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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 <fstream> |
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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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unsigned int pos = OutputFileName.rfind("."); |
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if(pos==string::npos) |
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OutputFileName += ".md"; |
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else |
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OutputFileName = OutputFileName.substr(0, pos) + ".md"; |
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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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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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OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol, vector<int>& fragment) { |
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|
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OBMol* newMol = new OBMol(); |
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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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findAngles(*newMol); |
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newMol->FindTorsions(); |
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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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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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|
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|
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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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|
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pmol->ConnectTheDots(); |
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pmol->PerceiveBondOrders(); |
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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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//atom |
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int ai = 0; |
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FOR_ATOMS_OF_MOL(atom, *pmol ) { |
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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 = " << "\"" << etab.GetSymbol(atom->GetAtomicNum()) << "\"" << ";\n"; |
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os << indentLevel2 << "type = " << "\"" << 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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//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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} |
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/* |
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//bend |
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OBGenericData* pGenericData = pmol->GetData(OBGenericDataType::AngleData); |
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OBAngleData* pAngleData = dynamic_cast<OBAngleData*>(pGenericData); |
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vector<OBAngle> angles = pAngleData->GetData(); |
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|
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os << indentLevel1 << "nBends = " << angles.size() << ";\n"; |
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int bendIndex = 0; |
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for (vector<OBAngle>::iterator ti = angles.begin(); ti != angles.end(); ++ti) |
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{ |
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triple<OBAtom*, OBAtom*, OBAtom*> bendAtoms = ti->getAtoms(); |
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os << indentLevel1 << "bend[" << bendIndex++ << "] {\n"; |
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os << indentLevel2 << "member(" << atomMap[bendAtoms.first] << ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n"; |
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os << indentLevel1 << "}\n"; |
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} |
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|
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//torsion |
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pGenericData = pmol->GetData(OBGenericDataType::TorsionData); |
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OBTorsionData* pTorsionData = dynamic_cast<OBTorsionData*>(pGenericData); |
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vector<OBTorsion> torsions = pTorsionData->GetData(); |
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vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > torsionArray; |
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for (vector<OBTorsion>::iterator ti = torsions.begin(); ti != torsions.end(); ++ti) |
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{ |
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vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > tmpTorsions = ti->getTorsions(); |
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torsionArray.insert(torsionArray.end(), tmpTorsions.begin(), tmpTorsions.end()); |
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} |
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|
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os << indentLevel1 << "nTorsions = " << torsionArray.size() << ";\n"; |
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int torsionIndex = 0; |
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for (vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> >::iterator ti = torsionArray.begin(); ti != torsionArray.end(); ++ti) |
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{ |
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os << indentLevel1 << "torsion[" << torsionIndex++ << "] {\n"; |
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os << indentLevel2 << "member(" << atomMap[ti->first] << ", " << atomMap[ti->second] <<", " << atomMap[ti->third] <<", " << atomMap[ti->forth] << ");\n"; |
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os << indentLevel1 << "}\n"; |
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} |
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*/ |
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os << "}" << endl; |
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os << endl; |
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|
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} |
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|
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os << endl; |
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|
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|
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for(i=0; i < mols.size(); ++i) { |
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os << "component{" << endl; |
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sprintf(buffer, "%d", i); |
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os << indentLevel1 << "type = " << molPrefix << buffer << ";" << endl; |
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os << indentLevel1 << "nMol = " << numMols[i]<< ";" << endl; |
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os << "}" << endl; |
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} |
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|
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os << " </MetaData>" << endl; |
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os << " <Snapshot>" << endl; |
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os << " <FrameData>" << endl; |
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|
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sprintf(buffer, " Time: %.10g", 0.0); |
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|
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os << buffer << endl; |
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|
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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); |
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|
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os << buffer << endl; |
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os << " </FrameData>" << endl; |
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os << " <StuntDoubles>" << endl; |
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|
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OBAtom *atom; |
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|
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for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i) { |
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atom = mol.GetAtom(*i); |
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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); |
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os << buffer << endl; |
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} |
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os << " </StuntDoubles>" << endl; |
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os << " </Snapshot>" << endl; |
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os << "</OOPSE>" << endl; |
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} |
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|
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} //namespace OpenBabel |
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|
