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/********************************************************************** |
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Copyright (C) 2000 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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Some portions Copyright (C) 2004 by Chris Morley |
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Some portions Copyright (C) 2008 by J. Daniel Gezelter |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#include <openbabel/babelconfig.h> |
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#include <openbabel/obmolecformat.h> |
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#include <openbabel/obiter.h> |
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#include <openbabel/mol.h> |
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#include <openbabel/chains.h> |
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#include <fstream> |
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|
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#include "utils/StringUtils.hpp" |
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|
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using namespace std; |
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namespace OpenBabel |
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{ |
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|
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class OOPSEFormat : public OBMoleculeFormat |
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{ |
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public: |
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//Register this format type ID |
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OOPSEFormat() |
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{ |
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OBConversion::RegisterFormat("md",this); |
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} |
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|
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virtual const char* Description() //required |
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{ |
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return |
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"OOPSE combined meta-data / cartesian coordinates format\nNo comments yet\n"; |
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}; |
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|
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virtual const char* SpecificationURL() |
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{return "http://www.oopse.org";}; //optional |
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|
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virtual const char* GetMIMEType() |
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{return "chemical/x-md"; }; |
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|
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virtual unsigned int Flags() |
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{ |
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return NOTREADABLE | WRITEONEONLY; |
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} |
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|
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//*** This section identical for most OBMol conversions *** |
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//////////////////////////////////////////////////// |
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/// The "API" interface functions |
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virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv); |
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|
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private: |
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bool AreSameFragments(OBMol& mol, vector<int>& frag1, vector<int>& frag2); |
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//void findAngles(OBMol& mol); |
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OBMol* createMolFromFragment(OBMol& mol, vector<int>& fragment); |
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void WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os, OBMol& mol, vector<int>& indices); |
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}; |
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|
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//Make an instance of the format class |
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OOPSEFormat theOOPSEFormat; |
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|
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///////////////////////////////////////////////////////////////// |
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|
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|
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bool OOPSEFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
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{ |
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OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
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if(pmol==NULL) |
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return false; |
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|
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vector<vector<int> > fragmentLists; |
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pmol->ContigFragList(fragmentLists); |
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OBBitVec unused; |
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vector<bool> used(fragmentLists.size(), 0); |
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vector<vector<int> > molecules; |
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vector<int> indices; |
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for(int i =0; i < used.size(); ++i) { |
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if (used[i]) |
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{ |
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continue; |
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} |
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used[i] = true; |
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vector<int> sameMolTypes; |
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sameMolTypes.push_back(i); |
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indices.insert(indices.end(), fragmentLists[i].begin(), |
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fragmentLists[i].end()); |
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for (int j = i + 1;j < used.size(); ++j) |
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{ |
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if (used[j]) |
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{ |
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continue; |
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} |
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|
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if (AreSameFragments(*pmol, fragmentLists[i], fragmentLists[j])) |
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{ |
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sameMolTypes.push_back(j); |
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indices.insert(indices.end(), fragmentLists[j].begin(), |
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fragmentLists[j].end()); |
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used[j]=true; |
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} |
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} |
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molecules.push_back(sameMolTypes); |
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|
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} |
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|
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// |
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vector<OBMol*> mdMols; |
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vector<int> numMols; |
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for(vector<vector<int> >::iterator i = molecules.begin(); |
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i != molecules.end(); ++i) |
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{ |
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mdMols.push_back(createMolFromFragment(*pmol, |
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fragmentLists[i->front()])); |
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numMols.push_back((*i).size()); |
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} |
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|
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string OutputFileName = pConv->GetInFilename(); |
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size_t pos = OutputFileName.rfind("."); |
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if(pos!=string::npos) |
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OutputFileName = OutputFileName.substr(0, pos) + ".md"; |
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else |
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OutputFileName += ".md"; |
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|
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ofstream ofs(OutputFileName.c_str()); |
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if(!ofs) |
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{ |
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cerr << "Cannot write to " << OutputFileName <<endl; |
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return false; |
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} |
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|
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WriteMDFile(mdMols, numMols, ofs, *pmol, indices); |
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|
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for(vector<OBMol*>::iterator i = mdMols.begin(); i != mdMols.end(); ++i) |
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{ |
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delete *i; |
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} |
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|
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// |
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|
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return(true); |
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} |
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|
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bool OOPSEFormat::AreSameFragments(OBMol& mol, vector<int>& frag1, |
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vector<int>& frag2) |
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{ |
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if (frag1.size() != frag2.size()) |
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{ |
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return false; |
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} |
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|
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//exact graph matching is a NP complete problem |
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/** @todo using sparse matrix to store the connectivities*/ |
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for (unsigned int i =0 ; i < frag1.size(); ++i) |
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{ |
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OBAtom* atom1 = mol.GetAtom(frag1[i]); |
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OBAtom* atom2 = mol.GetAtom(frag2[i]); |
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|
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if (atom1->GetAtomicNum() != atom2->GetAtomicNum()) |
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{ |
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return false; |
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} |
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} |
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return true; |
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} |
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|
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struct SameAngle |
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{ |
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bool operator()(const triple<OBAtom*,OBAtom*,OBAtom*> t1, |
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const triple<OBAtom*,OBAtom*,OBAtom*> t2) const |
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{ |
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return (t1.second == t2.second) && ( (t1.first == t2.first && t1.third == t2.third) || (t1.first == t2.third && t1.third == t2.first)); |
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} |
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}; |
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|
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/* |
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void OOPSEFormat::findAngles(OBMol& mol) { |
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|
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//if already has data return |
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if(mol.HasData(OBGenericDataType::AngleData)) |
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return; |
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|
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vector<OBEdgeBase*>::iterator bi1,bi2; |
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OBBond* bond; |
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OBAtom *a,*b,*c; |
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|
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set<triple<OBAtom*,OBAtom*,OBAtom*>, SameAngle> uniqueAngles; |
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//loop through all bonds generating torsions |
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for(bond = mol.BeginBond(bi1);bond;bond = mol.NextBond(bi1)) |
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{ |
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b = bond->GetBeginAtom(); |
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c = bond->GetEndAtom(); |
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if(b->IsHydrogen()) |
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continue; |
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|
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for(a = b->BeginNbrAtom(bi2);a;a = b->NextNbrAtom(bi2)) |
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{ |
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if(a == c) |
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continue; |
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|
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uniqueAngles.insert(triple<OBAtom*,OBAtom*,OBAtom*>(a, b, c)); |
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} |
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} |
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|
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//get new data and attach it to molecule |
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OBAngleData *angles = new OBAngleData; |
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mol.SetData(angles); |
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set<triple<OBAtom*,OBAtom*,OBAtom*>, SameAngle>::iterator i; |
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|
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for (i = uniqueAngles.begin(); i != uniqueAngles.end(); ++i) { |
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OBAngle angle; |
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angle.SetAtoms(i->first, i->second, i->second); |
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angles->SetData(angle); |
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} |
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|
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} |
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*/ |
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|
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OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol, vector<int>& fragment) { |
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|
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OBMol* newMol = new OBMol(); |
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OBChainsParser* chainParser = new OBChainsParser(); |
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newMol->ReserveAtoms(fragment.size()); |
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newMol->BeginModify(); |
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for(vector<int>::iterator i = fragment.begin(); i != fragment.end(); ++i) { |
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OBAtom* newAtom = newMol->NewAtom(); |
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*newAtom = *mol.GetAtom(*i); |
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} |
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newMol->EndModify(); |
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newMol->ConnectTheDots(); |
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newMol->PerceiveBondOrders(); |
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newMol->FindAngles(); |
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newMol->FindTorsions(); |
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//chainParser->PerceiveChains(*newMol, false); |
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|
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return newMol; |
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} |
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|
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void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os, OBMol& mol, vector<int>& indices) { |
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std::string indentLevel1(" "); |
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std::string indentLevel2(" "); |
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std::string molPrefix("MolName"); |
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std::string resName; |
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unsigned int i; |
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const int BUFFLEN = 1024; |
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char buffer[BUFFLEN]; |
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string str, str1; |
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OBAtom *a, *b, *c, *d; |
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OBChainsParser* chainParser = new OBChainsParser(); |
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OBResidue *r; |
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int resKey; |
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char type_name[10]; |
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char *element_name; |
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int res_num; |
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|
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std::cerr << "yo\n"; |
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os << "<OOPSE version=4>" << endl; |
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os << " <MetaData>" << endl << endl; |
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|
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for(i = 0; i < mols.size(); ++i) { |
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OBMol* pmol = mols[i]; |
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std::cerr << "yo1\n"; |
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pmol->ConnectTheDots(); |
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pmol->PerceiveBondOrders(); |
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chainParser->PerceiveChains(*pmol, false); |
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//pmol->FindSSSR(); |
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//pmol->SetAromaticPerceived(); |
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//pmol->Kekulize(); |
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|
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map<OBAtom*, int> atomMap; |
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os << "molecule {\n"; |
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sprintf(buffer, "%d", i); |
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os << indentLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n"; |
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|
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|
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//atom |
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|
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int ai = 0; |
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FOR_RESIDUES_OF_MOL(res, *pmol) { |
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|
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std::cerr << "found residue" << res->GetName() << "\n"; |
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} |
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|
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// FOR_RESIDUES_OF_MOL(res, *pmol) { |
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|
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// resName = res->GetName(); |
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// resKey = res->GetResKey(); |
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|
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|
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|
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// std::cerr << "found residue " << resName << "\n"; |
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// std::cerr << " num = " << res->GetNum() << "\n"; |
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// std::cerr << " numAtoms = " << res->GetNumAtoms() << "\n"; |
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// std::cerr << " num = " << res->GetNum() << "\n"; |
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// std::cerr << " chain = " << res->GetChain() << "\n"; |
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// std::cerr << " chainnum = " << res->GetChainNum() << "\n"; |
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// std::cerr << " idx = " << res->GetIdx() << "\n"; |
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// std::cerr << " key = " << res->GetResKey() << "\n"; |
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|
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|
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// FOR_ATOMS_OF_RESIDUE(atom, &*res) { |
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// str = atom->GetType(); |
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// ttab.SetFromType("INT"); |
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// ttab.SetToType("INT"); |
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// ttab.Translate(str1,str); |
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// os << indentLevel1 << "atom[" << ai << "] {\n"; |
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// os << indentLevel2 << "type = " << "\"" << resName << "-" << str1 << "\"" << ";\n"; |
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// os << indentLevel1 << "}\n"; |
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// atomMap[&(*atom)] = ai++; |
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// } |
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// os << "\n"; |
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|
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// } |
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|
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ai = 0; |
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FOR_ATOMS_OF_MOL(atom, *pmol ) { |
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str = atom->GetType(); |
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r = atom->GetResidue(); |
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|
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if (r == NULL) |
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resName = "NULL"; |
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else |
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resName = r->GetName(); |
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|
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if (resName.compare("NULL") ==0 || resName.compare("LIG") == 0 || resName.compare("UNK") == 0) { |
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// Either couldn't find a residue at all or couldn't find a reasonable |
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// residue name to use. We'll punt and use OpenBabel's internal atom typing: |
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ttab.SetFromType("INT"); |
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ttab.SetToType("INT"); |
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ttab.Translate(str1,str); |
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} else { |
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|
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|
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if (resName.compare("HOH") == 0) { |
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// HOH is a special residue name for water, and the standard atom types |
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// are OW and HW, so just append W to the string for the atom type: |
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ttab.SetFromType("INT"); |
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ttab.SetToType("XYZ"); |
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ttab.Translate(str1,str); |
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str1 += "W"; |
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} else { |
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|
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std::cerr << "found residue " << resName << "\n"; |
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|
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// If we know what residue we've got, the specific atom name can |
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// be used to help specify partial charges. |
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|
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str = r->GetAtomID(&*atom); |
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size_t startpos = str.find_first_not_of(" "); |
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size_t endpos = str.find_last_not_of(" "); |
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str = str.substr( startpos, endpos-startpos+1 ); |
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str1 = resName + "-" + str; |
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} |
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|
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} |
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|
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// os << indentLevel1 << "atom[" << ai << "] {\n"; |
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// os << indentLevel2 << "type = " << "\"" << str1 << "\"" << ";\n"; |
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// os << indentLevel1 << "}\n"; |
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os << "atom[" << ai << "] { "; |
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os << "type = " << "\"" << str1 << "\"" << "; "; |
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os << "}\n"; |
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atomMap[&(*atom)] = ai++; |
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} |
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os << "\n"; |
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|
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//bond |
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FOR_BONDS_OF_MOL(bond, *pmol ) { |
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// os << indentLevel1 << "bond {\n"; |
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// os << indentLevel2 << "members(" << atomMap[bond->GetBeginAtom()] << ", " << atomMap[bond->GetEndAtom()] << ");\n"; |
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// os << indentLevel1 << "}\n"; |
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os << "bond { "; |
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os << "members(" << atomMap[bond->GetBeginAtom()] << ", " << atomMap[bond->GetEndAtom()] << "); "; |
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os << "}\n"; |
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} |
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|
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FOR_ANGLES_OF_MOL(angle, *pmol) { |
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|
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// OpenBabel's getAtoms returns the 3 atom pointer for the |
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// angle with the vertex first. These need to be reordered |
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// for vertex-second ordering for OOPSE. |
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|
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b = pmol->GetAtom((*angle)[0] + 1); |
| 392 |
a = pmol->GetAtom((*angle)[1] + 1); |
| 393 |
c = pmol->GetAtom((*angle)[2] + 1); |
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|
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// 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 |
|
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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 |
/* |
| 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 |
|
