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))
{
_atom_stereo_flags = reaction.getInversionArray(i).ptr();
_bond_rc_flags = reaction.getReactingCenterArray(i).ptr();
_aam = reaction.getAAMArray(i).ptr();
_writeMolecule(reaction.getMolecule(i));
}
for (i = reaction.productBegin(); i < reaction.productEnd(); i = reaction.productNext(i))
{
_atom_stereo_flags = reaction.getInversionArray(i).ptr();
_bond_rc_flags = reaction.getReactingCenterArray(i).ptr();
_aam = reaction.getAAMArray(i).ptr();
_writeMolecule(reaction.getMolecule(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");
}
void CrfSaver::_writeReactionMolecule (Reaction &reaction, int i)
{
_atom_stereo_flags = reaction.getInversionArray(i).ptr();
_bond_rc_flags = reaction.getReactingCenterArray(i).ptr();
_aam = reaction.getAAMArray(i).ptr();
_writeMolecule(reaction.getMolecule(i));
}
void ReactionAtomNeighbourhoodCounters::calculate(Reaction &reac) {
int i;
_counters.resize(reac.count());
for (i = reac.begin(); i < reac.end(); i = reac.next(i))
_counters[i].calculate(reac.getMolecule(i));
}
void CrfLoader::_loadReactionMolecule (Reaction &reaction, int index, bool have_aam)
{
_bond_rc_flags = &reaction.getReactingCenterArray(index);
_atom_stereo_flags = &reaction.getInversionArray(index);
if (have_aam)
_aam = &reaction.getAAMArray(index);
_loadMolecule(reaction.getMolecule(index));
}
bool ReactionExactMatcher::_match_atoms (BaseReaction &query_, Reaction &target,
int sub_mol_idx, int sub_atom_idx, int super_mol_idx, int super_atom_idx,
void *context)
{
ReactionExactMatcher &self = *(ReactionExactMatcher *)context;
Reaction &query = query_.asReaction();
Molecule &submol = query.getMolecule(sub_mol_idx);
Molecule &supermol = target.getMolecule(super_mol_idx);
if (!MoleculeExactMatcher::matchAtoms(submol, supermol, sub_atom_idx, super_atom_idx, self.flags))
return false;
if (self.flags & CONDITION_AAM)
{
if ((query.getAAM(sub_mol_idx, sub_atom_idx) == 0) !=
(target.getAAM(super_mol_idx, super_atom_idx) == 0))
return false;
}
return true;
}
bool ReactionExactMatcher::_match_bonds (BaseReaction &query_, Reaction &target,
int sub_mol_idx, int sub_bond_idx, int super_mol_idx, int super_bond_idx,
AromaticityMatcher *am, void *context)
{
ReactionExactMatcher &self = *(ReactionExactMatcher *)context;
Reaction &query = query_.asReaction();
Molecule &submol = query.getMolecule(sub_mol_idx);
Molecule &supermol = target.getMolecule(super_mol_idx);
if (!MoleculeExactMatcher::matchBonds(submol, supermol, sub_bond_idx, super_bond_idx, self.flags))
return false;
if (self.flags & CONDITION_REACTING_CENTERS)
{
int sub_change = query.getReactingCenter(sub_mol_idx, sub_bond_idx);
int super_change = target.getReactingCenter(super_mol_idx, super_bond_idx);
if (sub_change != super_change)
return false;
}
return true;
}