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/**********************************************************************
Copyright (C) 2002 by Geoffrey Hutchison
Based on code Copyright (C) 1999 Jrg-Rdiger Hill
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 {
#define BOHR_TO_ANGSTROM 0.529177
bool ReadViewMol(istream &ifs,OBMol &mol,char *title)
{
char buffer[BUFF_SIZE];
OBAtom *atom;
float x,y,z, border;
int bgn, end, order;
vector<string> vs;
bool foundTitle = false;
bool foundBonds = false;
while (ifs.getline(buffer,BUFF_SIZE))
if (buffer[0] == '$') break;
mol.BeginModify();
while (ifs.getline(buffer,BUFF_SIZE))
{
if (strstr(buffer,"$title") != NULL)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return (false);
mol.SetTitle(buffer);
foundTitle = true;
}
else if (strstr(buffer,"$coord") != NULL)
{
while (ifs.getline(buffer,BUFF_SIZE))
{
if (buffer[0] == '$') break;
tokenize(vs,buffer);
if (vs.size() != 4) return(false);
atom = mol.NewAtom();
x = atof((char*)vs[0].c_str()) * BOHR_TO_ANGSTROM;
y = atof((char*)vs[1].c_str()) * BOHR_TO_ANGSTROM;
z = atof((char*)vs[2].c_str()) * BOHR_TO_ANGSTROM;
atom->SetVector(x,y,z); //set coordinates
atom->SetAtomicNum(etab.GetAtomicNum(vs[3].c_str()));
}
}
else if (strstr(buffer,"$bonds") != NULL)
{
foundBonds = true;
while (ifs.getline(buffer,BUFF_SIZE))
{
if (buffer[0] == '$') break;
sscanf(buffer,"%d %d %f",&bgn,&end, &border);
if (border > 1.0f)
order = int(border);
else
order = 1;
mol.AddBond(bgn+1,end+1,order);
}
}
else if (strstr(buffer,"$end") != NULL)
break;
} // while
mol.EndModify();
if (!foundTitle)
mol.SetTitle(title);
if (!foundBonds)
{
mol.ConnectTheDots();
mol.PerceiveBondOrders();
}
return(true);
}
bool WriteViewMol(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
if (strlen(mol.GetTitle()) > 0)
ofs << "$title" << endl << mol.GetTitle() << endl;
ofs << "$coord 1.0" << endl;
OBAtom *atom;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%22.14f%22.14f%22.14f %s",
atom->GetX(),
atom->GetY(),
atom->GetZ(),
etab.GetSymbol(atom->GetAtomicNum()));
ofs << buffer << endl;
}
ofs << "$end" << endl;
return(true);
}
}
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