void CrfSaver::_writeReactionInfo (Reaction &reaction)
{
_output.writePackedUInt(reaction.reactantsCount());
_output.writePackedUInt(reaction.productsCount());
byte features = CrfFeatureFlags::CRF_AAM;
if (reaction.catalystCount() > 0)
features |= CrfFeatureFlags::CRF_CATALYST;
_output.writeByte(features);
if (reaction.catalystCount() > 0)
_output.writePackedUInt(reaction.catalystCount());
}
void CrfSaver::saveReaction (Reaction &reaction)
{
_writeReactionInfo(reaction);
int i;
_atom_stereo_flags = 0;
_bond_rc_flags = 0;
_aam = 0;
for (i = reaction.reactantBegin(); i < reaction.reactantEnd(); i = reaction.reactantNext(i))
_writeReactionMolecule(reaction, i);
for (i = reaction.productBegin(); i < reaction.productEnd(); i = reaction.productNext(i))
_writeReactionMolecule(reaction, i);
if (reaction.catalystCount() > 0)
{
for (i = reaction.catalystBegin(); i < reaction.catalystEnd(); i = reaction.catalystNext(i))
_writeReactionMolecule(reaction, i);
}
if (_encoder.get() != 0)
_encoder->finish();
}
void ReactionCmlSaver::saveReaction (Reaction &rxn)
{
if (!skip_cml_tag)
{
_output.printf("<?xml version=\"1.0\" ?>\n");
_output.printf("<cml>\n");
}
if (rxn.name.ptr() != 0)
{
if (strchr(rxn.name.ptr(), '\"') != NULL)
throw Error("can not save reaction with '\"' in title");
_output.printf("<reaction title=\"%s\">\n", rxn.name.ptr());
}
else
_output.printf("<reaction>\n");
int i;
MoleculeCmlSaver molsaver(_output);
molsaver.skip_cml_tag = true;
if (rxn.reactantsCount() > 0)
{
_output.printf("<reactantList>\n");
for (i = rxn.reactantBegin(); i != rxn.reactantEnd(); i = rxn.reactantNext(i))
molsaver.saveMolecule(rxn.getMolecule(i));
_output.printf("</reactantList>\n");
}
if (rxn.productsCount() > 0)
{
_output.printf("<productList>\n");
for (i = rxn.productBegin(); i != rxn.productEnd(); i = rxn.productNext(i))
molsaver.saveMolecule(rxn.getMolecule(i));
_output.printf("</productList>\n");
}
if (rxn.catalystCount() > 0)
{
_output.printf("<spectatorList>\n");
for (i = rxn.catalystBegin(); i != rxn.catalystEnd(); i = rxn.catalystNext(i))
molsaver.saveMolecule(rxn.getMolecule(i));
_output.printf("</spectatorList>\n");
}
_output.printf("</reaction>\n");
if (!skip_cml_tag)
_output.printf("</cml>\n");
}