| 1 |
gezelter |
1210 |
/********************************************************************** |
| 2 |
|
|
Copyright (C) 2000 by OpenEye Scientific Software, Inc. |
| 3 |
|
|
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
| 4 |
|
|
Some portions Copyright (C) 2004 by Chris Morley |
| 5 |
|
|
Some portions Copyright (C) 2008 by J. Daniel Gezelter |
| 6 |
|
|
|
| 7 |
|
|
This program is free software; you can redistribute it and/or modify |
| 8 |
|
|
it under the terms of the GNU General Public License as published by |
| 9 |
|
|
the Free Software Foundation version 2 of the License. |
| 10 |
|
|
|
| 11 |
|
|
This program is distributed in the hope that it will be useful, |
| 12 |
|
|
but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 13 |
|
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 14 |
|
|
GNU General Public License for more details. |
| 15 |
|
|
***********************************************************************/ |
| 16 |
|
|
|
| 17 |
|
|
#include <openbabel/babelconfig.h> |
| 18 |
|
|
#include <openbabel/obmolecformat.h> |
| 19 |
gezelter |
1269 |
#include <openbabel/obiter.h> |
| 20 |
|
|
#include <openbabel/mol.h> |
| 21 |
|
|
#include <openbabel/chains.h> |
| 22 |
gezelter |
1210 |
#include <fstream> |
| 23 |
|
|
|
| 24 |
gezelter |
1269 |
#include "utils/StringUtils.hpp" |
| 25 |
|
|
|
| 26 |
gezelter |
1210 |
using namespace std; |
| 27 |
|
|
namespace OpenBabel |
| 28 |
|
|
{ |
| 29 |
|
|
|
| 30 |
|
|
class OOPSEFormat : public OBMoleculeFormat |
| 31 |
|
|
{ |
| 32 |
|
|
public: |
| 33 |
|
|
//Register this format type ID |
| 34 |
|
|
OOPSEFormat() |
| 35 |
|
|
{ |
| 36 |
|
|
OBConversion::RegisterFormat("md",this); |
| 37 |
|
|
} |
| 38 |
|
|
|
| 39 |
|
|
virtual const char* Description() //required |
| 40 |
|
|
{ |
| 41 |
|
|
return |
| 42 |
|
|
"OOPSE combined meta-data / cartesian coordinates format\nNo comments yet\n"; |
| 43 |
|
|
}; |
| 44 |
|
|
|
| 45 |
|
|
virtual const char* SpecificationURL() |
| 46 |
|
|
{return "http://www.oopse.org";}; //optional |
| 47 |
|
|
|
| 48 |
|
|
virtual const char* GetMIMEType() |
| 49 |
|
|
{return "chemical/x-md"; }; |
| 50 |
|
|
|
| 51 |
|
|
virtual unsigned int Flags() |
| 52 |
|
|
{ |
| 53 |
|
|
return NOTREADABLE | WRITEONEONLY; |
| 54 |
|
|
} |
| 55 |
|
|
|
| 56 |
|
|
//*** This section identical for most OBMol conversions *** |
| 57 |
|
|
//////////////////////////////////////////////////// |
| 58 |
|
|
/// The "API" interface functions |
| 59 |
|
|
virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv); |
| 60 |
|
|
|
| 61 |
|
|
private: |
| 62 |
|
|
bool AreSameFragments(OBMol& mol, vector<int>& frag1, vector<int>& frag2); |
| 63 |
gezelter |
1269 |
//void findAngles(OBMol& mol); |
| 64 |
gezelter |
1210 |
OBMol* createMolFromFragment(OBMol& mol, vector<int>& fragment); |
| 65 |
|
|
void WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os, OBMol& mol, vector<int>& indices); |
| 66 |
|
|
}; |
| 67 |
|
|
|
| 68 |
|
|
//Make an instance of the format class |
| 69 |
|
|
OOPSEFormat theOOPSEFormat; |
| 70 |
|
|
|
| 71 |
|
|
///////////////////////////////////////////////////////////////// |
| 72 |
|
|
|
| 73 |
|
|
|
| 74 |
|
|
bool OOPSEFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
| 75 |
|
|
{ |
| 76 |
|
|
OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
| 77 |
|
|
if(pmol==NULL) |
| 78 |
|
|
return false; |
| 79 |
|
|
|
| 80 |
|
|
vector<vector<int> > fragmentLists; |
| 81 |
|
|
pmol->ContigFragList(fragmentLists); |
| 82 |
|
|
OBBitVec unused; |
| 83 |
|
|
vector<bool> used(fragmentLists.size(), 0); |
| 84 |
|
|
vector<vector<int> > molecules; |
| 85 |
|
|
vector<int> indices; |
| 86 |
|
|
for(int i =0; i < used.size(); ++i) { |
| 87 |
|
|
if (used[i]) |
| 88 |
|
|
{ |
| 89 |
|
|
continue; |
| 90 |
|
|
} |
| 91 |
|
|
used[i] = true; |
| 92 |
|
|
vector<int> sameMolTypes; |
| 93 |
|
|
sameMolTypes.push_back(i); |
| 94 |
|
|
indices.insert(indices.end(), fragmentLists[i].begin(), |
| 95 |
|
|
fragmentLists[i].end()); |
| 96 |
|
|
for (int j = i + 1;j < used.size(); ++j) |
| 97 |
|
|
{ |
| 98 |
|
|
if (used[j]) |
| 99 |
|
|
{ |
| 100 |
|
|
continue; |
| 101 |
|
|
} |
| 102 |
|
|
|
| 103 |
|
|
if (AreSameFragments(*pmol, fragmentLists[i], fragmentLists[j])) |
| 104 |
|
|
{ |
| 105 |
|
|
sameMolTypes.push_back(j); |
| 106 |
|
|
indices.insert(indices.end(), fragmentLists[j].begin(), |
| 107 |
|
|
fragmentLists[j].end()); |
| 108 |
|
|
used[j]=true; |
| 109 |
|
|
} |
| 110 |
|
|
} |
| 111 |
|
|
molecules.push_back(sameMolTypes); |
| 112 |
|
|
|
| 113 |
|
|
} |
| 114 |
|
|
|
| 115 |
|
|
// |
| 116 |
|
|
vector<OBMol*> mdMols; |
| 117 |
|
|
vector<int> numMols; |
| 118 |
|
|
for(vector<vector<int> >::iterator i = molecules.begin(); |
| 119 |
|
|
i != molecules.end(); ++i) |
| 120 |
|
|
{ |
| 121 |
|
|
mdMols.push_back(createMolFromFragment(*pmol, |
| 122 |
|
|
fragmentLists[i->front()])); |
| 123 |
|
|
numMols.push_back((*i).size()); |
| 124 |
|
|
} |
| 125 |
|
|
|
| 126 |
|
|
string OutputFileName = pConv->GetInFilename(); |
| 127 |
gezelter |
1269 |
size_t pos = OutputFileName.rfind("."); |
| 128 |
|
|
if(pos!=string::npos) |
| 129 |
|
|
OutputFileName = OutputFileName.substr(0, pos) + ".md"; |
| 130 |
|
|
else |
| 131 |
gezelter |
1210 |
OutputFileName += ".md"; |
| 132 |
gezelter |
1269 |
|
| 133 |
gezelter |
1210 |
ofstream ofs(OutputFileName.c_str()); |
| 134 |
|
|
if(!ofs) |
| 135 |
|
|
{ |
| 136 |
|
|
cerr << "Cannot write to " << OutputFileName <<endl; |
| 137 |
|
|
return false; |
| 138 |
|
|
} |
| 139 |
|
|
|
| 140 |
|
|
WriteMDFile(mdMols, numMols, ofs, *pmol, indices); |
| 141 |
|
|
|
| 142 |
|
|
for(vector<OBMol*>::iterator i = mdMols.begin(); i != mdMols.end(); ++i) |
| 143 |
|
|
{ |
| 144 |
|
|
delete *i; |
| 145 |
|
|
} |
| 146 |
|
|
|
| 147 |
|
|
// |
| 148 |
|
|
|
| 149 |
|
|
return(true); |
| 150 |
|
|
} |
| 151 |
|
|
|
| 152 |
|
|
bool OOPSEFormat::AreSameFragments(OBMol& mol, vector<int>& frag1, |
| 153 |
|
|
vector<int>& frag2) |
| 154 |
|
|
{ |
| 155 |
|
|
if (frag1.size() != frag2.size()) |
| 156 |
|
|
{ |
| 157 |
|
|
return false; |
| 158 |
|
|
} |
| 159 |
|
|
|
| 160 |
|
|
//exact graph matching is a NP complete problem |
| 161 |
|
|
/** @todo using sparse matrix to store the connectivities*/ |
| 162 |
|
|
for (unsigned int i =0 ; i < frag1.size(); ++i) |
| 163 |
|
|
{ |
| 164 |
|
|
OBAtom* atom1 = mol.GetAtom(frag1[i]); |
| 165 |
|
|
OBAtom* atom2 = mol.GetAtom(frag2[i]); |
| 166 |
|
|
|
| 167 |
|
|
if (atom1->GetAtomicNum() != atom2->GetAtomicNum()) |
| 168 |
|
|
{ |
| 169 |
|
|
return false; |
| 170 |
|
|
} |
| 171 |
|
|
} |
| 172 |
|
|
return true; |
| 173 |
|
|
} |
| 174 |
|
|
|
| 175 |
|
|
struct SameAngle |
| 176 |
|
|
{ |
| 177 |
|
|
bool operator()(const triple<OBAtom*,OBAtom*,OBAtom*> t1, |
| 178 |
|
|
const triple<OBAtom*,OBAtom*,OBAtom*> t2) const |
| 179 |
|
|
{ |
| 180 |
|
|
return (t1.second == t2.second) && ( (t1.first == t2.first && t1.third == t2.third) || (t1.first == t2.third && t1.third == t2.first)); |
| 181 |
|
|
} |
| 182 |
|
|
}; |
| 183 |
gezelter |
1269 |
|
| 184 |
|
|
/* |
| 185 |
|
|
void OOPSEFormat::findAngles(OBMol& mol) { |
| 186 |
|
|
|
| 187 |
gezelter |
1210 |
//if already has data return |
| 188 |
|
|
if(mol.HasData(OBGenericDataType::AngleData)) |
| 189 |
|
|
return; |
| 190 |
|
|
|
| 191 |
|
|
vector<OBEdgeBase*>::iterator bi1,bi2; |
| 192 |
|
|
OBBond* bond; |
| 193 |
|
|
OBAtom *a,*b,*c; |
| 194 |
|
|
|
| 195 |
|
|
set<triple<OBAtom*,OBAtom*,OBAtom*>, SameAngle> uniqueAngles; |
| 196 |
|
|
//loop through all bonds generating torsions |
| 197 |
|
|
for(bond = mol.BeginBond(bi1);bond;bond = mol.NextBond(bi1)) |
| 198 |
|
|
{ |
| 199 |
|
|
b = bond->GetBeginAtom(); |
| 200 |
|
|
c = bond->GetEndAtom(); |
| 201 |
|
|
if(b->IsHydrogen()) |
| 202 |
|
|
continue; |
| 203 |
|
|
|
| 204 |
|
|
for(a = b->BeginNbrAtom(bi2);a;a = b->NextNbrAtom(bi2)) |
| 205 |
|
|
{ |
| 206 |
|
|
if(a == c) |
| 207 |
|
|
continue; |
| 208 |
|
|
|
| 209 |
|
|
uniqueAngles.insert(triple<OBAtom*,OBAtom*,OBAtom*>(a, b, c)); |
| 210 |
|
|
} |
| 211 |
|
|
} |
| 212 |
|
|
|
| 213 |
|
|
//get new data and attach it to molecule |
| 214 |
|
|
OBAngleData *angles = new OBAngleData; |
| 215 |
|
|
mol.SetData(angles); |
| 216 |
|
|
set<triple<OBAtom*,OBAtom*,OBAtom*>, SameAngle>::iterator i; |
| 217 |
|
|
|
| 218 |
|
|
for (i = uniqueAngles.begin(); i != uniqueAngles.end(); ++i) { |
| 219 |
|
|
OBAngle angle; |
| 220 |
|
|
angle.SetAtoms(i->first, i->second, i->second); |
| 221 |
|
|
angles->SetData(angle); |
| 222 |
|
|
} |
| 223 |
gezelter |
1269 |
|
| 224 |
gezelter |
1210 |
} |
| 225 |
gezelter |
1269 |
*/ |
| 226 |
gezelter |
1210 |
|
| 227 |
|
|
OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol, vector<int>& fragment) { |
| 228 |
|
|
|
| 229 |
|
|
OBMol* newMol = new OBMol(); |
| 230 |
gezelter |
1269 |
OBChainsParser* chainParser = new OBChainsParser(); |
| 231 |
gezelter |
1210 |
newMol->ReserveAtoms(fragment.size()); |
| 232 |
|
|
newMol->BeginModify(); |
| 233 |
|
|
for(vector<int>::iterator i = fragment.begin(); i != fragment.end(); ++i) { |
| 234 |
|
|
OBAtom* newAtom = newMol->NewAtom(); |
| 235 |
|
|
*newAtom = *mol.GetAtom(*i); |
| 236 |
|
|
} |
| 237 |
|
|
newMol->EndModify(); |
| 238 |
|
|
newMol->ConnectTheDots(); |
| 239 |
gezelter |
1269 |
newMol->PerceiveBondOrders(); |
| 240 |
|
|
newMol->FindAngles(); |
| 241 |
gezelter |
1210 |
newMol->FindTorsions(); |
| 242 |
gezelter |
1269 |
//chainParser->PerceiveChains(*newMol, false); |
| 243 |
|
|
|
| 244 |
gezelter |
1210 |
return newMol; |
| 245 |
|
|
} |
| 246 |
|
|
|
| 247 |
|
|
void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os, OBMol& mol, vector<int>& indices) { |
| 248 |
|
|
std::string indentLevel1(" "); |
| 249 |
|
|
std::string indentLevel2(" "); |
| 250 |
|
|
std::string molPrefix("MolName"); |
| 251 |
gezelter |
1269 |
std::string resName; |
| 252 |
gezelter |
1210 |
unsigned int i; |
| 253 |
|
|
const int BUFFLEN = 1024; |
| 254 |
|
|
char buffer[BUFFLEN]; |
| 255 |
|
|
string str, str1; |
| 256 |
gezelter |
1269 |
OBAtom *a, *b, *c, *d; |
| 257 |
|
|
OBChainsParser* chainParser = new OBChainsParser(); |
| 258 |
|
|
OBResidue *r; |
| 259 |
|
|
int resKey; |
| 260 |
|
|
char type_name[10]; |
| 261 |
|
|
char *element_name; |
| 262 |
|
|
int res_num; |
| 263 |
gezelter |
1210 |
|
| 264 |
gezelter |
1269 |
std::cerr << "yo\n"; |
| 265 |
gezelter |
1210 |
os << "<OOPSE version=4>" << endl; |
| 266 |
|
|
os << " <MetaData>" << endl << endl; |
| 267 |
|
|
|
| 268 |
|
|
for(i = 0; i < mols.size(); ++i) { |
| 269 |
|
|
OBMol* pmol = mols[i]; |
| 270 |
gezelter |
1269 |
std::cerr << "yo1\n"; |
| 271 |
gezelter |
1210 |
pmol->ConnectTheDots(); |
| 272 |
|
|
pmol->PerceiveBondOrders(); |
| 273 |
gezelter |
1269 |
chainParser->PerceiveChains(*pmol, false); |
| 274 |
gezelter |
1210 |
//pmol->FindSSSR(); |
| 275 |
|
|
//pmol->SetAromaticPerceived(); |
| 276 |
|
|
//pmol->Kekulize(); |
| 277 |
|
|
|
| 278 |
|
|
map<OBAtom*, int> atomMap; |
| 279 |
|
|
os << "molecule {\n"; |
| 280 |
|
|
sprintf(buffer, "%d", i); |
| 281 |
|
|
os << indentLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n"; |
| 282 |
|
|
|
| 283 |
gezelter |
1269 |
|
| 284 |
gezelter |
1210 |
//atom |
| 285 |
gezelter |
1269 |
|
| 286 |
gezelter |
1210 |
int ai = 0; |
| 287 |
gezelter |
1269 |
FOR_RESIDUES_OF_MOL(res, *pmol) { |
| 288 |
|
|
|
| 289 |
|
|
std::cerr << "found residue" << res->GetName() << "\n"; |
| 290 |
|
|
} |
| 291 |
|
|
|
| 292 |
|
|
// FOR_RESIDUES_OF_MOL(res, *pmol) { |
| 293 |
|
|
|
| 294 |
|
|
// resName = res->GetName(); |
| 295 |
|
|
// resKey = res->GetResKey(); |
| 296 |
|
|
|
| 297 |
|
|
|
| 298 |
|
|
|
| 299 |
|
|
// std::cerr << "found residue " << resName << "\n"; |
| 300 |
|
|
// std::cerr << " num = " << res->GetNum() << "\n"; |
| 301 |
|
|
// std::cerr << " numAtoms = " << res->GetNumAtoms() << "\n"; |
| 302 |
|
|
// std::cerr << " num = " << res->GetNum() << "\n"; |
| 303 |
|
|
// std::cerr << " chain = " << res->GetChain() << "\n"; |
| 304 |
|
|
// std::cerr << " chainnum = " << res->GetChainNum() << "\n"; |
| 305 |
|
|
// std::cerr << " idx = " << res->GetIdx() << "\n"; |
| 306 |
|
|
// std::cerr << " key = " << res->GetResKey() << "\n"; |
| 307 |
|
|
|
| 308 |
|
|
|
| 309 |
|
|
// FOR_ATOMS_OF_RESIDUE(atom, &*res) { |
| 310 |
|
|
// str = atom->GetType(); |
| 311 |
|
|
// ttab.SetFromType("INT"); |
| 312 |
|
|
// ttab.SetToType("INT"); |
| 313 |
|
|
// ttab.Translate(str1,str); |
| 314 |
|
|
// os << indentLevel1 << "atom[" << ai << "] {\n"; |
| 315 |
|
|
// os << indentLevel2 << "type = " << "\"" << resName << "-" << str1 << "\"" << ";\n"; |
| 316 |
|
|
// os << indentLevel1 << "}\n"; |
| 317 |
|
|
// atomMap[&(*atom)] = ai++; |
| 318 |
|
|
// } |
| 319 |
|
|
// os << "\n"; |
| 320 |
|
|
|
| 321 |
|
|
// } |
| 322 |
|
|
|
| 323 |
|
|
ai = 0; |
| 324 |
gezelter |
1210 |
FOR_ATOMS_OF_MOL(atom, *pmol ) { |
| 325 |
|
|
str = atom->GetType(); |
| 326 |
gezelter |
1269 |
r = atom->GetResidue(); |
| 327 |
|
|
|
| 328 |
|
|
if (r == NULL) |
| 329 |
|
|
resName = "NULL"; |
| 330 |
|
|
else |
| 331 |
|
|
resName = r->GetName(); |
| 332 |
|
|
|
| 333 |
|
|
if (resName.compare("NULL") ==0 || resName.compare("LIG") == 0 || resName.compare("UNK") == 0) { |
| 334 |
|
|
// Either couldn't find a residue at all or couldn't find a reasonable |
| 335 |
|
|
// residue name to use. We'll punt and use OpenBabel's internal atom typing: |
| 336 |
|
|
ttab.SetFromType("INT"); |
| 337 |
|
|
ttab.SetToType("INT"); |
| 338 |
|
|
ttab.Translate(str1,str); |
| 339 |
|
|
} else { |
| 340 |
|
|
|
| 341 |
|
|
|
| 342 |
|
|
if (resName.compare("HOH") == 0) { |
| 343 |
|
|
// HOH is a special residue name for water, and the standard atom types |
| 344 |
|
|
// are OW and HW, so just append W to the string for the atom type: |
| 345 |
|
|
ttab.SetFromType("INT"); |
| 346 |
|
|
ttab.SetToType("XYZ"); |
| 347 |
|
|
ttab.Translate(str1,str); |
| 348 |
|
|
str1 += "W"; |
| 349 |
|
|
} else { |
| 350 |
|
|
|
| 351 |
|
|
std::cerr << "found residue " << resName << "\n"; |
| 352 |
|
|
|
| 353 |
|
|
// If we know what residue we've got, the specific atom name can |
| 354 |
|
|
// be used to help specify partial charges. |
| 355 |
|
|
|
| 356 |
|
|
str = r->GetAtomID(&*atom); |
| 357 |
|
|
size_t startpos = str.find_first_not_of(" "); |
| 358 |
|
|
size_t endpos = str.find_last_not_of(" "); |
| 359 |
|
|
str = str.substr( startpos, endpos-startpos+1 ); |
| 360 |
|
|
str1 = resName + "-" + str; |
| 361 |
|
|
} |
| 362 |
|
|
|
| 363 |
|
|
} |
| 364 |
|
|
|
| 365 |
|
|
// os << indentLevel1 << "atom[" << ai << "] {\n"; |
| 366 |
|
|
// os << indentLevel2 << "type = " << "\"" << str1 << "\"" << ";\n"; |
| 367 |
|
|
// os << indentLevel1 << "}\n"; |
| 368 |
|
|
os << "atom[" << ai << "] { "; |
| 369 |
|
|
os << "type = " << "\"" << str1 << "\"" << "; "; |
| 370 |
|
|
os << "}\n"; |
| 371 |
gezelter |
1210 |
atomMap[&(*atom)] = ai++; |
| 372 |
|
|
} |
| 373 |
|
|
os << "\n"; |
| 374 |
|
|
|
| 375 |
|
|
//bond |
| 376 |
|
|
FOR_BONDS_OF_MOL(bond, *pmol ) { |
| 377 |
gezelter |
1269 |
// os << indentLevel1 << "bond {\n"; |
| 378 |
|
|
// os << indentLevel2 << "members(" << atomMap[bond->GetBeginAtom()] << ", " << atomMap[bond->GetEndAtom()] << ");\n"; |
| 379 |
|
|
// os << indentLevel1 << "}\n"; |
| 380 |
|
|
os << "bond { "; |
| 381 |
|
|
os << "members(" << atomMap[bond->GetBeginAtom()] << ", " << atomMap[bond->GetEndAtom()] << "); "; |
| 382 |
|
|
os << "}\n"; |
| 383 |
|
|
} |
| 384 |
|
|
|
| 385 |
|
|
FOR_ANGLES_OF_MOL(angle, *pmol) { |
| 386 |
|
|
|
| 387 |
|
|
// OpenBabel's getAtoms returns the 3 atom pointer for the |
| 388 |
|
|
// angle with the vertex first. These need to be reordered |
| 389 |
|
|
// for vertex-second ordering for OOPSE. |
| 390 |
|
|
|
| 391 |
|
|
b = pmol->GetAtom((*angle)[0] + 1); |
| 392 |
|
|
a = pmol->GetAtom((*angle)[1] + 1); |
| 393 |
|
|
c = pmol->GetAtom((*angle)[2] + 1); |
| 394 |
|
|
|
| 395 |
|
|
// os << indentLevel1 << "bend {\n"; |
| 396 |
|
|
// os << indentLevel2 << "members(" << atomMap[a] << ", " << atomMap[b] << ", " << atomMap[c] << ");\n"; |
| 397 |
|
|
// os << indentLevel1 << "}\n"; |
| 398 |
|
|
os << "bend { "; |
| 399 |
|
|
os << "members(" << atomMap[a] << ", " << atomMap[b] << ", " << atomMap[c] << "); "; |
| 400 |
|
|
os << "}\n"; |
| 401 |
|
|
} |
| 402 |
|
|
|
| 403 |
|
|
FOR_TORSIONS_OF_MOL(torsion, *pmol) { |
| 404 |
|
|
|
| 405 |
|
|
// OpenBabel's getAtoms returns the 3 atom pointer for the |
| 406 |
|
|
// angle with the vertex first. These need to be reordered |
| 407 |
|
|
// for vertex-second ordering for OOPSE. |
| 408 |
|
|
|
| 409 |
|
|
a = pmol->GetAtom((*torsion)[0] + 1); |
| 410 |
|
|
b = pmol->GetAtom((*torsion)[1] + 1); |
| 411 |
|
|
c = pmol->GetAtom((*torsion)[2] + 1); |
| 412 |
|
|
d = pmol->GetAtom((*torsion)[3] + 1); |
| 413 |
|
|
|
| 414 |
|
|
// os << indentLevel1 << "torsion {\n"; |
| 415 |
|
|
// os << indentLevel2 << "members(" << atomMap[a] << ", " << atomMap[b] << ", " << atomMap[c] << ", " << atomMap[d] << ");\n"; |
| 416 |
|
|
// os << indentLevel1 << "}\n"; |
| 417 |
|
|
|
| 418 |
|
|
os << "torsion { "; |
| 419 |
|
|
os << "members(" << atomMap[a] << ", " << atomMap[b] << ", " << atomMap[c] << ", " << atomMap[d] << "); "; |
| 420 |
|
|
os << "}\n"; |
| 421 |
|
|
} |
| 422 |
|
|
|
| 423 |
gezelter |
1210 |
/* |
| 424 |
|
|
//bend |
| 425 |
|
|
OBGenericData* pGenericData = pmol->GetData(OBGenericDataType::AngleData); |
| 426 |
|
|
OBAngleData* pAngleData = dynamic_cast<OBAngleData*>(pGenericData); |
| 427 |
|
|
vector<OBAngle> angles = pAngleData->GetData(); |
| 428 |
|
|
|
| 429 |
|
|
os << indentLevel1 << "nBends = " << angles.size() << ";\n"; |
| 430 |
|
|
int bendIndex = 0; |
| 431 |
|
|
for (vector<OBAngle>::iterator ti = angles.begin(); ti != angles.end(); ++ti) |
| 432 |
|
|
{ |
| 433 |
|
|
triple<OBAtom*, OBAtom*, OBAtom*> bendAtoms = ti->getAtoms(); |
| 434 |
|
|
os << indentLevel1 << "bend[" << bendIndex++ << "] {\n"; |
| 435 |
|
|
os << indentLevel2 << "member(" << atomMap[bendAtoms.first] << ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n"; |
| 436 |
|
|
os << indentLevel1 << "}\n"; |
| 437 |
|
|
} |
| 438 |
|
|
|
| 439 |
|
|
//torsion |
| 440 |
|
|
pGenericData = pmol->GetData(OBGenericDataType::TorsionData); |
| 441 |
|
|
OBTorsionData* pTorsionData = dynamic_cast<OBTorsionData*>(pGenericData); |
| 442 |
|
|
vector<OBTorsion> torsions = pTorsionData->GetData(); |
| 443 |
|
|
vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > torsionArray; |
| 444 |
|
|
for (vector<OBTorsion>::iterator ti = torsions.begin(); ti != torsions.end(); ++ti) |
| 445 |
|
|
{ |
| 446 |
|
|
vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > tmpTorsions = ti->getTorsions(); |
| 447 |
|
|
torsionArray.insert(torsionArray.end(), tmpTorsions.begin(), tmpTorsions.end()); |
| 448 |
|
|
} |
| 449 |
|
|
|
| 450 |
|
|
os << indentLevel1 << "nTorsions = " << torsionArray.size() << ";\n"; |
| 451 |
|
|
int torsionIndex = 0; |
| 452 |
|
|
for (vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> >::iterator ti = torsionArray.begin(); ti != torsionArray.end(); ++ti) |
| 453 |
|
|
{ |
| 454 |
|
|
os << indentLevel1 << "torsion[" << torsionIndex++ << "] {\n"; |
| 455 |
|
|
os << indentLevel2 << "member(" << atomMap[ti->first] << ", " << atomMap[ti->second] <<", " << atomMap[ti->third] <<", " << atomMap[ti->forth] << ");\n"; |
| 456 |
|
|
os << indentLevel1 << "}\n"; |
| 457 |
|
|
} |
| 458 |
|
|
*/ |
| 459 |
|
|
os << "}" << endl; |
| 460 |
|
|
os << endl; |
| 461 |
|
|
|
| 462 |
|
|
} |
| 463 |
|
|
|
| 464 |
|
|
os << endl; |
| 465 |
|
|
|
| 466 |
|
|
|
| 467 |
|
|
for(i=0; i < mols.size(); ++i) { |
| 468 |
|
|
os << "component{" << endl; |
| 469 |
|
|
sprintf(buffer, "%d", i); |
| 470 |
|
|
os << indentLevel1 << "type = " << molPrefix << buffer << ";" << endl; |
| 471 |
|
|
os << indentLevel1 << "nMol = " << numMols[i]<< ";" << endl; |
| 472 |
|
|
os << "}" << endl; |
| 473 |
|
|
} |
| 474 |
|
|
|
| 475 |
|
|
os << " </MetaData>" << endl; |
| 476 |
|
|
os << " <Snapshot>" << endl; |
| 477 |
|
|
os << " <FrameData>" << endl; |
| 478 |
|
|
|
| 479 |
|
|
sprintf(buffer, " Time: %.10g", 0.0); |
| 480 |
|
|
|
| 481 |
|
|
os << buffer << endl; |
| 482 |
|
|
|
| 483 |
|
|
sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}", 100.0, 0.0, 0.0, 0.0, 100.0, 0.0, 0.0, 0.0, 100.0); |
| 484 |
|
|
|
| 485 |
|
|
os << buffer << endl; |
| 486 |
|
|
os << " </FrameData>" << endl; |
| 487 |
|
|
os << " <StuntDoubles>" << endl; |
| 488 |
|
|
|
| 489 |
|
|
OBAtom *atom; |
| 490 |
|
|
|
| 491 |
|
|
for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i) { |
| 492 |
|
|
atom = mol.GetAtom(*i); |
| 493 |
|
|
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); |
| 494 |
|
|
os << buffer << endl; |
| 495 |
|
|
} |
| 496 |
|
|
os << " </StuntDoubles>" << endl; |
| 497 |
|
|
os << " </Snapshot>" << endl; |
| 498 |
|
|
os << "</OOPSE>" << endl; |
| 499 |
|
|
} |
| 500 |
|
|
|
| 501 |
|
|
} //namespace OpenBabel |
| 502 |
|
|
|
