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/**********************************************************************
Copyright (C) 2000-2006 by Geoffrey 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/obiter.h>
using namespace std;
namespace OpenBabel
{
#define BOHR_TO_ANGSTROM 0.529177249
class MPQCFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
MPQCFormat()
{
OBConversion::RegisterFormat("mpqc",this);
}
virtual const char* Description() //required
{
return
"MPQC output 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 "http://www.mpqc.org/mpqc-html/mpqcinp.html";}; //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 | READONEONLY;
};
////////////////////////////////////////////////////
/// The "API" interface functions
virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);
};
//Make an instance of the format class
MPQCFormat theMPQCFormat;
class MPQCInputFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
MPQCInputFormat()
{
OBConversion::RegisterFormat("mpqcin",this);
}
virtual const char* Description() //required
{
return
"MPQC simplified input format\n"
"No comments yet\n";
};
virtual const char* SpecificationURL()
{ return "http://www.mpqc.org/mpqc-html/mpqcinp.html";}; //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
MPQCInputFormat theMPQCInputFormat;
/////////////////////////////////////////////////////////////////
bool MPQCFormat::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();
char buffer[BUFF_SIZE];
string str,str1;
double x,y,z;
OBAtom *atom;
vector<string> vs;
bool bohr = true;
mol.BeginModify();
while (ifs.getline(buffer,BUFF_SIZE))
{
if (strstr(buffer, "<Molecule>:") != nullptr)
{
// mol.EndModify();
mol.Clear();
while (strstr(buffer, "geometry") == nullptr)
{
if (strstr(buffer, "angstrom") != nullptr)
bohr = false;
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
}
ifs.getline(buffer,BUFF_SIZE); // Now we're on the atoms
tokenize(vs,buffer);
while (vs.size() == 6)
{
if (bohr)
{
x = atof((char*)vs[3].c_str()) * BOHR_TO_ANGSTROM;
y = atof((char*)vs[4].c_str()) * BOHR_TO_ANGSTROM;
z = atof((char*)vs[5].c_str()) * BOHR_TO_ANGSTROM;
}
else
{
x = atof((char*)vs[3].c_str());
y = atof((char*)vs[4].c_str());
z = atof((char*)vs[5].c_str());
}
atom = mol.NewAtom();
atom->SetVector(x,y,z);
atom->SetAtomicNum(OBElements::GetAtomicNum(vs[1].c_str()));
if (!ifs.getline(buffer,BUFF_SIZE))
break;
tokenize(vs,buffer);
}
}
}
if (mol.NumAtoms() == 0) { // e.g., if we're at the end of a file PR#1737209
mol.EndModify();
return false;
}
if (!pConv->IsOption("b",OBConversion::INOPTIONS))
mol.ConnectTheDots();
if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
mol.PerceiveBondOrders();
mol.EndModify();
mol.SetTitle(title);
return(true);
}
bool MPQCInputFormat::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() << "\n";
ofs << "\n"; // keywords/direction lines here
ofs << "molecule:\n";
FOR_ATOMS_OF_MOL(atom, mol)
{
snprintf(buffer, BUFF_SIZE, "%4s %8.5f %8.5f %8.5f \n",
OBElements::GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer;
}
ofs << "\n\n\n";
return(true);
}
} //namespace OpenBabel