bool TinkerFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
bool mm2Types = false;
bool mmffTypes = pConv->IsOption("m",OBConversion::OUTOPTIONS) != NULL;
bool mm3Types = pConv->IsOption("3",OBConversion::OUTOPTIONS) != NULL;
bool classTypes = pConv->IsOption("c", OBConversion::OUTOPTIONS) != NULL;
unsigned int i;
char buffer[BUFF_SIZE];
OBBond *bond;
vector<OBBond*>::iterator j;
// Before we try output of MMFF94 atom types, check if it works
OBForceField *ff = OpenBabel::OBForceField::FindForceField("MMFF94");
if (mmffTypes && ff && ff->Setup(mol))
mmffTypes = ff->GetAtomTypes(mol);
else
mmffTypes = false; // either the force field isn't available, or it doesn't work
if (!mmffTypes && !mm3Types && !classTypes) {
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM2 parameters\n",mol.NumAtoms(),mol.GetTitle());
mm2Types = true;
}
else if (mm3Types)
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM3 parameters\n",mol.NumAtoms(),mol.GetTitle());
else if (classTypes)
snprintf(buffer, BUFF_SIZE, "%6d %-20s Custom parameters\n",mol.NumAtoms(),mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "%6d %-20s MMFF94 parameters\n",mol.NumAtoms(),mol.GetTitle());
ofs << buffer;
ttab.SetFromType("INT");
OBAtom *atom;
string str,str1;
int atomType;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
atomType = 0; // Something is very wrong if this doesn't get set below
if (mm2Types) {
ttab.SetToType("MM2");
ttab.Translate(str1,str);
atomType = atoi((char*)str1.c_str());
}
if (mmffTypes) {
// Override the MM2 typing
OBPairData *type = (OpenBabel::OBPairData*)atom->GetData("FFAtomType");
if (type) {
str1 = type->GetValue().c_str();
atomType = atoi((char*)str1.c_str());
}
}
if (mm3Types) {
// convert to integer for MM3 typing
atomType = SetMM3Type(atom);
}
if (classTypes) {
// Atom classes are set by the user, so use those
OBGenericData *data = atom->GetData("Atom Class");
if (data) {
OBPairInteger* acdata = dynamic_cast<OBPairInteger*>(data); // Could replace with C-style cast if willing to live dangerously
if (acdata) {
int ac = acdata->GetGenericValue();
if (ac >= 0)
atomType = ac;
}
}
}
snprintf(buffer, BUFF_SIZE, "%6d %2s %12.6f%12.6f%12.6f %5d",
i,
OBElements::GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atomType);
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
snprintf(buffer, BUFF_SIZE, "%6d", (bond->GetNbrAtom(atom))->GetIdx());
ofs << buffer;
}
ofs << endl;
}
return(true);
}
bool TinkerFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
bool mmffTypes = pConv->IsOption("m",OBConversion::OUTOPTIONS) != NULL;
bool mm3Types = pConv->IsOption("3",OBConversion::OUTOPTIONS) != NULL;
unsigned int i;
char buffer[BUFF_SIZE];
OBBond *bond;
vector<OBBond*>::iterator j;
// Before we try output of MMFF94 atom types, check if it works
OBForceField *ff = OpenBabel::OBForceField::FindForceField("MMFF94");
if (mmffTypes && ff && ff->Setup(mol))
mmffTypes = ff->GetAtomTypes(mol);
else
mmffTypes = false; // either the force field isn't available, or it doesn't work
if (!mmffTypes && !mm3Types)
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM2 parameters\n",mol.NumAtoms(),mol.GetTitle());
else if (mm3Types)
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM3 parameters\n",mol.NumAtoms(),mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "%6d %-20s MMFF94 parameters\n",mol.NumAtoms(),mol.GetTitle());
ofs << buffer;
ttab.SetFromType("INT");
OBAtom *atom;
string str,str1;
int atomType;
for(i = 1; i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.SetToType("MM2");
ttab.Translate(str1,str);
if (mmffTypes && !mm3Types) {
// Override the MM2 typing
OBPairData *type = (OpenBabel::OBPairData*)atom->GetData("FFAtomType");
if (type)
str1 = type->GetValue().c_str();
}
// convert to integer for MM3 typing
atomType = atoi((char*)str1.c_str());
if (mm3Types) {
atomType = SetMM3Type(atom);
}
snprintf(buffer, BUFF_SIZE, "%6d %2s %12.6f%12.6f%12.6f %5d",
i,
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atomType);
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
snprintf(buffer, BUFF_SIZE, "%6d", (bond->GetNbrAtom(atom))->GetIdx());
ofs << buffer;
}
ofs << endl;
}
return(true);
}
