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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/obutil.h>
using namespace std;
namespace OpenBabel
{
class FEATFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
FEATFormat()
{
OBConversion::RegisterFormat("feat",this);
}
virtual const char* Description() //required
{
return
"Feature format\n"
"Read Options e.g. -as\n"
" s Output single bonds only\n"
" b Disable bonding entirely\n\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 READONEONLY | WRITEONEONLY;
};
//*** This section identical for most OBMol conversions ***
////////////////////////////////////////////////////
/// The "API" interface functions
virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);
virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);
};
//***
//Make an instance of the format class
FEATFormat theFEATFormat;
/////////////////////////////////////////////////////////////////
bool FEATFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if (pmol == nullptr)
return false;
//Define some references so we can use the old parameter names
istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
mol.SetTitle( pConv->GetTitle()); //default title is the filename
char buffer[BUFF_SIZE];
int i,natoms;
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%d",&natoms);
mol.ReserveAtoms(natoms);
mol.BeginModify();
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
mol.SetTitle(buffer);
double x,y,z;
char type[32];
OBAtom *atom;
for (i = 0; i < natoms;i++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
sscanf(buffer,"%30s %lf %lf %lf",
type,
&x,
&y,
&z);
CleanAtomType(type);
atom = mol.NewAtom();
atom->SetVector(x,y,z);
atom->SetAtomicNum(OBElements::GetAtomicNum(type));
}
// clean out remaining blank lines
std::streampos ipos;
do
{
ipos = ifs.tellg();
ifs.getline(buffer,BUFF_SIZE);
}
while(strlen(buffer) == 0 && !ifs.eof() );
ifs.seekg(ipos);
if (!pConv->IsOption("b",OBConversion::INOPTIONS))
mol.ConnectTheDots();
if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
mol.PerceiveBondOrders();
mol.EndModify();
return(true);
}
////////////////////////////////////////////////////////////////
bool FEATFormat::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];
ofs << mol.NumAtoms() << endl;
ofs << mol.GetTitle() << endl;
OBAtom *atom;
vector<OBAtom*>::iterator i;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
snprintf(buffer, BUFF_SIZE, "%-3s %8.5f %8.5f %8.5f ",
OBElements::GetSymbol(atom->GetAtomicNum()),
atom->x(),
atom->y(),
atom->z());
ofs << buffer << endl;
}
return(true);
}
} //namespace OpenBabel