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// $Id: SmilesParse.cpp 1981 2012-03-01 09:49:40Z glandrum $
//
// Copyright (C) 2001-2010 Greg Landrum and Rational Discovery LLC
//
// @@ 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.
//
// ----------------------------------------------------------------------------------
// Despite the name of this file, both SMILES and SMARTS parsers are exposed here
//
// General comments about the parsers:
// - Atom numbering will be preserved, so input order of atoms==internal order
//
// - Bond ordering is not, in general, preserved. Specifically, ring closure
// bonds will occur at the end of the bond list in general. Basically ring
// closure bonds are not constructed until fragments are closed. This forces
// some form of reordering.
//
//
//
#include <GraphMol/RDKitBase.h>
#include "SmilesParse.h"
#include "SmilesParseOps.h"
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Invariant.h>
#include <boost/algorithm/string.hpp>
#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>
int yysmiles_parse (const char *,std::vector<RDKit::RWMol *>*,void *);
int yysmiles_lex_init (void **);
int yysmiles_lex_destroy (void *);
void setup_smiles_string(const std::string &text,void *);
extern int yysmiles_debug;
int yysmarts_parse (const char *,std::vector<RDKit::RWMol *>*,void *);
int yysmarts_lex_init (void **);
int yysmarts_lex_destroy (void *);
void setup_smarts_string(const std::string &text,void *);
extern int yysmarts_debug;
namespace RDKit{
namespace {
int smiles_parse(const std::string &inp,
std::vector<RDKit::RWMol *> &molVect){
void *scanner;
TEST_ASSERT(!yysmiles_lex_init(&scanner));
setup_smiles_string(inp,scanner);
int res=yysmiles_parse(inp.c_str(),&molVect,scanner);
yysmiles_lex_destroy(scanner);
return res;
}
int smarts_parse(const std::string &inp,
std::vector<RDKit::RWMol *> &molVect){
void *scanner;
TEST_ASSERT(!yysmarts_lex_init(&scanner));
setup_smarts_string(inp,scanner);
int res=yysmarts_parse(inp.c_str(),&molVect,scanner);
yysmarts_lex_destroy(scanner);
return res;
}
typedef enum {
BASE=0,
BRANCH,
RECURSE
} SmaState;
std::string labelRecursivePatterns(std::string sma){
#ifndef NO_AUTOMATIC_SMARTS_RELABELLING
std::list<SmaState> state;
std::list<unsigned int> startRecurse;
std::map<std::string, std::string> patterns;
std::string res="";
state.push_back(BASE);
unsigned int pos=0;
while(pos<sma.size()){
res += sma[pos];
if(sma[pos]=='$' && pos+1<sma.size() && sma[pos+1]=='('){
state.push_back(RECURSE);
startRecurse.push_back(pos);
++pos;
res += sma[pos];
} else if(sma[pos]=='('){
state.push_back(BRANCH);
} else if(sma[pos]==')'){
SmaState currState=state.back();
state.pop_back();
if(currState==RECURSE){
unsigned int dollarPos=startRecurse.back();
startRecurse.pop_back();
if(pos+1>=sma.size() || sma[pos+1] !='_'){
std::string recurs = sma.substr(dollarPos,pos-dollarPos+1);
std::string label;
if(patterns.find(recurs)!=patterns.end()){
// seen this one before, add the label
label=patterns[recurs];
} else {
label=boost::lexical_cast<std::string>(patterns.size()+100);
patterns[recurs]=label;
}
res += "_" + label;
}
} else if(currState==BRANCH) {
// no need to do anything here.
}
}
++pos;
}
//std::cerr<< " >"<<sma<<"->"<<res<<std::endl;
return res;
#else
return sma;
#endif
}
} // end of local namespace
RWMol *toMol(std::string inp,int func(const std::string &,
std::vector<RDKit::RWMol *> &),
std::string origInp){
RWMol *res;
std::vector<RDKit::RWMol *> molVect;
try {
func(inp,molVect);
if(molVect.size()<=0){
res = 0;
} else {
res = molVect[0];
molVect[0]=0;
SmilesParseOps::CloseMolRings(res,false);
SmilesParseOps::AdjustAtomChiralityFlags(res);
// No sense leaving this bookmark intact:
if(res->hasAtomBookmark(ci_RIGHTMOST_ATOM)){
res->clearAtomBookmark(ci_RIGHTMOST_ATOM);
}
}
} catch (SmilesParseException &e) {
std::string nm="SMILES";
if(func==smarts_parse){
nm="SMARTS";
}
BOOST_LOG(rdErrorLog) << nm<<" Parse Error: "<< e.message() << " for input: "<< origInp << std::endl;
res = 0;
}
BOOST_FOREACH(RDKit::RWMol *molPtr,molVect){
if(molPtr) delete molPtr;
}
return res;
}
RWMol *SmilesToMol(std::string smi,int debugParse,bool sanitize,
std::map<std::string,std::string> *replacements){
yysmiles_debug = debugParse;
// strip any leading/trailing whitespace:
boost::trim_if(smi,boost::is_any_of(" \t\r\n"));
if(replacements){
bool loopAgain=true;
while(loopAgain){
loopAgain=false;
for(std::map<std::string, std::string>::const_iterator replIt=replacements->begin();
replIt!=replacements->end();++replIt){
if(boost::find_first(smi,replIt->first)){
loopAgain=true;
boost::replace_all(smi,replIt->first,replIt->second);
}
}
}
}
RWMol *res = toMol(smi,smiles_parse,smi);
if(sanitize && res){
// we're going to remove explicit Hs from the graph,
// this triggers a sanitization, so we do not need to
// worry about doing one here:
ROMol *tmp = MolOps::removeHs(*res,false,false);
delete res;
res = static_cast<RWMol *>(tmp);
// figure out stereochemistry:
MolOps::assignStereochemistry(*res,true);
}
return res;
};
RWMol *SmartsToMol(std::string sma,int debugParse,bool mergeHs,
std::map<std::string, std::string> *replacements){
yysmarts_debug = debugParse;
boost::trim_if(sma,boost::is_any_of(" \t\r\n"));
if(replacements){
bool loopAgain=true;
while(loopAgain){
loopAgain=false;
for(std::map<std::string, std::string>::const_iterator replIt=replacements->begin();
replIt!=replacements->end();++replIt){
if(boost::find_first(sma,replIt->first)){
loopAgain=true;
boost::replace_all(sma,replIt->first,replIt->second);
}
}
}
}
std::string oInput=sma;
sma=labelRecursivePatterns(sma);
RWMol *res = toMol(sma,smarts_parse,oInput);
if(res && mergeHs){
ROMol *tmp = MolOps::mergeQueryHs(*res);
delete res;
res = static_cast<RWMol *>(tmp);
}
return res;
};
}
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