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root/OpenMD/trunk/src/openbabel/gromos96format.cpp
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Comparing trunk/src/openbabel/gromos96format.cpp (file contents):
Revision 1080 by tim, Wed Nov 16 21:22:51 2005 UTC vs.
Revision 1081 by gezelter, Thu Oct 19 20:49:05 2006 UTC

# Line 1 | Line 1 | Copyright (C) 1998-2001 by OpenEye Scientific Software
1   /**********************************************************************
2   Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
3 < Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
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
# Line 50 | Line 50 | GNU General Public License for more details.
50           *** But now handled by a command line option in new framework.
51   */
52  
53 < #include "gromos96format.hpp"
53 > #include "mol.hpp"
54 > #include "obconversion.hpp"
55  
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);
# Line 67 | Line 129 | bool GROMOS96Format::WriteMolecule(OBBase* pOb, OBConv
129      OBMol &mol = *pmol;
130      double fac = pConv->IsOption("n") ? 0.1 : 1.0; //new framework
131  
132 <    char type_name[10];
133 <    char res_name[10],padded_name[10];
132 >    char type_name[16];
133 >    char res_name[16];
134      char buffer[BUFF_SIZE];
135      int res_num;
136  
137 <    sprintf(buffer,"#GENERATED BY OPEN BABEL %s",BABEL_VERSION);
138 <    ofs << buffer << endl;
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 <    sprintf(buffer,"TITLE\n%s\nEND",mol.GetTitle());
142 <    ofs << buffer << endl;
81 <    ofs << "POSITION" << endl;
141 >    ofs << "TITLE\n" << mol.GetTitle() << "\nEND\n";
142 >    ofs << "POSITION\n";
143  
144      OBAtom *atom;
145      OBResidue *res;
# Line 88 | Line 149 | bool GROMOS96Format::WriteMolecule(OBBase* pOb, OBConv
149      {
150        if ( (res = atom->GetResidue()) )
151          {
152 <            strcpy(res_name,(char*)res->GetName().c_str());
153 <            strcpy(type_name,(char*)res->GetAtomID(atom).c_str());
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 <            strcpy(type_name,etab.GetSymbol(atom->GetAtomicNum()));
161 >            strncpy(type_name,etab.GetSymbol(atom->GetAtomicNum()), 16);
162              strcpy(res_name,"UNK");
99 –            sprintf(padded_name,"%2s",type_name);
100 –            strcpy(type_name,padded_name);
163              res_num = 1;
164          }
165  
166 <        sprintf(buffer,"%5d %5s %5s %6d %15.5f %15.5f %15.5f",
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 << endl;
169 >        ofs << buffer;
170  
171          if (!(atom->GetIdx()%10))
172          {
173 <            sprintf(buffer,"# %d",atom->GetIdx());
174 <            ofs << buffer << endl;
173 >            sprintf(buffer,"# %d\n",atom->GetIdx());
174 >            ofs << buffer;
175          }
176      }
177  
178 <    ofs << "END" << endl;
178 >    ofs << "END\n";
179  
180      return(true);
181   }

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