void ReactionCdxLoader::loadReaction (Reaction &rxn)
{
rxn.clear();
QS_DEF(Array<char>, buf);
_scanner.readAll(buf);
buf.push(0);
}
void CrfLoader::loadReaction (Reaction &reaction)
{
int i;
int nreactants = _scanner.readPackedUInt();
int nproducts = _scanner.readPackedUInt();
byte flags = _scanner.readByte();
int ncatalyst = 0;
if (flags & CrfFeatureFlags::CRF_CATALYST)
ncatalyst = _scanner.readPackedUInt();
reaction.clear();
_bond_rc_flags = 0;
_atom_stereo_flags = 0;
_aam = 0;
bool have_aam = (flags != 0);
for (i = 0; i < nreactants; i++)
{
int index = reaction.addReactant();
_loadReactionMolecule(reaction, index, have_aam);
}
for (i = 0; i < nproducts; i++)
{
int index = reaction.addProduct();
_loadReactionMolecule(reaction, index, have_aam);
}
for (i = 0; i < ncatalyst; i++)
{
int index = reaction.addCatalyst();
_loadReactionMolecule(reaction, index, have_aam);
}
}
void ReactionCmlLoader::loadReaction (Reaction &rxn)
{
rxn.clear();
QS_DEF(Array<char>, buf);
_scanner.readAll(buf);
buf.push(0);
TiXmlDocument xml;
xml.Parse(buf.ptr());
if (xml.Error())
throw Error("XML parsing error: %s", xml.ErrorDesc());
TiXmlHandle hxml(&xml);
TiXmlElement *elem;
TiXmlHandle hroot(0);
elem = hxml.FirstChild("reaction").Element();
if (elem == 0)
elem = hxml.FirstChild("cml").FirstChild("reaction").Element();
if (elem == 0)
throw Error("no <reaction>?");
hroot = TiXmlHandle(elem);
const char *title = elem->Attribute("title");
if (title != 0)
rxn.name.readString(title, true);
QS_DEF(Molecule, mol);
elem = hroot.FirstChild("reactantList").FirstChild().Element();
for (; elem; elem = elem->NextSiblingElement())
{
if (strcasecmp(elem->Value(), "molecule") != 0)
continue;
TiXmlHandle handle(elem);
MoleculeCmlLoader loader(handle);
loader.stereochemistry_options = stereochemistry_options;
loader.loadMolecule(mol);
rxn.addReactantCopy(mol, 0, 0);
}
elem = hroot.FirstChild("productList").FirstChild().Element();
for (; elem; elem = elem->NextSiblingElement())
{
if (strcasecmp(elem->Value(), "molecule") != 0)
continue;
TiXmlHandle handle(elem);
MoleculeCmlLoader loader(handle);
loader.stereochemistry_options = stereochemistry_options;
loader.loadMolecule(mol);
rxn.addProductCopy(mol, 0, 0);
}
elem = hroot.FirstChild("spectatorList").FirstChild().Element();
for (; elem; elem = elem->NextSiblingElement())
{
if (strcasecmp(elem->Value(), "molecule") != 0)
continue;
TiXmlHandle handle(elem);
MoleculeCmlLoader loader(handle);
loader.stereochemistry_options = stereochemistry_options;
loader.loadMolecule(mol);
rxn.addCatalystCopy(mol, 0, 0);
}
}