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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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|
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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 "mol.hpp" |
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#include "obconversion.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 TinkerFormat : public OBFormat |
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{ |
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public: |
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//Register this format type ID |
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TinkerFormat() |
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{ |
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OBConversion::RegisterFormat("txyz",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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"Tinker MM2 format\n \ |
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No 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://dasher.wustl.edu/tinker/";}; //optional |
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|
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//Flags() can return be any the following combined by | or be omitted if none apply |
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// NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY |
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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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//////////////////////////////////////////////////// |
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/// The "Convert" interface functions |
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virtual bool WriteChemObject(OBConversion* pConv) |
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{ |
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//Retrieve the target OBMol |
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OBBase* pOb = pConv->GetChemObject(); |
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OBMol* pmol = dynamic_cast<OBMol*> (pOb); |
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bool ret=false; |
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if(pmol) |
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ret=WriteMolecule(pmol,pConv); |
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|
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std::string auditMsg = "OpenBabel::Write molecule "; |
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std::string description(Description()); |
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auditMsg += description.substr( 0, description.find('\n') ); |
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obErrorLog.ThrowError(__func__, |
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auditMsg, |
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obAuditMsg); |
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|
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delete pOb; |
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return ret; |
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}; |
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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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TinkerFormat theTinkerFormat; |
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|
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///////////////////////////////////////////////////////////////// |
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|
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bool TinkerFormat::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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//Define some references so we can use the old parameter names |
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ostream &ofs = *pConv->GetOutStream(); |
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OBMol &mol = *pmol; |
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|
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unsigned int i; |
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char buffer[BUFF_SIZE]; |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator j; |
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|
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snprintf(buffer, BUFF_SIZE, "%6d %-20s MM2 parameters\n",mol.NumAtoms(),mol.GetTitle()); |
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ofs << buffer; |
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|
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ttab.SetFromType("INT"); |
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|
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OBAtom *atom; |
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string str,str1; |
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for(i = 1;i <= mol.NumAtoms(); i++) |
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{ |
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atom = mol.GetAtom(i); |
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str = atom->GetType(); |
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ttab.SetToType("MM2"); |
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ttab.Translate(str1,str); |
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snprintf(buffer, BUFF_SIZE, "%6d %2s %12.6f%12.6f%12.6f %5d", |
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i, |
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etab.GetSymbol(atom->GetAtomicNum()), |
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atom->GetX(), |
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atom->GetY(), |
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atom->GetZ(), |
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atoi((char*)str1.c_str())); |
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ofs << buffer; |
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|
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for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j)) |
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{ |
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snprintf(buffer, BUFF_SIZE, "%6d", (bond->GetNbrAtom(atom))->GetIdx()); |
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ofs << buffer; |
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} |
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|
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ofs << endl; |
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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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} //namespace OpenBabel |
