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/**********************************************************************
Copyright (C) 2000 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.
***********************************************************************/
#include <openbabel/babelconfig.h>
#include <openbabel/obmolecformat.h>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/elements.h>
#include <openbabel/bond.h>
#include <openbabel/data.h>
#include <cstdlib>
using namespace std;
namespace OpenBabel
{
class XEDFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
XEDFormat()
{
OBConversion::RegisterFormat("xed",this);
}
virtual const char* Description() //required
{
return
"XED format\n"
"No comments yet\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);
};
//Make an instance of the format class
XEDFormat theXEDFormat;
////////////////////////////////////////////////////////////////
bool XEDFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if (pmol == nullptr)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
unsigned int i;
char buffer[BUFF_SIZE];
int type_name, mass;
OBAtom *atom;
OBBond *bond;
string str,str1;
ttab.SetFromType("INT");
ttab.SetToType("XED");
snprintf(buffer, BUFF_SIZE, "%10.3f%10i%10i",
mol.GetEnergy(),mol.NumAtoms(),mol.NumBonds());
ofs << buffer << endl;
ofs << "File conversion by Open Babel" << endl;
for (i = 0; i < mol.NumBonds(); i++)
{
bond = mol.GetBond(i);
snprintf(buffer, BUFF_SIZE, "%8i%8i",
bond->GetBeginAtomIdx(),
bond->GetEndAtomIdx());
ofs << buffer;
if ( !((i+1) % 5) )
ofs << endl;
}
if (mol.NumBonds()%5)
ofs << endl;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.Translate(str1,str);
type_name = atoi((char*) str1.c_str());
switch (type_name)
{
case 1:
case 2:
case 3:
case 4:
mass=6;
break;
case 5:
case 6:
case 7:
case 8:
case 9:
case 23:
case 25:
mass=7;
break;
case 10:
case 11:
case 22:
case 24:
case 26:
mass=8;
break;
case 12:
case 13:
mass=16;
break;
case 14:
mass=15;
break;
case 15:
mass=1;
break;
case 16:
mass=9;
break;
case 17:
mass=17;
break;
case 18:
mass=35;
break;
case 19:
mass=53;
break;
default:
mass=0;
}
snprintf(buffer, BUFF_SIZE, "%6i%15.6f%15.6f%15.6f%6i%12.4f",
mass, atom->GetX(),atom->GetY(),atom->GetZ(), type_name, 0.0);
ofs << buffer << endl;
}
ofs << " 1 0.0000 0 0.0000" << endl;
return(true);
}
} //namespace OpenBabel