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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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#include "obmolecformat.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 AmberPrepFormat : public OBMoleculeFormat |
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{ |
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public: |
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//Register this format type ID |
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AmberPrepFormat() |
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{ |
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OBConversion::RegisterFormat("prep",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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"Amber Prep format\n \ |
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Read Options e.g. -as\n\ |
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s Output single bonds only\n\ |
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b Disable bonding entirely\n\n"; |
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}; |
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|
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virtual const char* SpecificationURL() |
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{return "http://amber.scripps.edu/doc/prep.html";}; |
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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 NOTWRITABLE; |
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}; |
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|
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//////////////////////////////////////////////////// |
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/// The "API" interface functions |
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virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv); |
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}; |
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|
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//Make an instance of the format class |
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AmberPrepFormat theAmberPrepFormat; |
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|
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///////////////////////////////////////////////////////////////// |
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bool AmberPrepFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) |
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{ |
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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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istream &ifs = *pConv->GetInStream(); |
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OBMol &mol = *pmol; |
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const char* title = pConv->GetTitle(); |
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|
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char buffer[BUFF_SIZE]; |
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string str,str1; |
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OBAtom *atom; |
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OBInternalCoord *coord; |
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vector<string> vs; |
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vector<OBInternalCoord*> internals; |
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|
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mol.BeginModify(); |
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|
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while (ifs.getline(buffer,BUFF_SIZE)) |
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{ |
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tokenize(vs,buffer); |
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if (vs.size() == 10) |
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{ |
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atom = mol.NewAtom(); |
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coord = new OBInternalCoord(); |
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if (mol.NumAtoms() > 1) |
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coord->_a = mol.GetAtom(atoi(vs[4].c_str())); |
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if (mol.NumAtoms() > 2) |
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coord->_b = mol.GetAtom(atoi(vs[5].c_str())); |
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if (mol.NumAtoms() > 3) |
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coord->_c = mol.GetAtom(atoi(vs[6].c_str())); |
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coord->_dst = atof(vs[7].c_str()); |
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coord->_ang = atof(vs[8].c_str()); |
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coord->_tor = atof(vs[9].c_str()); |
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internals.push_back(coord); |
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|
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atom->SetAtomicNum(etab.GetAtomicNum(vs[1].c_str())); |
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|
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if (!ifs.getline(buffer,BUFF_SIZE)) |
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break; |
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tokenize(vs,buffer); |
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} |
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} |
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|
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if (internals.size() > 0) |
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InternalToCartesian(internals,mol); |
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|
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if (!pConv->IsOption("b",OBConversion::INOPTIONS)) |
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mol.ConnectTheDots(); |
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if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS)) |
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mol.PerceiveBondOrders(); |
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|
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mol.EndModify(); |
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mol.SetTitle(title); |
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return(true); |
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} |
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|
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} //namespace OpenBabel |
