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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/bond.h>
#include <openbabel/obiter.h>
#include <openbabel/elements.h>
#include <cstdlib>
using namespace std;
namespace OpenBabel
{
class HINFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
HINFormat()
{
OBConversion::RegisterFormat("hin",this, "chemical/x-hin");
}
virtual const char* Description() //required
{
return "HyperChem HIN format\n"
"No comments yet\n";
};
virtual const char* SpecificationURL()
{ return "";}; //optional
virtual const char* GetMIMEType()
{ return "chemical/x-hin";}; //optional
//*** 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
HINFormat theHINFormat;
/////////////////////////////////////////////////////////////////
bool HINFormat::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();
// Right now only read in the first molecule
int i;
int max, bo;
char buffer[BUFF_SIZE];
string str,str1;
double x,y,z;
OBAtom *atom;
vector<string> vs;
ifs.getline(buffer, BUFF_SIZE);
while (ifs.good() && (strstr(buffer, "mol") == nullptr || buffer[0] == ';')) //The "mol" in comment line should be ignored.
{
ifs.getline(buffer, BUFF_SIZE);
if (ifs.peek() == EOF || !ifs.good())
return false;
}
ifs.getline(buffer, BUFF_SIZE);
if (!ifs.good())
return false; // ended early
mol.BeginModify();
while (ifs.good() && strstr(buffer, "endmol") == nullptr)
{
if(buffer[0]==';'){
ifs.getline(buffer, BUFF_SIZE);
continue; //The comment Line in HIN should be ignored.
}
tokenize(vs,buffer); // Don't really know how long it'll be
if (vs.size() < 11)
{
ifs.getline(buffer, BUFF_SIZE);
continue;
}
atom = mol.NewAtom();
atom->SetAtomicNum(OBElements::GetAtomicNum(vs[3].c_str()));
atom->SetPartialCharge(atof(vs[6].c_str()));
x = atof((char*)vs[7].c_str());
y = atof((char*)vs[8].c_str());
z = atof((char*)vs[9].c_str());
atom->SetVector(x,y,z);
max = 11 + 2 * atoi((char *)vs[10].c_str());
for (i = 11; i < max; i+=2)
{
switch(((char*)vs[i+1].c_str())[0]) // First char in next token
{
case 's':
bo = 1;
break;
case 'd':
bo = 2;
break;
case 't':
bo = 3;
break;
case 'a':
bo = 5;
break;
default :
bo = 1;
break;
}
mol.AddBond(mol.NumAtoms(), atoi((char *)vs[i].c_str()), bo);
}
ifs.getline(buffer, BUFF_SIZE);
}
// clean out remaining blank lines
// blank lines cleaning codes rewritten for avoiding peek() and tellg() bugs
// https://github.com/openbabel/openbabel/issues/1569
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);
mol.SetPartialChargesPerceived();
return(true);
}
////////////////////////////////////////////////////////////////
bool HINFormat::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, file_num = 1;
string str,str1;
char buffer[BUFF_SIZE];
OBAtom *atom;
OBBond *bond;
vector<OBBond*>::iterator j;
char bond_char;
// make sure to escape titles in double quotes
// PR#1501694
ofs << "mol " << file_num << " \"" << mol.GetTitle() << "\"\n";
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, "atom %d - %-3s ** - %8.5f %8.5f %8.5f %8.5f %d ",
i,
OBElements::GetSymbol(atom->GetAtomicNum()),
atom->GetPartialCharge(),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atom->GetExplicitDegree());
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
switch(bond->GetBondOrder())
{
case 1 :
bond_char = 's';
break;
case 2 :
bond_char = 'd';
break;
case 3 :
bond_char = 't';
break;
case 5 :
bond_char = 'a';
break;
default:
bond_char = 's';
break;
}
if (bond->IsAromatic())
bond_char = 'a';
snprintf(buffer,BUFF_SIZE, "%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);
ofs << buffer;
}
ofs << endl;
}
ofs << "endmol " << file_num << endl;
return(true);
}
} //namespace OpenBabel