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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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#ifndef OB_GROMOS96FORMAT_HPP |
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#define OB_GROMOS96FORMAT_HPP |
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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 GROMOS96Format : public OBFormat |
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{ |
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public: |
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//Register this format type ID |
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GROMOS96Format() |
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{ |
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OBConversion::RegisterFormat("gr96",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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"GROMOS96 format\n \ |
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Write Options e.g. -xn\n\ |
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n output nm (not Angstroms)\n"; |
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}; |
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|
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virtual const char* SpecificationURL() |
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{ |
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return ""; |
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}; //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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//////////////////////////////////////////////////// |
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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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#endif |
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