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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 <cstdlib>
using namespace std;
namespace OpenBabel
{
class CCCFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
CCCFormat()
{
OBConversion::RegisterFormat("ccc",this);
}
virtual const char* Description() //required
{
return
"CCC 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 NOTWRITABLE;
};
////////////////////////////////////////////////////
/// The "API" interface functions
virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);
};
//Make an instance of the format class
CCCFormat theCCCFormat;
/////////////////////////////////////////////////////////////////
bool CCCFormat::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];
ifs.getline(buffer,BUFF_SIZE);
if (strlen(buffer) > 5)
mol.SetTitle(&buffer[5]);
mol.SetEnergy(0.0);
int natoms;
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%*s%d",&natoms);
mol.ReserveAtoms(natoms);
mol.BeginModify();
int end,order;
double x,y,z;
OBAtom atom;
vector3 v;
vector<string> vs;
char element[3];
element[2] = '\0';
for (int i = 1;i <= natoms;i++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
atom.Clear();
element[0] = buffer[0];
element[1] = (buffer[1] != ' ') ? buffer[1]:'\0';
atom.SetAtomicNum(OBElements::GetAtomicNum(element));
sscanf(&buffer[15],"%lf%lf%lf",&x,&y,&z);
v.Set(x,y,z);
atom.SetVector(v);
if (!mol.AddAtom(atom))
return(false);
tokenize(vs,&buffer[60]);
vector<string>::iterator j;
for (j = vs.begin();j != vs.end();++j)
if (!j->empty())
{
//get the bond order
switch((char)(*j)[j->size()-1])
{
case 'S':
order = 1;
break;
case 'D':
order = 2;
break;
case 'T':
order = 3;
break;
default:
order = 1;
}
(*j)[j->size()-1] = ' ';
end = atoi(j->c_str());
if (i>end)
mol.AddBond(i,end,order);
}
}
mol.EndModify();
return(true);
}
} //namespace OpenBabel