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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 <cstdlib>
using namespace std;
namespace OpenBabel
{
class UniChemFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
UniChemFormat()
{
OBConversion::RegisterFormat("unixyz",this);
}
virtual const char* Description() //required
{
return
"UniChem XYZ 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
UniChemFormat theUniChemFormat;
/////////////////////////////////////////////////////////////////
bool UniChemFormat::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;
const char* title = pConv->GetTitle();
int i;
int natoms;
char buffer[BUFF_SIZE];
ifs.getline(buffer,BUFF_SIZE);
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%d", &natoms);
if (!natoms)
return(false);
mol.ReserveAtoms(natoms);
mol.BeginModify();
string str;
double x,y,z;
OBAtom *atom;
vector<string> vs;
for (i = 1; i <= natoms; i ++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
tokenize(vs,buffer);
if (vs.size() != 4)
return(false);
atom = mol.NewAtom();
x = atof((char*)vs[1].c_str());
y = atof((char*)vs[2].c_str());
z = atof((char*)vs[3].c_str());
atom->SetVector(x,y,z); //set coordinates
//set atomic number
atom->SetAtomicNum(atoi((char*)vs[0].c_str()));
}
if (!pConv->IsOption("b",OBConversion::INOPTIONS))
mol.ConnectTheDots();
if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
mol.PerceiveBondOrders();
// 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);
mol.EndModify();
mol.SetTitle(title);
return(true);
}
////////////////////////////////////////////////////////////////
bool UniChemFormat::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];
ofs << mol.GetTitle() << endl;
ofs << mol.NumAtoms() << endl;
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE,
"%3d%15.5f%15.5f%15.5f",
atom->GetAtomicNum(),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
return(true);
}
} //namespace OpenBabel