src/openbabel/gromos96format.cpp

/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
Some portions Copyright (C) 2004 by Chris Morley
 
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

/* contributed by Walter Scott (wscott@igc.phys.chem.ethz.ch)
 
   (Actually the routine was copied from write_xyz and and write_pdb and
   then modified...)
 
   This is a small routine to write a GROMOS96 formatted 
   "position coordinate block" (POSITION) or a
   "reduced position coordinate block" (POSITIONRED)
   The former has name information (atom and residue names) while
   the latter only has coordinates.
   This version does not support the writing of binary
   GROMOS files.
 
   NOTE 1: the actual formats used in writing out the coordinates
   do not matter, as GROMOS96 uses free formatted reads.
   Each line may not be longer than 80 characters.
 
   (Note, however, in the POSITION block, the first 24 (twenty four)
   character on each line are ignored when the line is read in by GROMOS)
   Comments lines, beginning with hash (#) may occur within a block and are
   used as delimiters for easier reading.
 
   NOTE 2: Many programs specify the units of the coordinates (e.g. Angstrom).
   GROMOS96 does NOT, as all physical constants, from K_B to EPS are 
   NOT hardwired into the code, but specified by the user.
   This allows some (mostly Americans) to use GROMOS96 in KCal and
   Angstrom and the rest of us to use kJoule and nm.
   It also makes it easy to use reduced units.
 
   We get around this by supplying a routine, wr_sco_gr96, which
   will scale the coordinates by a factor before writing.
   This routine is then called with the factor set to 1.0 in 
   write_gr96A, or to 0.1 in write_gr96N depending on the users choice.
   Thus, we always assume that we have read coordinates in Angstrom.
         *** But now handled by a command line option in new framework.
*/

#include "mol.hpp"
#include "obconversion.hpp"

using namespace std;
namespace OpenBabel
{

class GROMOS96Format : public OBFormat
{
public:
    //Register this format type ID
    GROMOS96Format()
    {
        OBConversion::RegisterFormat("gr96",this);
    }

  virtual const char* Description() //required
  {
    return
      "GROMOS96 format\n \
       Write Options e.g. -xn\n\
        n output nm (not Angstroms)\n";
  };

    virtual const char* SpecificationURL()
    {
        return "";
    }; //optional

    //Flags() can return be any the following combined by | or be omitted if none apply
    // NOTREADABLE  READONEONLY  NOTWRITABLE  WRITEONEONLY
    virtual unsigned int Flags()
    {
        return NOTREADABLE | WRITEONEONLY;
    };

    ////////////////////////////////////////////////////
    /// The "API" interface functions
    virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);

    ////////////////////////////////////////////////////
    /// The "Convert" interface functions
    virtual bool WriteChemObject(OBConversion* pConv)
    {
        //Retrieve the target OBMol
        OBBase* pOb = pConv->GetChemObject();
        OBMol* pmol = dynamic_cast<OBMol*> (pOb);
        bool ret=false;
        if(pmol)
            ret=WriteMolecule(pmol,pConv);

        std::string auditMsg = "OpenBabel::Write molecule ";
        std::string description(Description());
        auditMsg += description.substr( 0, description.find('\n') );
        obErrorLog.ThrowError(__func__,
                              auditMsg,
                              obAuditMsg);

        delete pOb;
        return ret;
    };
};

//Make an instance of the format class
GROMOS96Format theGROMOS96Format;

////////////////////////////////////////////////////////////////

bool GROMOS96Format::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
        return false;

    //Define some references so we can use the old parameter names
    ostream &ofs = *pConv->GetOutStream();
    OBMol &mol = *pmol;
    double fac = pConv->IsOption("n") ? 0.1 : 1.0; //new framework

    char type_name[16];
    char res_name[16];
    char buffer[BUFF_SIZE];
    int res_num;

    snprintf(buffer, BUFF_SIZE, "#GENERATED BY OPEN BABEL %s\n",BABEL_VERSION);
    ofs << buffer;

    /* GROMOS wants a TITLE block, so let's write one*/
    ofs << "TITLE\n" << mol.GetTitle() << "\nEND\n";
    ofs << "POSITION\n";

    OBAtom *atom;
    OBResidue *res;
    vector<OBNodeBase*>::iterator i;

    for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
    {
      if ( (res = atom->GetResidue()) )
        {
            // 16 = sizeof(res_name) and sizeof(type_name)
            strncpy(res_name,(char*)res->GetName().c_str(), 16);
            res_name[15] = '\0';
            strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16);
            type_name[15] = '\0';
            res_num = res->GetNum();
        }
        else
        {
            strncpy(type_name,etab.GetSymbol(atom->GetAtomicNum()), 16);
            strcpy(res_name,"UNK");
            res_num = 1;
        }

        snprintf(buffer, BUFF_SIZE, "%5d %5s %5s %6d %15.5f %15.5f %15.5f\n",
                res_num,res_name,type_name,atom->GetIdx(),
                atom->x()*fac,atom->y()*fac,atom->z()*fac);
        ofs << buffer;

        if (!(atom->GetIdx()%10))
        {
            sprintf(buffer,"# %d\n",atom->GetIdx());
            ofs << buffer;
        }
    }

    ofs << "END\n";

    return(true);
}

} //namespace OpenBabel
Revision:	1081
Committed:	Thu Oct 19 20:49:05 2006 UTC (19 years ago) by gezelter
File size:	6012 byte(s)
Log Message:	updated OpenBabel to version 2.0.2
#	Content
1	/**********************************************************************
2	Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
3	Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
4	Some portions Copyright (C) 2004 by Chris Morley
5
6	This program is free software; you can redistribute it and/or modify
7	it under the terms of the GNU General Public License as published by
8	the Free Software Foundation version 2 of the License.
9
10	This program is distributed in the hope that it will be useful,
11	but WITHOUT ANY WARRANTY; without even the implied warranty of
12	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13	GNU General Public License for more details.
14	***********************************************************************/
15
16	/* contributed by Walter Scott (wscott@igc.phys.chem.ethz.ch)
17
18	(Actually the routine was copied from write_xyz and and write_pdb and
19	then modified...)
20
21	This is a small routine to write a GROMOS96 formatted
22	"position coordinate block" (POSITION) or a
23	"reduced position coordinate block" (POSITIONRED)
24	The former has name information (atom and residue names) while
25	the latter only has coordinates.
26	This version does not support the writing of binary
27	GROMOS files.
28
29	NOTE 1: the actual formats used in writing out the coordinates
30	do not matter, as GROMOS96 uses free formatted reads.
31	Each line may not be longer than 80 characters.
32
33	(Note, however, in the POSITION block, the first 24 (twenty four)
34	character on each line are ignored when the line is read in by GROMOS)
35	Comments lines, beginning with hash (#) may occur within a block and are
36	used as delimiters for easier reading.
37
38	NOTE 2: Many programs specify the units of the coordinates (e.g. Angstrom).
39	GROMOS96 does NOT, as all physical constants, from K_B to EPS are
40	NOT hardwired into the code, but specified by the user.
41	This allows some (mostly Americans) to use GROMOS96 in KCal and
42	Angstrom and the rest of us to use kJoule and nm.
43	It also makes it easy to use reduced units.
44
45	We get around this by supplying a routine, wr_sco_gr96, which
46	will scale the coordinates by a factor before writing.
47	This routine is then called with the factor set to 1.0 in
48	write_gr96A, or to 0.1 in write_gr96N depending on the users choice.
49	Thus, we always assume that we have read coordinates in Angstrom.
50	*** But now handled by a command line option in new framework.
51	*/
52
53	#include "mol.hpp"
54	#include "obconversion.hpp"
55
56	using namespace std;
57	namespace OpenBabel
58	{
59
60	class GROMOS96Format : public OBFormat
61	{
62	public:
63	//Register this format type ID
64	GROMOS96Format()
65	{
66	OBConversion::RegisterFormat("gr96",this);
67	}
68
69	virtual const char* Description() //required
70	{
71	return
72	"GROMOS96 format\n \
73	Write Options e.g. -xn\n\
74	n output nm (not Angstroms)\n";
75	};
76
77	virtual const char* SpecificationURL()
78	{
79	return "";
80	}; //optional
81
82	//Flags() can return be any the following combined by \| or be omitted if none apply
83	// NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY
84	virtual unsigned int Flags()
85	{
86	return NOTREADABLE \| WRITEONEONLY;
87	};
88
89	////////////////////////////////////////////////////
90	/// The "API" interface functions
91	virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);
92
93	////////////////////////////////////////////////////
94	/// The "Convert" interface functions
95	virtual bool WriteChemObject(OBConversion* pConv)
96	{
97	//Retrieve the target OBMol
98	OBBase* pOb = pConv->GetChemObject();
99	OBMol* pmol = dynamic_cast<OBMol*> (pOb);
100	bool ret=false;
101	if(pmol)
102	ret=WriteMolecule(pmol,pConv);
103
104	std::string auditMsg = "OpenBabel::Write molecule ";
105	std::string description(Description());
106	auditMsg += description.substr( 0, description.find('\n') );
107	obErrorLog.ThrowError(__func__,
108	auditMsg,
109	obAuditMsg);
110
111	delete pOb;
112	return ret;
113	};
114	};
115
116	//Make an instance of the format class
117	GROMOS96Format theGROMOS96Format;
118
119	////////////////////////////////////////////////////////////////
120
121	bool GROMOS96Format::WriteMolecule(OBBase* pOb, OBConversion* pConv)
122	{
123	OBMol* pmol = dynamic_cast<OBMol*>(pOb);
124	if(pmol==NULL)
125	return false;
126
127	//Define some references so we can use the old parameter names
128	ostream &ofs = *pConv->GetOutStream();
129	OBMol &mol = *pmol;
130	double fac = pConv->IsOption("n") ? 0.1 : 1.0; //new framework
131
132	char type_name[16];
133	char res_name[16];
134	char buffer[BUFF_SIZE];
135	int res_num;
136
137	snprintf(buffer, BUFF_SIZE, "#GENERATED BY OPEN BABEL %s\n",BABEL_VERSION);
138	ofs << buffer;
139
140	/* GROMOS wants a TITLE block, so let's write one*/
141	ofs << "TITLE\n" << mol.GetTitle() << "\nEND\n";
142	ofs << "POSITION\n";
143
144	OBAtom *atom;
145	OBResidue *res;
146	vector<OBNodeBase*>::iterator i;
147
148	for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
149	{
150	if ( (res = atom->GetResidue()) )
151	{
152	// 16 = sizeof(res_name) and sizeof(type_name)
153	strncpy(res_name,(char*)res->GetName().c_str(), 16);
154	res_name[15] = '\0';
155	strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16);
156	type_name[15] = '\0';
157	res_num = res->GetNum();
158	}
159	else
160	{
161	strncpy(type_name,etab.GetSymbol(atom->GetAtomicNum()), 16);
162	strcpy(res_name,"UNK");
163	res_num = 1;
164	}
165
166	snprintf(buffer, BUFF_SIZE, "%5d %5s %5s %6d %15.5f %15.5f %15.5f\n",
167	res_num,res_name,type_name,atom->GetIdx(),
168	atom->x()fac,atom->y()fac,atom->z()*fac);
169	ofs << buffer;
170
171	if (!(atom->GetIdx()%10))
172	{
173	sprintf(buffer,"# %d\n",atom->GetIdx());
174	ofs << buffer;
175	}
176	}
177
178	ofs << "END\n";
179
180	return(true);
181	}
182
183	} //namespace OpenBabel