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/********************************************************************** |
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Copyright (C) 1998-2001 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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/* contributed by Walter Scott (wscott@igc.phys.chem.ethz.ch) |
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|
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(Actually the routine was copied from write_xyz and and write_pdb and |
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then modified...) |
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|
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This is a small routine to write a GROMOS96 formatted |
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"position coordinate block" (POSITION) or a |
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"reduced position coordinate block" (POSITIONRED) |
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The former has name information (atom and residue names) while |
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the latter only has coordinates. |
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This version does not support the writing of binary |
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GROMOS files. |
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|
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NOTE 1: the actual formats used in writing out the coordinates |
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do not matter, as GROMOS96 uses free formatted reads. |
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Each line may not be longer than 80 characters. |
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|
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(Note, however, in the POSITION block, the first 24 (twenty four) |
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character on each line are ignored when the line is read in by GROMOS) |
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Comments lines, beginning with hash (#) may occur within a block and are |
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used as delimiters for easier reading. |
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|
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NOTE 2: Many programs specify the units of the coordinates (e.g. Angstrom). |
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GROMOS96 does NOT, as all physical constants, from K_B to EPS are |
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NOT hardwired into the code, but specified by the user. |
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This allows some (mostly Americans) to use GROMOS96 in KCal and |
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Angstrom and the rest of us to use kJoule and nm. |
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It also makes it easy to use reduced units. |
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|
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We get around this by supplying a routine, wr_sco_gr96, which |
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will scale the coordinates by a factor before writing. |
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This routine is then called with the factor set to 1.0 in |
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write_gr96A, or to 0.1 in write_gr96N depending on the users choice. |
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Thus, we always assume that we have read coordinates in Angstrom. |
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*** But now handled by a command line option in new framework. |
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*/ |
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|
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#include "gromos96format.hpp" |
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|
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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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bool GROMOS96Format::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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double fac = pConv->IsOption("n") ? 0.1 : 1.0; //new framework |
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|
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char type_name[10]; |
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char res_name[10],padded_name[10]; |
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char buffer[BUFF_SIZE]; |
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int res_num; |
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|
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sprintf(buffer,"#GENERATED BY OPEN BABEL %s",BABEL_VERSION); |
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ofs << buffer << endl; |
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|
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/* GROMOS wants a TITLE block, so let's write one*/ |
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sprintf(buffer,"TITLE\n%s\nEND",mol.GetTitle()); |
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ofs << buffer << endl; |
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ofs << "POSITION" << endl; |
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|
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OBAtom *atom; |
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OBResidue *res; |
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vector<OBNodeBase*>::iterator i; |
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|
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for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
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{ |
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if ( (res = atom->GetResidue()) ) |
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{ |
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strcpy(res_name,(char*)res->GetName().c_str()); |
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strcpy(type_name,(char*)res->GetAtomID(atom).c_str()); |
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res_num = res->GetNum(); |
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} |
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else |
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{ |
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strcpy(type_name,etab.GetSymbol(atom->GetAtomicNum())); |
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strcpy(res_name,"UNK"); |
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sprintf(padded_name,"%2s",type_name); |
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strcpy(type_name,padded_name); |
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res_num = 1; |
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} |
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|
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sprintf(buffer,"%5d %5s %5s %6d %15.5f %15.5f %15.5f", |
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res_num,res_name,type_name,atom->GetIdx(), |
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atom->x()*fac,atom->y()*fac,atom->z()*fac); |
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ofs << buffer << endl; |
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|
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if (!(atom->GetIdx()%10)) |
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{ |
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sprintf(buffer,"# %d",atom->GetIdx()); |
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ofs << buffer << endl; |
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} |
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} |
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|
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ofs << "END" << endl; |
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|
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return(true); |
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} |
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|
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} //namespace OpenBabel |
