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/**********************************************************************
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.
***********************************************************************/
#include <openbabel/babelconfig.h>
#include <openbabel/obmolecformat.h>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/elements.h>
#include <openbabel/generic.h>
using namespace std;
namespace OpenBabel
{
class CSSRFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
CSSRFormat()
{
OBConversion::RegisterFormat("cssr",this);
}
virtual const char* Description() //required
{
return
"CSD CSSR 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;
};
////////////////////////////////////////////////////
/// The "API" interface functions
virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);
};
//Make an instance of the format class
CSSRFormat theCSSRFormat;
////////////////////////////////////////////////////////////////
bool CSSRFormat::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;
char buffer[BUFF_SIZE];
if (!mol.HasData(OBGenericDataType::UnitCell))
{
snprintf(buffer, BUFF_SIZE,
" REFERENCE STRUCTURE = 00000 A,B,C =%8.3f%8.3f%8.3f",
1.0,1.0,1.0);
ofs << buffer << endl;
snprintf(buffer, BUFF_SIZE,
" ALPHA,BETA,GAMMA =%8.3f%8.3f%8.3f SPGR = P1"
, 90.0f, 90.0f, 90.0f);
ofs << buffer << endl;
}
else
{
OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
snprintf(buffer, BUFF_SIZE,
" REFERENCE STRUCTURE = 00000 A,B,C =%8.3f%8.3f%8.3f",
uc->GetA(), uc->GetB(), uc->GetC());
ofs << buffer << endl;
snprintf(buffer, BUFF_SIZE,
" ALPHA,BETA,GAMMA =%8.3f%8.3f%8.3f SPGR = P1",
uc->GetAlpha() , uc->GetBeta(), uc->GetGamma());
ofs << buffer << endl;
}
snprintf(buffer, BUFF_SIZE, "%4d 1 %s\n",mol.NumAtoms(), mol.GetTitle());
ofs << buffer << endl << endl;
OBAtom *atom,*nbr;
vector<OBAtom*>::iterator i;
vector<OBBond*>::iterator j;
vector<int> vtmp(106,0);
int bonds;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
//assign_pdb_number(pdb_types,atom->GetIdx());
vtmp[atom->GetAtomicNum()]++;
snprintf(buffer, BUFF_SIZE, "%4d%2s%-3d %9.5f %9.5f %9.5f ",
atom->GetIdx(),
OBElements::GetSymbol(atom->GetAtomicNum()),
vtmp[atom->GetAtomicNum()],
atom->x(),
atom->y(),
atom->z());
ofs << buffer;
bonds = 0;
for (nbr = atom->BeginNbrAtom(j); nbr; nbr = atom->NextNbrAtom(j))
{
if (bonds > 8) break;
snprintf(buffer, BUFF_SIZE, "%4d",nbr->GetIdx());
ofs << buffer;
bonds++;
}
for (; bonds < 8; bonds ++)
{
snprintf(buffer, BUFF_SIZE, "%4d",0);
ofs << buffer;
}
snprintf(buffer, BUFF_SIZE, " %7.3f%4d", atom->GetPartialCharge(), 1);
ofs << buffer << endl;
}
return(true);
}
} //namespace OpenBabel