| 173 |
|
vector<int>& fragment) { |
| 174 |
|
|
| 175 |
|
OBMol* newMol = new OBMol(); |
| 176 |
– |
OBChainsParser* chainParser = new OBChainsParser(); |
| 177 |
– |
bool molIsWater = false; |
| 176 |
|
|
| 177 |
|
newMol->ReserveAtoms(fragment.size()); |
| 178 |
|
newMol->BeginModify(); |
| 198 |
|
const int BUFFLEN = 1024; |
| 199 |
|
char buffer[BUFFLEN]; |
| 200 |
|
string str, str1, str2, str3; |
| 203 |
– |
OBAtom *a, *b, *c, *d; |
| 201 |
|
bool molIsWater = false; |
| 202 |
|
OBResidue *r; |
| 206 |
– |
int resKey, myserial; |
| 207 |
– |
char type_name[10]; |
| 208 |
– |
char *element_name; |
| 209 |
– |
int res_num; |
| 210 |
– |
OBChainsParser* chainParser = new OBChainsParser(); |
| 203 |
|
double min_x, max_x, min_y, max_y, min_z, max_z; /* Edges of bounding box */ |
| 204 |
|
|
| 205 |
< |
os << "<OpenMD version=1>" << endl; |
| 205 |
> |
os << "<OpenMD version=2>" << endl; |
| 206 |
|
os << " <MetaData>" << endl << endl; |
| 207 |
|
|
| 208 |
|
for(i = 0; i < mols.size(); ++i) { |
| 209 |
|
OBMol* pmol = mols[i]; |
| 210 |
|
map<OBAtom*, int> atomMap; |
| 211 |
|
|
| 220 |
– |
|
| 221 |
– |
//chainParser->PerceiveChains(*pmol, false); |
| 212 |
|
molIsWater = false; |
| 213 |
|
FOR_RESIDUES_OF_MOL(residue, *pmol) { |
| 214 |
|
if (residue->GetName().compare("HOH") == 0) { |
| 223 |
|
} else { |
| 224 |
|
|
| 225 |
|
os << "molecule {\n"; |
| 226 |
< |
sprintf(buffer, "%d", i); |
| 226 |
> |
sprintf(buffer, "%u", i); |
| 227 |
|
os << " name = \"" << molPrefix << buffer << "\";\n"; |
| 228 |
|
|
| 229 |
|
int ai = 0; |
| 387 |
|
if (std::string(pmol->GetTitle()).compare("HOH") == 0) { |
| 388 |
|
os << " type = " << "\"HOH\"" << "; // change to appropriate water model" << endl; |
| 389 |
|
} else { |
| 390 |
< |
sprintf(buffer, "%d", i); |
| 390 |
> |
sprintf(buffer, "%u", i); |
| 391 |
|
os << " type = " << molPrefix << buffer << ";" << endl; |
| 392 |
|
} |
| 393 |
|
os << " nMol = " << numMols[i]<< ";" << endl; |
