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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
Some portions Copyright (C) 2013 by Schrodinger Inc.
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/generic.h>
#include <cstdlib>
using namespace std;
namespace OpenBabel
{
class CARFormat : public OBMoleculeFormat
{
public:
//Register this format type ID
CARFormat()
{
OBConversion::RegisterFormat("car",this, "chemical/x-msi-car");
OBConversion::RegisterFormat("arc",this, "chemical/x-msi-car");
}
virtual const char* Description() //required
{
return
"Accelrys/MSI Biosym/Insight II CAR 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.centrcn.umontreal.ca/accelrys/life/insight2000.1/formats980/Files980TOC.doc.html";}; //optional
virtual const char* GetMIMEType()
{ return "chemical/x-msi-car"; };
virtual unsigned int Flags()
{
return NOTWRITABLE;
};
////////////////////////////////////////////////////
/// The "API" interface functions
virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);
};
//Make an instance of the format class
CARFormat theCARFormat;
/////////////////////////////////////////////////////////////////
bool CARFormat::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();
bool hasPartialCharges = false;
char buffer[BUFF_SIZE];
string str;
double x,y,z;
OBAtom *atom;
vector<string> vs;
mol.BeginModify();
while (ifs.getline(buffer,BUFF_SIZE))
{
if(strstr(buffer, "end") != nullptr)
{
if (mol.NumAtoms() > 0) // we've already read in a molecule, so exit
break;
// else, we hit the end of the previous molecular system
// (in a multimolecule file)
ifs.getline(buffer,BUFF_SIZE); // title
ifs.getline(buffer,BUFF_SIZE); // DATE
}
if (strncmp(buffer, "!BIOSYM", 7) == 0)
{
continue;
}
if (strstr(buffer, "PBC") != nullptr)
{
if (strstr(buffer, "ON") != nullptr)
{
ifs.getline(buffer,BUFF_SIZE); // title
ifs.getline(buffer,BUFF_SIZE); // DATE
ifs.getline(buffer,BUFF_SIZE); // PBC a b c alpha beta gamma SG
string str = buffer;
// parse cell parameters
tokenize(vs,str," \t\r\n", 7);
if (vs.size() >= 7)
{
//parse cell values
double A,B,C,Alpha,Beta,Gamma;
A = atof((char*)vs[1].c_str());
B = atof((char*)vs[2].c_str());
C = atof((char*)vs[3].c_str());
Alpha = atof((char*)vs[4].c_str());
Beta = atof((char*)vs[5].c_str());
Gamma = atof((char*)vs[6].c_str());
OBUnitCell *uc = new OBUnitCell;
uc->SetOrigin(fileformatInput);
uc->SetData(A, B, C, Alpha, Beta, Gamma);
if(vs.size() > 7)
{
string& space_group = vs[7];
// Remove parentheses enclosing the space
// group and remove white space from front
// and back of string.
Trim(space_group);
if(space_group[0] == '(')
{
space_group.erase(0, 1);
space_group.erase(space_group.size()-1);
}
Trim(space_group);
uc->SetSpaceGroup(space_group);
}
mol.SetData(uc);
}
}
else // PBC=OFF
{
ifs.getline(buffer,BUFF_SIZE); // title
ifs.getline(buffer,BUFF_SIZE); // !DATE
}
continue;
} // PBC
// reading real data!
tokenize(vs,buffer);
if (vs.size() < 8) {
break;
}
atom = mol.NewAtom();
atom->SetAtomicNum(OBElements::GetAtomicNum(vs[7].c_str()));
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);
// vs[0] contains atom label
// vs[4] contains "type of residue containing atom"
// vs[5] contains "residue sequence name"
// vs[6] contains "potential type of atom"
if (vs.size() == 9)
{
atom->SetPartialCharge(atof((char*)vs[8].c_str()));
hasPartialCharges = true;
}
}
if (!pConv->IsOption("b",OBConversion::INOPTIONS))
mol.ConnectTheDots();
if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
mol.PerceiveBondOrders();
mol.EndModify();
if (hasPartialCharges)
mol.SetPartialChargesPerceived();
mol.SetTitle(title);
return(true);
}
} //namespace OpenBabel