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rdkit/Code/GraphMol/SmilesParse/SmilesWrite.cpp
Greg Landrum 506ae022ae move GetAtomSmiles/GetAtomSmarts/GetBondSmiles/GetBondSmarts into separate namespaces; 
a couple of little hacks to cleanup the smiles produced from a substructure query (not guaranteed to be correct, but better);
additional internal consistency checks;
stop throwing an exception from inside the smarts parser... that just screws up later parses (this should be fixed!);
better cleanup from failed parsing;
2007-08-04 05:11:27 +00:00

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// $Id$
//
// Copyright (C) 2002-2006 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include "SmilesWrite.h"
#include <GraphMol/Canon.h>
#include <sstream>
#include <map>
namespace RDKit{
namespace SmilesWrite{
const int atomicSmiles[] = {5,6,7,8,15,16,9,17,35,53,-1};
std::string GetAtomSmiles(const Atom *atom,bool doKekule){
PRECONDITION(atom,"bad atom");
int i;
static bool firstCall=true;
static INT_VECT atomicSmilesVect;
if(firstCall){
i = 0;
while(atomicSmiles[i] != -1){
atomicSmilesVect.push_back(atomicSmiles[i]);
i++;
}
firstCall = false;
}
std::stringstream res;
int fc = atom->getFormalCharge();
int num = atom->getAtomicNum();
int numExplicit = atom->getNumExplicitHs();
double massDiff=fabs(PeriodicTable::getTable()->getAtomicWeight(num)-atom->getMass());
std::string symb = atom->getSymbol();
bool needsBracket=false;
if(std::find(atomicSmilesVect.begin(),atomicSmilesVect.end(),num) !=
atomicSmilesVect.end()){
// it's a member of the organic subset
if(!doKekule && atom->getIsAromatic() && symb[0] < 'a') symb[0] -= ('A'-'a');
// -----
// figure out if we need to put a bracket around the atom,
// the conditions for this are:
// - formal charge specified
// - the atom has explicit Hs
// - chirality present and writing isomeric smiles
// - non-default isotope and writing isomeric smiles
if(fc || numExplicit){
needsBracket=true;
}
if(atom->getOwningMol().hasProp("_doIsoSmiles")){
if( atom->getChiralTag()!=Atom::CHI_UNSPECIFIED ){
needsBracket = true;
} else if(massDiff>0.01){
needsBracket=true;
}
}
} else {
needsBracket = true;
}
if( needsBracket ) res << "[";
if(massDiff>0.01 && atom->getOwningMol().hasProp("_doIsoSmiles")){
int iMass=static_cast<int>(atom->getMass()+.1);
res <<iMass;
}
res << symb;
bool chiralityIncluded=false;
if(atom->getOwningMol().hasProp("_doIsoSmiles") &&
atom->getChiralTag()!=Atom::CHI_UNSPECIFIED ){
INT_LIST trueOrder;
atom->getProp("_TraversalBondIndexOrder",trueOrder);
#ifdef VERBOSE_CANON
std::copy(trueOrder.begin(),trueOrder.end(),
std::ostream_iterator<int>(std::cout," "));
std::cout << std::endl;
#endif
int nSwaps = atom->getPerturbationOrder(trueOrder);
//std::cout << "\t\tnSwaps: " << nSwaps << std::endl;
std::string atStr="";
switch(atom->getChiralTag()){
case Atom::CHI_TETRAHEDRAL_CW:
//std::cout << "\tcw" << std::endl;
if(!(nSwaps%2))
atStr = "@@";
else
atStr = "@";
chiralityIncluded=true;
break;
case Atom::CHI_TETRAHEDRAL_CCW:
//std::cout << "\tccw" << std::endl;
if(!(nSwaps%2))
atStr = "@";
else
atStr = "@@";
chiralityIncluded=true;
break;
}
//std::cout << "\tats: " << atStr << std::endl;
res << atStr;
}
if(needsBracket){
unsigned int totNumHs=atom->getTotalNumHs();
if(totNumHs > 0){
res << "H";
if(totNumHs > 1) res << totNumHs;
}
if(fc > 0){
res << "+";
if(fc > 1) res << fc;
} else if(fc < 0) {
res << "-";
if(fc < -1) res << -fc;
}
res << "]";
}
// If the atom has this property, the contained string will
// be inserted directly in the SMILES:
if(atom->hasProp("_supplementalSmilesLabel")){
std::string label;
atom->getProp("_supplementalSmilesLabel",label);
res << label;
}
return res.str();
}
std::string GetBondSmiles(const Bond *bond,int atomToLeftIdx,bool doKekule){
PRECONDITION(bond,"bad bond");
if(atomToLeftIdx<0) atomToLeftIdx=bond->getBeginAtomIdx();
std::stringstream res;
bool aromatic=false;
if( !doKekule &&
(bond->getBondType() == Bond::SINGLE ||
bond->getBondType() == Bond::DOUBLE ||
bond->getBondType() == Bond::AROMATIC) ){
Atom *a1,*a2;
a1 = bond->getOwningMol().getAtomWithIdx(atomToLeftIdx);
a2 = bond->getOwningMol().getAtomWithIdx(bond->getOtherAtomIdx(atomToLeftIdx));
if(a1->getIsAromatic() && a2->getIsAromatic()) aromatic=true;
}
Bond::BondDir dir= bond->getBondDir();
//if(bond->getBeginAtomIdx() != atomToLeftIdx) {
// if(dir==Bond::ENDDOWNRIGHT) dir = Bond::ENDUPRIGHT;
// else if(dir==Bond::ENDUPRIGHT) dir = Bond::ENDDOWNRIGHT;
//}
Bond::BondType btype = bond->getBondType();
int oaid = bond->getOtherAtomIdx(atomToLeftIdx);
switch(bond->getBondType()){
case Bond::SINGLE:
if( dir != Bond::NONE && dir != Bond::UNKNOWN ){
switch(dir){
case Bond::ENDDOWNRIGHT:
if(bond->getOwningMol().hasProp("_doIsoSmiles")) res << "\\";
break;
case Bond::ENDUPRIGHT:
if(bond->getOwningMol().hasProp("_doIsoSmiles")) res << "/";
break;
default:
break;
}
} else {
// if the bond is marked as aromatic and the two atoms
// are aromatic, we need no marker (this arises in kekulized
// molecules).
// FIX: we should be able to dump kekulized smiles
// currently this is possible by removing all
// isAromatic flags, but there should maybe be another way
if( aromatic && !bond->getIsAromatic() ) res << "-";
}
break;
case Bond::DOUBLE:
// see note above
if( !aromatic || !bond->getIsAromatic() ) res << "=";
break;
case Bond::TRIPLE: res << "#"; break;
case Bond::AROMATIC:
if ( dir != Bond::NONE && dir != Bond::UNKNOWN ){
switch(dir){
case Bond::ENDDOWNRIGHT:
if(bond->getOwningMol().hasProp("_doIsoSmiles")) res << "\\";
break;
case Bond::ENDUPRIGHT:
if(bond->getOwningMol().hasProp("_doIsoSmiles")) res << "/";
break;
default:
break;
}
}
if(!aromatic) res << ":";
break;
case Bond::DATIVE:
if(bond->getBeginAtomIdx() == atomToLeftIdx) res << ">";
else res << "<";
break;
default:
res << "?";
}
return res.str();
}
std::string FragmentSmilesConstruct(ROMol &mol,int atomIdx,
std::vector<Canon::AtomColors> &colors,
INT_VECT &ranks,bool doKekule){
Canon::MolStack molStack;
// try to prevent excessive reallocation
molStack.reserve(mol.getNumAtoms()+
mol.getNumBonds());
std::stringstream res;
std::map<int,int> ringClosureMap;
int ringIdx,closureVal;
Canon::canonicalizeFragment(mol,atomIdx,colors,ranks,
molStack);
Canon::MolStack::const_iterator msCI,tmpIt;
Bond *bond;
for(msCI=molStack.begin();msCI!=molStack.end();msCI++){
switch(msCI->type){
case Canon::MOL_STACK_ATOM:
res << GetAtomSmiles(msCI->obj.atom,doKekule);
break;
case Canon::MOL_STACK_BOND:
bond = msCI->obj.bond;
// FIX: This is kind of a hacky fix to a problem.
// What's going on here is that the traversal code currently
// (June 2004) puts ring-closure bonds with the final atom in
// the ring (choices are first and last atom). The bond
// directions calculated in the canonicalization code are
// configured to be correct if the bond dir goes from the
// first to the last atom. So if we have a bond closing a
// ring that has direction indicated, that direction will end
// up being wrong. The "correct" solution would be to go and
// change the traversal code to insert the bond into the stack
// after the initial atom, but that will break loads of
// existing canonical smiles and, potentially, open another
// can of bugs... so what we'll do instead here is look ahead
// in the stack and reverse the direction on ring-closure
// bonds at the time of writing. It's a hack, but a simple
// and functional hack.
// This fixes Issue 184.
#if 0
tmpIt = msCI+1;
if(tmpIt!=molStack.end()&&tmpIt->type==MOL_STACK_RING){
tmpDir = bond->getBondDir();
switch(tmpDir){
case Bond::ENDUPRIGHT:
bond->setBondDir(Bond::ENDDOWNRIGHT);
break;
case Bond::ENDDOWNRIGHT:
bond->setBondDir(Bond::ENDUPRIGHT);
break;
}
res << GetBondSmiles(bond,msCI->number);
bond->setBondDir(tmpDir);
} else {
res << GetBondSmiles(bond,msCI->number);
}
#else
res << GetBondSmiles(bond,msCI->number,doKekule);
#endif
break;
case Canon::MOL_STACK_RING:
ringIdx = msCI->number;
if(ringClosureMap.count(ringIdx)){
// the index is already in the map ->
// we're closing a ring, so grab
// the index and then delete the value:
closureVal = ringClosureMap[ringIdx];
ringClosureMap.erase(ringIdx);
} else {
// we're opening a new ring, find the index for it:
closureVal = 1;
bool done=false;
// EFF: there's got to be a more efficient way to do this
while(!done){
std::map<int,int>::iterator mapIt;
for(mapIt=ringClosureMap.begin();
mapIt!=ringClosureMap.end();
mapIt++){
if(mapIt->second==closureVal) break;
}
if(mapIt==ringClosureMap.end()){
done=true;
} else {
closureVal+=1;
}
}
ringClosureMap[ringIdx]=closureVal;
}
if(closureVal >= 10){
res << "%";
}
res << closureVal;
break;
case Canon::MOL_STACK_BRANCH_OPEN:
res << "(";
break;
case Canon::MOL_STACK_BRANCH_CLOSE:
res << ")";
break;
default:
break;
}
}
return res.str();
}
} // end of namespace SmilesWrite
// NOTE: I did not forget the const here... Producing SMILES for
// a molecule actually can change the molecule. Specifically,
// things like the directionality of bonds may be changed when
// the molecule is canonicalized.
// Odds are good that this may be one of those foot-shooting
// decisions and I'm gonna want to smack myself for doing this,
// but we'll try anyway.
std::string MolToSmiles(ROMol &mol,bool doIsomericSmiles,
bool doKekule,int rootedAtAtom){
PRECONDITION(rootedAtAtom<0||static_cast<unsigned int>(rootedAtAtom)<mol.getNumAtoms(),
"rootedAtomAtom must be less than the number of atoms");
if(doIsomericSmiles){
mol.setProp("_doIsoSmiles",1);
} else if(mol.hasProp("_doIsoSmiles")){
mol.clearProp("_doIsoSmiles");
}
#if 0
std::cout << "----------------------------" << std::endl;
std::cout << "MolToSmiles:"<< std::endl;
mol.debugMol(std::cout);
std::cout << "----------------------------" << std::endl;
#endif
std::string res;
for(ROMol::AtomIterator atIt=mol.beginAtoms();atIt!=mol.endAtoms();atIt++){
(*atIt)->updatePropertyCache();
}
unsigned int nAtoms=mol.getNumAtoms();
INT_VECT ranks(nAtoms,-1);
// clean up the chirality on any atom that is marked as chiral,
// but that should not be:
if(doIsomericSmiles){
MolOps::assignAtomChiralCodes(mol,true);
MolOps::rankAtoms(mol,ranks,ComprehensiveInvariants,
true,0,true);
} else {
MolOps::rankAtoms(mol,ranks);
}
#ifdef VERBOSE_CANON
for(int tmpI=0;tmpI<ranks.size();tmpI++){
std::cout << tmpI << " " << ranks[tmpI] << " " << *(mol.getAtomWithIdx(tmpI)) << std::endl;
}
#endif
std::vector<Canon::AtomColors> colors(nAtoms,Canon::WHITE_NODE);
std::vector<Canon::AtomColors>::iterator colorIt;
colorIt = colors.begin();
// loop to deal with the possibility that there might be disconnected fragments
while(colorIt != colors.end()){
int nextAtomIdx;
std::string subSmi;
// find the next atom for a traverse
if(rootedAtAtom>=0){
nextAtomIdx=rootedAtAtom;
rootedAtAtom=-1;
} else {
int nextRank = nAtoms+1;
for(unsigned int i=0;i<nAtoms;i++){
if( colors[i] == Canon::WHITE_NODE && ranks[i] < nextRank ){
nextRank = ranks[i];
nextAtomIdx = i;
}
}
}
subSmi = SmilesWrite::FragmentSmilesConstruct(mol, nextAtomIdx, colors,
ranks,doKekule);
res += subSmi;
colorIt = std::find(colors.begin(),colors.end(),Canon::WHITE_NODE);
if(colorIt != colors.end()){
res += ".";
}
}
return res;
}
}
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