices.push_back(pMap[*beg]->getIdx());
|
|
if(pMap[*beg]->getBeginAtomIdx()!=heavyAtom->getIdx() &&
|
|
pMap[*beg]->getOtherAtom(heavyAtom)->getIdx()<heavyAtom->getIdx() ){
|
|
++atomsBeforeHeavy;
|
|
}
|
|
}
|
|
++beg;
|
|
}
|
|
if(atomsBeforeHeavy){
|
|
neighborIndices.insert(++neighborIndices.begin(),bond->getIdx());
|
|
} else {
|
|
neighborIndices.push_front(bond->getIdx());
|
|
}
|
|
|
|
int nSwaps = heavyAtom->getPerturbationOrder(neighborIndices);
|
|
//std::cerr << " swaps: " << nSwaps << " " << atomsBeforeHeavy << std::endl;
|
|
if(nSwaps%2){
|
|
heavyAtom->invertChirality();
|
|
}
|
|
}
|
|
res->removeAtom(atom);
|
|
} else {
|
|
// only increment the atom idx if we don't remove the atom
|
|
currIdx++;
|
|
}
|
|
} else {
|
|
// only increment the atom idx if we don't remove the atom
|
|
currIdx++;
|
|
if(atom->hasProp("origNoImplicit")){
|
|
// we'll get in here if we haven't already processed the atom's implicit
|
|
// hydrogens. (this is protection for the case that removeHs() is called
|
|
// multiple times on a single molecule without intervening addHs() calls)
|
|
bool tmpBool;
|
|
atom->getProp("origNoImplicit",tmpBool);
|
|
atom->setNoImplicit(tmpBool);
|
|
atom->clearProp("origNoImplicit");
|
|
}
|
|
}
|
|
}
|
|
//
|
|
// If we didn't only remove implicit Hs, which are guaranteed to
|
|
// be the highest numbered atoms, we may have altered atom indices.
|
|
// This can screw up derived properties (such as ring members), so
|
|
// do some checks:
|
|
//
|
|
if(!implicitOnly){
|
|
if(sanitize){
|
|
sanitizeMol(*res);
|
|
}
|
|
if(mol.hasProp("_StereochemDone")){
|
|
// stereochem had been perceived in the original molecule,
|
|
// loop over the bonds and fix their stereoAtoms fields:
|
|
for(ROMol::BondIterator bondIt=res->beginBonds();
|
|
bondIt!=res->endBonds();
|
|
++bondIt){
|
|
Bond *bond=*bondIt;
|
|
if( bond->getBondType()==Bond::DOUBLE &&
|
|
bond->getStereo()!=Bond::STEREONONE){
|
|
for(INT_VECT_I it=bond->getStereoAtoms().begin();it!=bond->getStereoAtoms().end();++it){
|
|
*it = idxMap[*it];
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
return static_cast<ROMol *>(res);
|
|
};
|
|
|
|
//
|
|
// This routine removes explicit hydrogens (and bonds to them) from
|
|
// the molecular graph and adds them as queries to the heavy atoms
|
|
// to which they are bound. If the heavy atoms (or atom queries)
|
|
// already have hydrogen-count queries, they will be updated.
|
|
//
|
|
// NOTE:
|
|
// - Hydrogens which aren't connected to a heavy atom will not be
|
|
// removed. This prevents molecules like "[H][H]" from having
|
|
// all atoms removed.
|
|
//
|
|
ROMol *mergeQueryHs(const ROMol &mol){
|
|
unsigned int currIdx=0;
|
|
RWMol *res = new RWMol(mol);
|
|
while(currIdx < res->getNumAtoms()){
|
|
Atom *atom = res->getAtomWithIdx(currIdx);
|
|
if(atom->getAtomicNum()==1){
|
|
bool removeIt=false;
|
|
ROMol::ADJ_ITER begin,end;
|
|
boost::tie(begin,end) = res->getAtomNeighbors(atom);
|
|
while(begin!=end){
|
|
if(res->getAtomWithIdx(*begin)->getAtomicNum() > 1){
|
|
removeIt=true;
|
|
break;
|
|
}
|
|
begin++;
|
|
}
|
|
if(removeIt){
|
|
ROMol::ADJ_ITER begin,end;
|
|
boost::tie(begin,end) = res->getAtomNeighbors(atom);
|
|
Atom *nbr = res->getAtomWithIdx(*begin);
|
|
//
|
|
// We've found the neighbor.
|
|
// 1) If the neighbor has no H query already:
|
|
// - add a generic H query
|
|
// else:
|
|
// - do nothing
|
|
// 2) Remove the atom from the molecular graph
|
|
//
|
|
// Examples:
|
|
// C[H] -> [C;!H0]
|
|
// [C;H1][H] -> [C;H1]
|
|
// [C;H2][H] -> [C;H2]
|
|
//
|
|
// FIX: this is going to behave oddly in the case of a contradictory
|
|
// SMARTS like: [C;H0][H], where it will give the equivalent of:
|
|
// [C;H0] I think this is actually correct, but I can be persuaded
|
|
// otherwise.
|
|
//
|
|
// First we'll search for an H query:
|
|
bool hasHQuery=false;
|
|
if(nbr->hasQuery()){
|
|
std::list<QueryAtom::QUERYATOM_QUERY::CHILD_TYPE> childStack;
|
|
QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI child1;
|
|
for(child1=nbr->getQuery()->beginChildren();
|
|
child1!=nbr->getQuery()->endChildren();
|
|
child1++){
|
|
childStack.push_back(*child1);
|
|
}
|
|
while( !hasHQuery && childStack.size() ){
|
|
QueryAtom::QUERYATOM_QUERY::CHILD_TYPE query = childStack.front();
|
|
childStack.pop_front();
|
|
if(query->getDescription()=="AtomHCount"){
|
|
hasHQuery=true;
|
|
} else {
|
|
for(child1=query->beginChildren();
|
|
child1!=query->endChildren();
|
|
child1++){
|
|
childStack.push_back(*child1);
|
|
}
|
|
}
|
|
}
|
|
|
|
if(!hasHQuery){
|
|
ATOM_EQUALS_QUERY *tmp=makeAtomHCountQuery(0);
|
|
tmp->setNegation(true);
|
|
nbr->expandQuery(tmp);
|
|
}
|
|
} else {
|
|
// it wasn't a query atom, we need to replace it:
|
|
ATOM_EQUALS_QUERY *tmp=makeAtomHCountQuery(0);
|
|
tmp->setNegation(true);
|
|
QueryAtom *newAt = new QueryAtom;
|
|
newAt->setQuery(tmp);
|
|
res->replaceAtom(nbr->getIdx(),newAt);
|
|
delete newAt;
|
|
}
|
|
res->removeAtom(atom);
|
|
} else {
|
|
// only increment the atom idx if we don't remove the atom
|
|
currIdx++;
|
|
}
|
|
} else {
|
|
currIdx++;
|
|
}
|
|
}
|
|
return static_cast<ROMol *>(res);
|
|
};
|
|
}; // end of namespace MolOps
|
|
}; // end of namespace RDKit
|