| 179 |
|
} |
| 180 |
|
|
| 181 |
|
void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os, OBMol& mol, vector<int>& indices) { |
| 182 |
< |
std::string indentLevel1("\t"); |
| 183 |
< |
std::string indentLevel2("\t\t"); |
| 182 |
> |
std::string indentLevel1(" "); |
| 183 |
> |
std::string indentLevel2(" "); |
| 184 |
|
std::string molPrefix("MolName"); |
| 185 |
|
unsigned int i; |
| 186 |
|
const int BUFFLEN = 1024; |
| 187 |
|
char buffer[BUFFLEN]; |
| 188 |
+ |
string str, str1; |
| 189 |
|
|
| 190 |
|
|
| 191 |
|
os << "<OOPSE version=4>" << endl; |
| 192 |
< |
os << " <MetaData>" << endl; |
| 192 |
> |
os << " <MetaData>" << endl << endl; |
| 193 |
|
|
| 194 |
|
for(i = 0; i < mols.size(); ++i) { |
| 195 |
|
OBMol* pmol = mols[i]; |
| 196 |
+ |
|
| 197 |
+ |
pmol->ConnectTheDots(); |
| 198 |
+ |
pmol->PerceiveBondOrders(); |
| 199 |
+ |
//pmol->FindSSSR(); |
| 200 |
+ |
//pmol->SetAromaticPerceived(); |
| 201 |
+ |
//pmol->Kekulize(); |
| 202 |
+ |
|
| 203 |
|
map<OBAtom*, int> atomMap; |
| 204 |
|
os << "molecule {\n"; |
| 205 |
|
sprintf(buffer, "%d", i); |
| 206 |
|
os << indentLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n"; |
| 207 |
< |
|
| 200 |
< |
|
| 207 |
> |
|
| 208 |
|
//atom |
| 209 |
|
int ai = 0; |
| 210 |
|
FOR_ATOMS_OF_MOL(atom, *pmol ) { |
| 211 |
+ |
str = atom->GetType(); |
| 212 |
+ |
ttab.SetFromType("INT"); |
| 213 |
+ |
ttab.SetToType("INT"); |
| 214 |
+ |
ttab.Translate(str1,str); |
| 215 |
|
os << indentLevel1 << "atom[" << ai << "] {\n"; |
| 216 |
< |
os << indentLevel2 << "type = " << "\"" << etab.GetSymbol(atom->GetAtomicNum()) << "\"" << ";\n"; |
| 216 |
> |
// os << indentLevel2 << "type = " << "\"" << etab.GetSymbol(atom->GetAtomicNum()) << "\"" << ";\n"; |
| 217 |
> |
os << indentLevel2 << "type = " << "\"" << str1 << "\"" << ";\n"; |
| 218 |
|
os << indentLevel1 << "}\n"; |
| 219 |
|
atomMap[&(*atom)] = ai++; |
| 220 |
|
} |
| 268 |
|
} |
| 269 |
|
|
| 270 |
|
os << endl; |
| 271 |
< |
os << "nComponents = " << mols.size() << ";" << endl; |
| 271 |
> |
|
| 272 |
|
|
| 273 |
|
for(i=0; i < mols.size(); ++i) { |
| 274 |
|
os << "component{" << endl; |
| 275 |
|
sprintf(buffer, "%d", i); |
| 276 |
< |
os << "type = " << molPrefix << buffer << ";\n"; |
| 277 |
< |
os << "nMol = " << numMols[i]<< ";\n"; |
| 278 |
< |
os << "}\n"; |
| 276 |
> |
os << indentLevel1 << "type = " << molPrefix << buffer << ";" << endl; |
| 277 |
> |
os << indentLevel1 << "nMol = " << numMols[i]<< ";" << endl; |
| 278 |
> |
os << "}" << endl; |
| 279 |
|
} |
| 280 |
|
|
| 281 |
|
os << " </MetaData>" << endl; |
| 293 |
|
os << " <StuntDoubles>" << endl; |
| 294 |
|
|
| 295 |
|
OBAtom *atom; |
| 284 |
– |
string str,str1; |
| 296 |
|
|
| 297 |
|
for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i) { |
| 298 |
|
atom = mol.GetAtom(*i); |
| 299 |
< |
sprintf(buffer, "%d\tpv\t%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g", *i - 1, atom->GetX(), atom->GetY(), atom->GetZ(), 0.0, 0.0, 0.0); |
| 299 |
> |
sprintf(buffer, "%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e", *i - 1, "pv", atom->GetX(), atom->GetY(), atom->GetZ(), 0.0, 0.0, 0.0); |
| 300 |
|
os << buffer << endl; |
| 301 |
|
} |
| 302 |
|
os << " </StuntDoubles>" << endl; |
