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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) 2001-2006 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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Some portions Copyright (C) 2008-2009 by J. Daniel Gezelter |
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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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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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"OpenMD combined meta-data / cartesian coordinates format\n\ |
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No comments yet\n"; |
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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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{return "http://www.openmd.org";}; //optional |
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virtual const char* GetMIMEType() |
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{return "chemical/x-md"; }; |
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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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for(std::size_t i =0; i < used.size(); ++i) { |
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if (used[i]) |
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continue; |
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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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for (std::size_t j = i + 1; j < used.size(); ++j) { |
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if (used[j]) |
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continue; |
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return false; |
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} |
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WriteMDFile(mdMols, numMols, ofs, *pmol, indices); |
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for(vector<OBMol*>::iterator i = mdMols.begin(); i != mdMols.end(); ++i) { |
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vector<int>& fragment) { |
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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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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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os << "<OpenMD version=1>" << endl; |
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os << "<OpenMD version=2>" << endl; |
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os << " <MetaData>" << endl << endl; |
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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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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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} else { |
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os << "molecule {\n"; |
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sprintf(buffer, "%d", i); |
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sprintf(buffer, "%u", i); |
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os << " name = \"" << molPrefix << buffer << "\";\n"; |
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int ai = 0; |
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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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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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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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os << " type = " << "\"HOH\"" << "; // change to appropriate water model" << endl; |
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} else { |
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sprintf(buffer, "%d", i); |
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sprintf(buffer, "%u", 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 << buffer << endl; |
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os << " </FrameData>" << endl; |
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os << " <StuntDoubles>" << endl; |
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OBAtom *atom; |
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// still to do: intercept waters and recompute pvqj lines |
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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, |
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"pv", atom->GetX(), atom->GetY(), atom->GetZ(), 0.0, 0.0, 0.0); |
