bool OpExtraOut::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
/*
OptionText contains an output filename with a format extension.
Make an OBConversion object with this as output destination.
Make a copy the current OBConversion and replace the output format by
an instance of ExtraFormat. This then does all the subsequent work.
*/
if(!pConv || !OptionText || *OptionText=='\0')
return true; //silent no-op. false would prevent the main output
if(pConv->IsFirstInput())
{
OBConversion* pExtraConv = new OBConversion(*pConv); //copy ensures OBConversion::Index>-1
std::ofstream* ofs;
if( (ofs = new std::ofstream(OptionText)) ) // extra parens to indicate truth value
pExtraConv->SetOutStream(ofs);
if(!ofs || !pExtraConv->SetOutFormat(OBConversion::FormatFromExt(OptionText)))
{
obErrorLog.ThrowError(__FUNCTION__, "Error setting up extra output file", obError);
return true;
}
OBConversion* pOrigConv = new OBConversion(*pConv);
//Make an instance of ExtraFormat and divert the output to it. It will delete itself.
pConv->SetOutFormat(new ExtraFormat(pOrigConv, pExtraConv));
}
return true;
}
bool ReactionInChIFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if (pmol == NULL || !pmol->IsReaction())
return false;
ostream &ofs = *pConv->GetOutStream();
OBFormat* pInChIFormat = OBConversion::FindFormat("inchi");
if (!pInChIFormat)
return false;
bool isEquilibrium = pConv->IsOption("e");
OBConversion inchiconv;
inchiconv.SetOutFormat(pInChIFormat);
stringstream ss;
inchiconv.SetOutStream(&ss);
#define M_REACTANTS 0
#define M_PRODUCTS 1
#define M_AGENTS 2
OBReactionFacade facade(pmol);
std::vector<std::vector<std::string> > inchis(3);
unsigned int nonInchi[3] = { 0, 0, 0 };
bool hasNonInchi = false;
OBMol mol;
for (int part = 0; part <= 2; ++part) {
unsigned int N;
switch (part) {
case M_REACTANTS: N = facade.NumComponents(REACTANT); break;
case M_PRODUCTS: N = facade.NumComponents(PRODUCT); break;
case M_AGENTS: N = facade.NumComponents(AGENT); break;
}
for (unsigned int i = 0; i < N; ++i) {
mol.Clear();
switch (part) {
case M_REACTANTS: facade.GetComponent(&mol, REACTANT, i); break;
case M_PRODUCTS: facade.GetComponent(&mol, PRODUCT, i); break;
case M_AGENTS: facade.GetComponent(&mol, AGENT, i); break;
}
if (mol.NumAtoms() == 1 && mol.GetFirstAtom()->GetAtomicNum() == 0) {
// This represents an unknown component
nonInchi[part]++;
hasNonInchi = true;
}
else {
bool ok = inchiconv.Write(&mol);
if (!ok) {
nonInchi[part]++;
hasNonInchi = true;
}
else {
string inchi = ss.str();
if (strncmp(inchi.c_str(), "InChI=1S/", 9) != 0)
return false;
inchis[part].push_back(TrimInChI(inchi.c_str()));
}
ss.str("");
}
}
}
std::sort(inchis[M_REACTANTS].begin(), inchis[M_REACTANTS].end());
std::sort(inchis[M_PRODUCTS].begin(), inchis[M_PRODUCTS].end());
std::sort(inchis[M_AGENTS].begin(), inchis[M_AGENTS].end());
std::string reactants_string = "";
const int rsize = inchis[M_REACTANTS].size();
for (int i = 0; i < rsize; ++i) {
if (i > 0)
reactants_string += '!';
reactants_string += inchis[M_REACTANTS][i];
}
std::string products_string = "";
const int psize = inchis[M_PRODUCTS].size();
for (int i = 0; i < psize; ++i) {
if (i > 0)
products_string += '!';
products_string += inchis[M_PRODUCTS][i];
}
bool reactants_first = reactants_string <= products_string;
ofs << RINCHI_VERSION_STRING;
if (rsize > 0 || psize > 0 || !inchis[M_AGENTS].empty()) {
ofs << (reactants_first ? reactants_string : products_string);
ofs << "<>";
ofs << (reactants_first ? products_string : reactants_string);
if (!inchis[M_AGENTS].empty()) {
ofs << "<>";
for (std::vector<std::string>::const_iterator vit = inchis[M_AGENTS].begin(); vit != inchis[M_AGENTS].end(); ++vit) {
if (vit != inchis[M_AGENTS].begin())
ofs << '!';
ofs << *vit;
}
}
}
ofs << "/d";
if (isEquilibrium)
ofs << '=';
else
ofs << (reactants_first ? '+' : '-');
if (hasNonInchi) {
ofs << "/u" << (reactants_first ? nonInchi[M_REACTANTS] : nonInchi[M_PRODUCTS]) << '-'
<< (reactants_first ? nonInchi[M_PRODUCTS] : nonInchi[M_REACTANTS]) << '-'
<< nonInchi[M_AGENTS];
}
ofs << '\n';
return true;
}