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/**********************************************************************
Copyright (C) 2000 by OpenEye Scientific Software, 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 "mol.h"
using namespace std;
namespace OpenBabel {
bool ReadMOPAC(istream &ifs,OBMol &mol,char *title)
{
char buffer[BUFF_SIZE];
string str,str1;
float x,y,z;
OBAtom *atom;
vector<string> vs;
bool hasPartialCharges = false;
double energy;
mol.BeginModify();
while (ifs.getline(buffer,BUFF_SIZE))
{
if(strstr(buffer,"CARTESIAN COORDINATES") != NULL)
{
// mol.EndModify();
mol.Clear();
hasPartialCharges = false;
mol.BeginModify();
ifs.getline(buffer,BUFF_SIZE); // blank
ifs.getline(buffer,BUFF_SIZE); // column headings
ifs.getline(buffer,BUFF_SIZE); // blank
ifs.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
while (vs.size() == 5)
{
atom = mol.NewAtom();
atom->SetAtomicNum(etab.GetAtomicNum(vs[1].c_str()));
x = atof((char*)vs[2].c_str());
y = atof((char*)vs[3].c_str());
z = atof((char*)vs[4].c_str());
atom->SetVector(x,y,z);
if (!ifs.getline(buffer,BUFF_SIZE)) break;
tokenize(vs,buffer);
}
}
else if(strstr(buffer,"FINAL HEAT") != NULL)
{
sscanf(buffer,"%*s%*s%*s%*s%*s%lf",&energy);
mol.SetEnergy(energy);
}
else if(strstr(buffer,"NET ATOMIC CHARGES") != NULL)
{
hasPartialCharges = true;
ifs.getline(buffer,BUFF_SIZE); // blank
ifs.getline(buffer,BUFF_SIZE); // column headings
ifs.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
while (vs.size() == 4)
{
atom = mol.GetAtom(atoi(vs[0].c_str()));
atom->SetPartialCharge(atof(vs[2].c_str()));
if (!ifs.getline(buffer,BUFF_SIZE)) break;
tokenize(vs,buffer);
}
}
}
mol.EndModify();
mol.ConnectTheDots();
mol.PerceiveBondOrders();
if (hasPartialCharges)
mol.SetPartialChargesPerceived();
mol.SetTitle(title);
return(true);
}
bool ReadMOPACCartesian(istream &ifs,OBMol &mol,char *title)
{
char buffer[BUFF_SIZE];
string str;
float x,y,z;
OBAtom *atom;
vector<string> vs;
ifs.getline(buffer,BUFF_SIZE); // keywords
ifs.getline(buffer,BUFF_SIZE); // filename
ifs.getline(buffer,BUFF_SIZE); // title (currently ignored)
mol.BeginModify();
while (ifs.getline(buffer,BUFF_SIZE))
{
tokenize(vs,buffer);
if (vs.size() < 7) return(false);
atom = mol.NewAtom();
x = atof((char*)vs[1].c_str());
y = atof((char*)vs[3].c_str());
z = atof((char*)vs[5].c_str());
atom->SetVector(x,y,z); //set coordinates
//set atomic number
atom->SetAtomicNum(etab.GetAtomicNum(vs[0].c_str()));
}
mol.EndModify();
mol.ConnectTheDots();
mol.PerceiveBondOrders();
mol.SetTitle(title);
return(true);
}
bool WriteMOPACCartesian(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
ofs << "PUT KEYWORDS HERE" << endl;
ofs << endl;
ofs << mol.GetTitle() << endl;
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%-3s%8.5f 1 %8.5f 1 %8.5f 1",
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
return(true);
}
}
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