| 1 |
/********************************************************************** |
| 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 |
|
| 6 |
This program is free software; you can redistribute it and/or modify |
| 7 |
it under the terms of the GNU General Public License as published by |
| 8 |
the Free Software Foundation version 2 of the License. |
| 9 |
|
| 10 |
This program is distributed in the hope that it will be useful, |
| 11 |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 12 |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 13 |
GNU General Public License for more details. |
| 14 |
***********************************************************************/ |
| 15 |
|
| 16 |
#include "oopseformat.hpp" |
| 17 |
namespace OpenBabel |
| 18 |
{ |
| 19 |
|
| 20 |
bool OOPSEFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
| 21 |
{ |
| 22 |
OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
| 23 |
if(pmol==NULL) |
| 24 |
return false; |
| 25 |
|
| 26 |
vector<vector<int> > fragmentLists; |
| 27 |
pmol->ContigFragList(fragmentLists); |
| 28 |
OBBitVec unused; |
| 29 |
vector<bool> used(fragmentLists.size(), 0); |
| 30 |
vector<vector<int> > molecules; |
| 31 |
vector<int> indices; |
| 32 |
for(int i =0; i < used.size(); ++i) { |
| 33 |
if (used[i]) |
| 34 |
{ |
| 35 |
continue; |
| 36 |
} |
| 37 |
used[i] = true; |
| 38 |
vector<int> sameMolTypes; |
| 39 |
sameMolTypes.push_back(i); |
| 40 |
indices.insert(indices.end(), fragmentLists[i].begin(), fragmentLists[i].end()); |
| 41 |
for (int j = i + 1;j < used.size(); ++j) |
| 42 |
{ |
| 43 |
if (used[j]) |
| 44 |
{ |
| 45 |
continue; |
| 46 |
} |
| 47 |
|
| 48 |
if (AreSameFragments(*pmol, fragmentLists[i], fragmentLists[j])) |
| 49 |
{ |
| 50 |
sameMolTypes.push_back(j); |
| 51 |
indices.insert(indices.end(), fragmentLists[j].begin(), fragmentLists[j].end()); |
| 52 |
used[j]=true; |
| 53 |
} |
| 54 |
} |
| 55 |
molecules.push_back(sameMolTypes); |
| 56 |
|
| 57 |
} |
| 58 |
|
| 59 |
// |
| 60 |
vector<OBMol*> mdMols; |
| 61 |
vector<int> numMols; |
| 62 |
for(vector<vector<int> >::iterator i = molecules.begin(); i != molecules.end(); ++i) |
| 63 |
{ |
| 64 |
mdMols.push_back(createMolFromFragment(*pmol, fragmentLists[i->front()])); |
| 65 |
numMols.push_back((*i).size()); |
| 66 |
} |
| 67 |
|
| 68 |
WriteMDFile(mdMols, numMols); |
| 69 |
|
| 70 |
for(vector<OBMol*>::iterator i = mdMols.begin(); i != mdMols.end(); ++i) |
| 71 |
{ |
| 72 |
delete *i; |
| 73 |
} |
| 74 |
|
| 75 |
// |
| 76 |
WriteINFile(*pmol, *pConv->GetOutStream(), indices); |
| 77 |
|
| 78 |
|
| 79 |
|
| 80 |
return(true); |
| 81 |
} |
| 82 |
|
| 83 |
bool OOPSEFormat::AreSameFragments(OBMol& mol, vector<int>& frag1, vector<int>& frag2) |
| 84 |
{ |
| 85 |
if (frag1.size() != frag2.size()) |
| 86 |
{ |
| 87 |
return false; |
| 88 |
} |
| 89 |
|
| 90 |
//exact graph matching is a NP complete problem, |
| 91 |
for (unsigned int i =0 ; i < frag1.size(); ++i) |
| 92 |
{ |
| 93 |
if (strcmp(mol.GetAtom(frag1[i])->GetType(), mol.GetAtom(frag2[i])->GetType()) ) |
| 94 |
{ |
| 95 |
return false; |
| 96 |
} |
| 97 |
} |
| 98 |
return true; |
| 99 |
} |
| 100 |
|
| 101 |
struct SameAngle |
| 102 |
{ |
| 103 |
bool operator()(const triple<OBAtom*,OBAtom*,OBAtom*> t1, const triple<OBAtom*,OBAtom*,OBAtom*> t2) const |
| 104 |
{ |
| 105 |
return (t1.second == t2.second) && ( (t1.first == t2.first && t1.third == t2.third) || (t1.first == t2.third && t1.third == t2.first)); |
| 106 |
} |
| 107 |
}; |
| 108 |
|
| 109 |
void OOPSEFormat::findAngles(OBMol& mol) |
| 110 |
{ |
| 111 |
/* |
| 112 |
//if already has data return |
| 113 |
if(mol.HasData(OBGenericDataType::AngleData)) |
| 114 |
return; |
| 115 |
|
| 116 |
vector<OBEdgeBase*>::iterator bi1,bi2; |
| 117 |
OBBond* bond; |
| 118 |
OBAtom *a,*b,*c; |
| 119 |
|
| 120 |
set<triple<OBAtom*,OBAtom*,OBAtom*>, SameAngle> uniqueAngles; |
| 121 |
//loop through all bonds generating torsions |
| 122 |
for(bond = mol.BeginBond(bi1);bond;bond = mol.NextBond(bi1)) |
| 123 |
{ |
| 124 |
b = bond->GetBeginAtom(); |
| 125 |
c = bond->GetEndAtom(); |
| 126 |
if(b->IsHydrogen()) |
| 127 |
continue; |
| 128 |
|
| 129 |
for(a = b->BeginNbrAtom(bi2);a;a = b->NextNbrAtom(bi2)) |
| 130 |
{ |
| 131 |
if(a == c) |
| 132 |
continue; |
| 133 |
|
| 134 |
uniqueAngles.insert(triple<OBAtom*,OBAtom*,OBAtom*>(a, b, c)); |
| 135 |
} |
| 136 |
} |
| 137 |
|
| 138 |
//get new data and attach it to molecule |
| 139 |
OBAngleData *angles = new OBAngleData; |
| 140 |
mol.SetData(angles); |
| 141 |
set<triple<OBAtom*,OBAtom*,OBAtom*>, SameAngle>::iterator i; |
| 142 |
|
| 143 |
for (i = uniqueAngles.begin(); i != uniqueAngles.end(); ++i) { |
| 144 |
OBAngle angle; |
| 145 |
angle.SetAtoms(i->first, i->second, i->second); |
| 146 |
angles->SetData(angle); |
| 147 |
} |
| 148 |
*/ |
| 149 |
} |
| 150 |
OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol, vector<int>& fragment) |
| 151 |
{ |
| 152 |
OBMol* newMol = new OBMol(); |
| 153 |
newMol->ReserveAtoms(fragment.size()); |
| 154 |
newMol->BeginModify(); |
| 155 |
for(vector<int>::iterator i = fragment.begin(); i != fragment.end(); ++i) |
| 156 |
{ |
| 157 |
OBAtom* newAtom = newMol->NewAtom(); |
| 158 |
*newAtom = *mol.GetAtom(*i); |
| 159 |
} |
| 160 |
newMol->EndModify(); |
| 161 |
newMol->ConnectTheDots(); |
| 162 |
findAngles(*newMol); |
| 163 |
newMol->FindTorsions(); |
| 164 |
return newMol; |
| 165 |
} |
| 166 |
void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols) |
| 167 |
{ |
| 168 |
std::string identLevel1("\t"); |
| 169 |
std::string identLevel2("\t\t"); |
| 170 |
std::string molPrefix("MolName"); |
| 171 |
ostream& ofs = std::cout; |
| 172 |
const int BUFFLEN = 1024; |
| 173 |
char buffer[BUFFLEN]; |
| 174 |
|
| 175 |
for(unsigned int i = 0; i < mols.size(); ++i) |
| 176 |
{ |
| 177 |
OBMol* pmol = mols[i]; |
| 178 |
map<OBAtom*, int> atomMap; |
| 179 |
ofs << "molecule {\n"; |
| 180 |
sprintf(buffer, "%d", i); |
| 181 |
ofs << identLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n"; |
| 182 |
|
| 183 |
|
| 184 |
//atom |
| 185 |
ofs << identLevel1 << "nAtoms = " << pmol->NumAtoms() << ";\n"; |
| 186 |
int ai = 0; |
| 187 |
FOR_ATOMS_OF_MOL(atom, *pmol ) { |
| 188 |
ofs << identLevel1 << "atom[" << ai << "] {\n"; |
| 189 |
ofs << identLevel2 << "type = " << "\"" << atom->GetType() << "\"" << ";\n"; |
| 190 |
ofs << identLevel2 << "position(" << atom->GetX() << ", " << atom->GetY() << ", " << atom->GetZ() << ");\n"; |
| 191 |
ofs << identLevel1 << "}\n"; |
| 192 |
atomMap[&(*atom)] = ai++; |
| 193 |
} |
| 194 |
|
| 195 |
//bond |
| 196 |
ofs << identLevel1 << "nBonds = " << pmol->NumBonds() << ";\n"; |
| 197 |
int bi = 0; |
| 198 |
FOR_BONDS_OF_MOL(bond, *pmol ) { |
| 199 |
ofs << identLevel1 << "bond[" << bi++ << "] {\n"; |
| 200 |
ofs << identLevel2 << "member(" << atomMap[bond->GetBeginAtom()] << ", " << atomMap[bond->GetEndAtom()] << ");\n"; |
| 201 |
ofs << identLevel1 << "}\n"; |
| 202 |
} |
| 203 |
/* |
| 204 |
//bend |
| 205 |
OBGenericData* pGenericData = pmol->GetData(OBGenericDataType::AngleData); |
| 206 |
OBAngleData* pAngleData = dynamic_cast<OBAngleData*>(pGenericData); |
| 207 |
vector<OBAngle> angles = pAngleData->GetData(); |
| 208 |
|
| 209 |
ofs << identLevel1 << "nBends = " << angles.size() << ";\n"; |
| 210 |
int bendIndex = 0; |
| 211 |
for (vector<OBAngle>::iterator ti = angles.begin(); ti != angles.end(); ++ti) |
| 212 |
{ |
| 213 |
triple<OBAtom*, OBAtom*, OBAtom*> bendAtoms = ti->getAtoms(); |
| 214 |
ofs << identLevel1 << "bend[" << bendIndex++ << "] {\n"; |
| 215 |
ofs << identLevel2 << "member(" << atomMap[bendAtoms.first] << ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n"; |
| 216 |
ofs << identLevel1 << "}\n"; |
| 217 |
} |
| 218 |
|
| 219 |
//torsion |
| 220 |
pGenericData = pmol->GetData(OBGenericDataType::TorsionData); |
| 221 |
OBTorsionData* pTorsionData = dynamic_cast<OBTorsionData*>(pGenericData); |
| 222 |
vector<OBTorsion> torsions = pTorsionData->GetData(); |
| 223 |
vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > torsionArray; |
| 224 |
for (vector<OBTorsion>::iterator ti = torsions.begin(); ti != torsions.end(); ++ti) |
| 225 |
{ |
| 226 |
vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > tmpTorsions = ti->getTorsions(); |
| 227 |
torsionArray.insert(torsionArray.end(), tmpTorsions.begin(), tmpTorsions.end()); |
| 228 |
} |
| 229 |
|
| 230 |
ofs << identLevel1 << "nTorsions = " << torsionArray.size() << ";\n"; |
| 231 |
int torsionIndex = 0; |
| 232 |
for (vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> >::iterator ti = torsionArray.begin(); ti != torsionArray.end(); ++ti) |
| 233 |
{ |
| 234 |
ofs << identLevel1 << "torsion[" << torsionIndex++ << "] {\n"; |
| 235 |
ofs << identLevel2 << "member(" << atomMap[ti->first] << ", " << atomMap[ti->second] <<", " << atomMap[ti->third] <<", " << atomMap[ti->forth] << ");\n"; |
| 236 |
ofs << identLevel1 << "}\n"; |
| 237 |
} |
| 238 |
*/ |
| 239 |
ofs << "}\n"; |
| 240 |
} |
| 241 |
|
| 242 |
ofs << "nComponents = " << mols.size() << ";\n"; |
| 243 |
|
| 244 |
for(unsigned int i =0; i < mols.size(); ++i) |
| 245 |
{ |
| 246 |
ofs << "component{\n"; |
| 247 |
sprintf(buffer, "%d", i); |
| 248 |
ofs << "type = " << molPrefix << buffer << ";\n"; |
| 249 |
ofs << "nMol = " << numMols[i]<< ";\n"; |
| 250 |
ofs << "}\n"; |
| 251 |
} |
| 252 |
} |
| 253 |
void OOPSEFormat::WriteINFile(OBMol& mol, ostream& ofs, vector<int>& indices) |
| 254 |
{ |
| 255 |
unsigned int i; |
| 256 |
char buffer[BUFF_SIZE]; |
| 257 |
|
| 258 |
sprintf(buffer,"%d", mol.NumAtoms()); |
| 259 |
ofs << buffer << endl; |
| 260 |
//sprintf(buffer,"0;%f, 0, 0; 0, %15.7f, 0; 0, 0, %15.7f;", boxx, boxy, boxz); |
| 261 |
sprintf(buffer, "0;%f, 0, 0; 0, %15.7f, 0; 0, 0, %15.7f;", 100.0, 100.0, 100.0); |
| 262 |
ofs << buffer << endl; |
| 263 |
|
| 264 |
OBAtom *atom; |
| 265 |
string str,str1; |
| 266 |
|
| 267 |
for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i) |
| 268 |
{ |
| 269 |
atom = mol.GetAtom(*i); |
| 270 |
sprintf(buffer,"%15s%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f", |
| 271 |
atom->GetType(), |
| 272 |
atom->GetX(), atom->GetY(), atom->GetZ(), |
| 273 |
0.0, 0.0, 0.0, |
| 274 |
0.0, 0.0, 0.0, 0.0, |
| 275 |
0.0, 0.0, 0.0 |
| 276 |
); |
| 277 |
ofs << buffer << endl; |
| 278 |
} |
| 279 |
|
| 280 |
} |
| 281 |
|
| 282 |
} //namespace OpenBabel |
| 283 |
|
