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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 <openbabel/data.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 OpenMDFormat : public OBMoleculeFormat |
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{ |
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public: |
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//Register this format type ID |
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OpenMDFormat() |
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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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"OpenMD 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.openmd.net";}; //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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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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OBMol* createMolFromFragment(OBMol& mol, vector<int>& fragment); |
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void WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os, |
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OBMol& mol, vector<int>& indices); |
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void CalcBoundingBox(OBMol &mol, |
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double &min_x, double &max_x, |
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double &min_y, double &max_y, |
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double &min_z, double &max_z); |
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|
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}; |
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|
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//Make an instance of the format class |
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OpenMDFormat theOpenMDFormat; |
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|
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bool OpenMDFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) { |
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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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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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if (used[j]) |
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continue; |
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|
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if (AreSameFragments(*pmol, fragmentLists[i], fragmentLists[j])) { |
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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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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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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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delete *i; |
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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 OpenMDFormat::AreSameFragments(OBMol& mol, vector<int>& frag1, |
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vector<int>& frag2) { |
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if (frag1.size() != frag2.size()) |
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return false; |
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|
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// Exact graph matching is an NP complete problem. |
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// This just matches all of the atom atomic numbers and may falsely |
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// detect identical fragments which aren't really identical. |
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// @todo using sparse matrix to store the connectivities |
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|
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for (unsigned int i =0 ; i < frag1.size(); ++i) { |
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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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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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bool operator()(const triple<OBAtom*,OBAtom*,OBAtom*> t1, |
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const triple<OBAtom*,OBAtom*,OBAtom*> t2) const { |
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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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OBMol* OpenMDFormat::createMolFromFragment(OBMol& mol, |
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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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|
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newMol->EndModify(); |
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newMol->ConnectTheDots(); |
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newMol->PerceiveBondOrders(); |
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|
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return newMol; |
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} |
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|
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void OpenMDFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols, |
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ostream& os, OBMol& mol, |
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vector<int>& indices) { |
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|
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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, str2, str3; |
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OBAtom *a, *b, *c, *d; |
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bool molIsWater = false; |
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OBResidue *r; |
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int resKey, myserial; |
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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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OBChainsParser* chainParser = new OBChainsParser(); |
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double min_x, max_x, min_y, max_y, min_z, max_z; /* Edges of bounding box */ |
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|
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os << "<OpenMD version=1>" << 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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map<OBAtom*, int> atomMap; |
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|
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chainParser->PerceiveChains(*pmol, false); |
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molIsWater = false; |
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FOR_RESIDUES_OF_MOL(residue, *pmol) { |
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std::cerr << "residue = " << residue->GetName() << "\n"; |
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if (residue->GetName().compare("HOH") == 0) { |
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molIsWater = true; |
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} |
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} |
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|
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if (molIsWater) { |
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// water include files define all of the known water types |
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os << "#include \"water.md\";\n"; |
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pmol->SetTitle("HOH"); |
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} else { |
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|
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os << "molecule {\n"; |
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sprintf(buffer, "%d", i); |
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os << " name = \"" << molPrefix << buffer << "\";\n"; |
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|
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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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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 || |
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resName.compare("LIG") == 0 || |
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resName.compare("UNK") == 0) { |
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// Either couldn't find a residue at all or couldn't find a |
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// reasonable residue name to use. We'll punt and use |
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// 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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// 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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//resdat.SetResName(resName); |
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|
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// atom type from residue: |
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str = r->GetAtomID(&*atom); |
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|
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// arginine has separate indices for chemically-identical |
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// nitrogen atoms: |
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if (resName.compare("ARG") == 0) { |
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if (str.compare("NH1") == 0 || str.compare("NH2") == 0) { |
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str = "NH"; |
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} |
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} |
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if (resName.compare("VAL") == 0) { |
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if (str.compare("CG1") == 0 || str.compare("CG2") == 0) { |
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str = "CG"; |
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} |
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} |
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if (resName.compare("LEU") == 0) { |
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if (str.compare("CD1") == 0 || str.compare("CD2") == 0) { |
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str = "CD"; |
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} |
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} |
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if (resName.compare("ASP") == 0) { |
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if (str.compare("OD1") == 0 || str.compare("OD2") == 0) { |
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str = "OD"; |
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} |
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} |
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if (resName.compare("GLU") == 0) { |
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if (str.compare("OE1") == 0 || str.compare("OE2") == 0) { |
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str = "OE"; |
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} |
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} |
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if (resName.compare("TYR") == 0) { |
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if (str.compare("CD1") == 0 || str.compare("CD2") == 0) { |
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str = "CD"; |
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} |
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if (str.compare("CE1") == 0 || str.compare("CE2") == 0) { |
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str = "CE"; |
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} |
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} |
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|
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|
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if ((&*atom)->IsHydrogen()) { |
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FOR_NBORS_OF_ATOM(nbr, *atom) { |
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str2 = r->GetAtomID(&*nbr); |
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size_t startpos = str2.find_first_not_of(" "); |
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size_t endpos = str2.find_last_not_of(" "); |
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if ((endpos - startpos) < 1) { |
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// if the bonded atom type has only one character (i.e. N) |
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// then the hydrogen will be labeled "HN" to show what |
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// kind of proton it is: |
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str3 = str2; |
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} else { |
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if (str2.compare("OH") == 0) { |
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str3 = "O"; |
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} else { |
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// When the bonded atom type is more specific, we drop |
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// the first character: i.e. H bonded to OG1 is HG1 type: |
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str3 = str2.substr(startpos+1, endpos-startpos); |
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} |
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} |
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str = "H" + str3; |
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} |
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// same problem with arginine NH atoms, but now for connected hydrogens |
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if (resName.compare("ARG") == 0) { |
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if (str.compare("HH1") == 0 || str.compare("HH2") == 0) { |
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str = "HH"; |
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} |
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} |
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if (resName.compare("VAL") == 0) { |
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if (str.compare("HG1") == 0 || str.compare("HG2") == 0) { |
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str = "HG"; |
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} |
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} |
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if (resName.compare("LEU") == 0) { |
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if (str.compare("HD1") == 0 || str.compare("HD2") == 0) { |
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str = "HD"; |
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} |
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} |
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if (resName.compare("TYR") == 0) { |
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if (str.compare("HD1") == 0 || str.compare("HD2") == 0) { |
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str = "HD"; |
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} |
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if (str.compare("HE1") == 0 || str.compare("HE2") == 0) { |
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str = "HE"; |
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} |
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} |
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|
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} |
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|
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// atom type from residue table: |
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//resdat.LookupType(str, str2, hyb); |
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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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os << " atom[" << ai << "] { "; |
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os << "type = " << "\"" << str1 << "\"" << "; "; |
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os << "position( " << atom->GetX() << ", " << atom->GetY() << ", " << atom->GetZ() << ");"; |
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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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|
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int b1, b2; |
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FOR_BONDS_OF_MOL(bond, *pmol ) { |
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b1 = atomMap[bond->GetBeginAtom()]; |
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b2 = atomMap[bond->GetEndAtom()]; |
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|
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os << " bond { "; |
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|
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if (b1 < b2) |
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os << "members(" << b1 << ", " << b2 << "); "; |
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else |
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os << "members(" << b2 << ", " << b1 << "); "; |
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|
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os << "}" << endl; |
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} |
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|
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os << endl; |
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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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for(i=0; i < mols.size(); ++i) { |
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OBMol* pmol = mols[i]; |
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os << "component{" << endl; |
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if (std::string(pmol->GetTitle()).compare("HOH") == 0) { |
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os << " type = " << "HOH" << ";" << endl; |
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} else { |
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sprintf(buffer, "%d", i); |
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os << " type = " << molPrefix << buffer << ";" << endl; |
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} |
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os << " 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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CalcBoundingBox(mol, min_x, max_x, min_y, max_y, min_z, max_z); |
| 410 |
|
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// still to do: should compute a bounding box here |
| 412 |
sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}", |
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max_x - min_x, 0.0, 0.0, 0.0, max_y - min_y, 0.0, 0.0, 0.0, max_z - min_z); |
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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; |
| 418 |
|
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OBAtom *atom; |
| 420 |
|
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// still to do: intercept waters and recompute pvqj lines |
| 422 |
|
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for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i) { |
| 424 |
atom = mol.GetAtom(*i); |
| 425 |
sprintf(buffer, "%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e", *i - 1, |
| 426 |
"pv", atom->GetX(), atom->GetY(), atom->GetZ(), 0.0, 0.0, 0.0); |
| 427 |
os << buffer << endl; |
| 428 |
} |
| 429 |
os << " </StuntDoubles>" << endl; |
| 430 |
os << " </Snapshot>" << endl; |
| 431 |
os << "</OpenMD>" << endl; |
| 432 |
} |
| 433 |
|
| 434 |
void OpenMDFormat::CalcBoundingBox(OBMol &mol, |
| 435 |
double &min_x, double &max_x, |
| 436 |
double &min_y, double &max_y, |
| 437 |
double &min_z, double &max_z |
| 438 |
) |
| 439 |
{ |
| 440 |
/* ---- Init bounding-box variables ---- */ |
| 441 |
min_x = (double) 0.0; |
| 442 |
max_x = (double) 0.0; |
| 443 |
min_y = (double) 0.0; |
| 444 |
max_y = (double) 0.0; |
| 445 |
min_z = (double) 0.0; |
| 446 |
max_z = (double) 0.0; |
| 447 |
|
| 448 |
/* ---- Check all atoms ---- */ |
| 449 |
for(unsigned int i = 1; i <= mol.NumAtoms(); ++i) |
| 450 |
{ |
| 451 |
|
| 452 |
/* ---- Get a pointer to ith atom ---- */ |
| 453 |
OBAtom *atom = mol.GetAtom(i); |
| 454 |
|
| 455 |
/* ---- Check for minimal/maximal x-position ---- */ |
| 456 |
if (atom -> GetX() < min_x) |
| 457 |
min_x = atom -> GetX(); |
| 458 |
if (atom -> GetX() > max_x) |
| 459 |
max_x = atom -> GetX(); |
| 460 |
|
| 461 |
/* ---- Check for minimal/maximal y-position ---- */ |
| 462 |
if (atom -> GetY() < min_y) |
| 463 |
min_y = atom -> GetY(); |
| 464 |
if (atom -> GetY() > max_y) |
| 465 |
max_y = atom -> GetY(); |
| 466 |
|
| 467 |
/* ---- Check for minimal/maximal z-position ---- */ |
| 468 |
if (atom -> GetZ() < min_z) |
| 469 |
min_z = atom -> GetZ(); |
| 470 |
if (atom -> GetZ() > max_z) |
| 471 |
max_z = atom -> GetZ(); |
| 472 |
|
| 473 |
} |
| 474 |
} |
| 475 |
} //namespace OpenBabel |
| 476 |
|
