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/**********************************************************************
Copyright (C) 1998-2001 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 ReadBox(istream &ifs, OBMol &mol,char *title)
{
char buffer[BUFF_SIZE];
vector<string> vs;
vector<string>::iterator i;
OBAtom atom;
mol.BeginModify();
while (ifs.getline(buffer,BUFF_SIZE) && !EQn(buffer,"END",3))
{
if (EQn(buffer,"ATOM",4))
{
string sbuf = &buffer[6];
/* X, Y, Z */
string x = sbuf.substr(24,8);
string y = sbuf.substr(32,8);
string z = sbuf.substr(40,8);
Vector v(atof(x.c_str()),atof(y.c_str()),atof(z.c_str()));
atom.SetVector(v);
if (!mol.AddAtom(atom)) return(false);
}
if (EQn(buffer,"CONECT",6))
{
tokenize(vs,buffer);
if (!vs.empty() && vs.size() > 2)
for (i = vs.begin(),i+=2;i != vs.end();i++)
mol.AddBond(atoi(vs[1].c_str()),atoi((*i).c_str()),1);
}
}
mol.EndModify();
mol.SetTitle(title);
return(true);
}
bool WriteBox(ostream &ofs,OBMol &mol,float margin)
{
char buffer[BUFF_SIZE];
Vector vcenter,vmin,vmax,vmid,vdim;
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
vmax.Set(-10E10,-10E10,-10E10);
vmin.Set( 10E10, 10E10, 10E10);
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
vcenter += atom->GetVector();
if (atom->x() < vmin.x()) vmin.SetX(atom->x());
if (atom->y() < vmin.y()) vmin.SetY(atom->y());
if (atom->z() < vmin.z()) vmin.SetZ(atom->z());
if (atom->x() > vmax.x()) vmax.SetX(atom->x());
if (atom->y() > vmax.y()) vmax.SetY(atom->y());
if (atom->z() > vmax.z()) vmax.SetZ(atom->z());
}
vcenter /= (float)mol.NumAtoms();
Vector vmarg(margin,margin,margin);
vmin -= vmarg; vmax += vmarg;
vdim = vmax - vmin;
vmid = vmin+vmax; vmid /= 2.0f;
ofs << "HEADER CORNERS OF BOX" << endl;
sprintf(buffer,"REMARK CENTER (X Y Z) %10.3f %10.3f %10.3f",
vmid.x(),vmid.y(),vmid.z()); ofs << buffer << endl;
sprintf(buffer,"REMARK DIMENSIONS (X Y Z) %10.3f %10.3f %10.3f",
vdim.x(),vdim.y(),vdim.z()); ofs << buffer << endl;
vdim /= 2.0f;
Vector vtmp;
int j;
for (j = 1;j <= 8;j++)
{
switch(j)
{
case 1: vtmp = vmid-vdim; break;
case 2: vtmp.SetX(vmid.x()+vdim.x()); break;
case 3: vtmp.SetZ(vmid.z()+vdim.z()); break;
case 4: vtmp.SetX(vmid.x()-vdim.x()); break;
case 5:
vtmp = vmid-vdim; vtmp.SetY(vmid.y()+vdim.y());
break;
case 6:
vtmp = vmid+vdim; vtmp.SetZ(vmid.z()-vdim.z());
break;
case 7: vtmp = vmid+vdim; break;
case 8: vtmp.SetX(vmid.x()-vdim.x()); break;
}
sprintf(buffer,"ATOM %d DUA BOX 1 %8.3f%8.3f%8.3f",
j,vtmp.x(),vtmp.y(),vtmp.z());
ofs << buffer << endl;
}
ofs << "CONECT 1 2 4 5" << endl;
ofs << "CONECT 2 1 3 6" << endl;
ofs << "CONECT 3 2 4 7" << endl;
ofs << "CONECT 4 1 3 8" << endl;
ofs << "CONECT 5 1 6 8" << endl;
ofs << "CONECT 6 2 5 7" << endl;
ofs << "CONECT 7 3 6 8" << endl;
ofs << "CONECT 8 4 5 7" << endl;
return(true);
}
}
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