bool FastSearchFormat::ObtainTarget(OBConversion* pConv, vector<OBMol>& patternMols, const string& indexname)
{
//Obtains an OBMol from:
// the filename in the -s option or
// the SMARTS string in the -s option or
// by converting the file in the -S or -aS options (deprecated).
// If there is no -s -S or -aS option, information on the index file is displayed.
OBMol patternMol;
patternMol.SetIsPatternStructure();
const char* p = pConv->IsOption("s",OBConversion::GENOPTIONS);
bool OldSOption=false;
//If no -s option, make OBMol from file in -S option or -aS option (both deprecated)
if(!p)
{
p = pConv->IsOption("S",OBConversion::GENOPTIONS);
if(!p)
p = pConv->IsOption("S",OBConversion::INOPTIONS);//for GUI mainly
OldSOption = true;
}
if(p)
{
vector<string> vec;
tokenize(vec, p);
//ignore leading ~ (not relevant to fastsearch)
if(vec[0][0]=='~')
vec[0].erase(0,1);
if(vec.size()>1 && vec[1]=="exact")
pConv->AddOption("e", OBConversion::INOPTIONS);
OBConversion patternConv;
OBFormat* pFormat;
//Interpret as a filename if possible
string& txt =vec [0];
if( txt.empty() ||
txt.find('.')==string::npos ||
!(pFormat = patternConv.FormatFromExt(txt.c_str())) ||
!patternConv.SetInFormat(pFormat) ||
!patternConv.ReadFile(&patternMol, txt) ||
patternMol.NumAtoms()==0)
//if false, have a valid patternMol from a file
{
//is SMARTS/SMILES
//Replace e.g. [#6] in SMARTS by C so that it can be converted as SMILES
//for the fingerprint phase, but allow more generality in the SMARTS phase.
for(;;)
{
string::size_type pos1, pos2;
pos1 = txt.find("[#");
if(pos1==string::npos)
break;
pos2 = txt.find(']');
int atno;
if(pos2!=string::npos && (atno = atoi(txt.substr(pos1+2, pos2-pos1-2).c_str())) && atno>0)
txt.replace(pos1, pos2-pos1+1, etab.GetSymbol(atno));
else
{
obErrorLog.ThrowError(__FUNCTION__,"Ill-formed [#n] atom in SMARTS", obError);
return false;
}
}
bool hasTildeBond;
if( (hasTildeBond = (txt.find('~')!=string::npos)) ) // extra parens to indicate truth value
{
//Find ~ bonds and make versions of query molecule with a single and aromatic bonds
//To avoid having to parse the SMILES here, replace ~ by $ (quadruple bond)
//and then replace this in patternMol. Check first that there are no $ already
//Sadly, isocynanides may have $ bonds.
if(txt.find('$')!=string::npos)
{
obErrorLog.ThrowError(__FUNCTION__,
"Cannot use ~ bonds in patterns with $ (quadruple) bonds.)", obError);
return false;
}
replace(txt.begin(),txt.end(), '~' , '$');
}
//read as standard SMILES
patternConv.SetInFormat("smi");
if(!patternConv.ReadString(&patternMol, vec[0]))
{
obErrorLog.ThrowError(__FUNCTION__,"Cannot read the SMILES string",obError);
return false;
}
if(hasTildeBond)
{
AddPattern(patternMols, patternMol, 0); //recursively add all combinations of tilde bond values
return true;
}
}
else
{
// target(s) are in a file
patternMols.push_back(patternMol);
while(patternConv.Read(&patternMol))
patternMols.push_back(patternMol);
return true;
}
}
if(OldSOption) //only when using deprecated -S and -aS options
{
//make -s option for later SMARTS test
OBConversion conv;
if(conv.SetOutFormat("smi"))
{
string optiontext = conv.WriteString(&patternMol, true);
pConv->AddOption("s", OBConversion::GENOPTIONS, optiontext.c_str());
}
}
if(!p)
{
//neither -s or -S options provided. Output info rather than doing search
const FptIndexHeader& header = fs.GetIndexHeader();
string id(header.fpid);
if(id.empty())
id = "default";
clog << indexname << " is an index of\n " << header.datafilename
<< ".\n It contains " << header.nEntries
<< " molecules. The fingerprint type is " << id << " with "
<< OBFingerprint::Getbitsperint() * header.words << " bits.\n"
<< "Typical usage for a substructure search:\n"
<< "obabel indexfile.fs -osmi -sSMILES\n"
<< "(-s option in GUI is 'Convert only if match SMARTS or mols in file')" << endl;
return false;
}
patternMols.push_back(patternMol);
return true;
}
bool FastSearchFormat::ObtainTarget(OBConversion* pConv, OBMol& patternMol, const string& indexname)
{
//Obtains an OBMol
// either from the SMARTS string in the -s option
// or by converting the file in the -S option
//or, if neither option is provided, displays information on the index file.
stringstream smiles(stringstream::out);
ifstream patternstream;
OBConversion PatternConv(&patternstream,&smiles);
const char* p = pConv->IsOption("s",OBConversion::GENOPTIONS);
string txt;
if(p)
{
// Use the -s option
txt=p;
stringstream smarts(txt, stringstream::in);
OBConversion Convsm(&smarts);
if(!Convsm.SetInFormat("smi")) return false;
Convsm.Read(&patternMol);
//erase -s option in GeneralOptions since it will be rewritten
pConv->RemoveOption("s",OBConversion::GENOPTIONS);
if(patternMol.Empty())
{
obErrorLog.ThrowError(__FUNCTION__,
"Could not make a molecule from " + smarts.str()
+ "\nThis needs to be valid SMILES when using fastsearch."
"You can use the more versatile SMARTS in a normal substructure search." , obError);
return false;
}
}
else
{
// or Make OBMol from file in -S option or -aS option
p = pConv->IsOption("S",OBConversion::GENOPTIONS);
if(!p)
p = pConv->IsOption("S",OBConversion::INOPTIONS);//for GUI mainly
}
if(!p)
{
//neither -s or -S options provided. Output info rather than doing search
const FptIndexHeader& header = fs.GetIndexHeader();
string id(header.fpid);
if(id.empty())
id = "default";
clog << indexname << " is an index of\n " << header.datafilename
<< ".\n It contains " << header.nEntries
<< " molecules. The fingerprint type is " << id << " with "
<< OBFingerprint::Getbitsperint() * header.words << " bits.\n"
<< "Typical usage for a substructure search:\n"
<< "babel indexfile.fs -osmi -sSMILES" << endl;
return false;
}
if(p && patternMol.Empty())
{
txt=p;
string::size_type pos = txt.find_last_of('.');
if(pos==string::npos)
{
obErrorLog.ThrowError(__FUNCTION__, "Filename of pattern molecule in -S option must have an extension", obError);
return false;
}
patternstream.open(txt.c_str());
if(!patternstream)
{
stringstream errorMsg;
errorMsg << "Cannot open " << txt << endl;
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);
return false;
}
PatternConv.SetOneObjectOnly();
if(PatternConv.SetInFormat(txt.substr(pos+1).c_str()))
PatternConv.Read(&patternMol);
}
if(patternMol.Empty())
{
obErrorLog.ThrowError(__FUNCTION__, "Cannot derive a molecule from the -s or -S options", obWarning);
return false;
}
patternMol.ConvertDativeBonds();//use standard form for dative bonds
//Convert to SMILES and generate a -s option for use in the final filtering
if(!PatternConv.SetOutFormat("smi"))
return false;
PatternConv.Write(&patternMol);
//remove name to leave smiles string
string smilesstr(smiles.str());
string::size_type pos = smilesstr.find_first_of(" \t\r\n");
if(pos!=string::npos)
smilesstr = smilesstr.substr(0,pos);
pConv->AddOption("s", OBConversion::GENOPTIONS, smilesstr.c_str());
return true;
}