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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 ReadAlchemy(istream &ifs,OBMol &mol,char *title)
{
int i;
int natoms,nbonds;
char buffer[BUFF_SIZE];
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%d %*s %d", &natoms, &nbonds);
if (!natoms) return(false);
mol.ReserveAtoms(natoms);
ttab.SetFromType("ALC");
string str;
float x,y,z;
OBAtom *atom;
vector<string> vs;
for (i = 1; i <= natoms; i ++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
tokenize(vs,buffer);
if (vs.size() != 6) return(false);
atom = mol.NewAtom();
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); //set coordinates
//set atomic number
ttab.SetToType("ATN"); ttab.Translate(str,vs[1]);
atom->SetAtomicNum(atoi(str.c_str()));
//set type
ttab.SetToType("INT"); ttab.Translate(str,vs[1]);
atom->SetType(str);
}
char bobuf[100];
string bostr;
int bgn,end,order;
for (i = 0; i < nbonds; i++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
sscanf(buffer,"%*d%d%d%s",&bgn,&end,bobuf);
bostr = bobuf; order = 1;
if (bostr == "DOUBLE") order = 2;
else if (bostr == "TRIPLE") order = 3;
else if (bostr == "AROMATIC") order = 5;
mol.AddBond(bgn,end,order);
}
mol.SetTitle(title);
return(true);
}
bool WriteAlchemy(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
char bond_string[10];
snprintf(buffer, BUFF_SIZE, "%5d ATOMS, %5d BONDS, 0 CHARGES",
mol.NumAtoms(),
mol.NumBonds());
ofs << buffer << endl;
ttab.SetFromType("INT"); ttab.SetToType("ALC");
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.Translate(str1,str);
snprintf(buffer, BUFF_SIZE, "%5d %-6s%8.4f %8.4f %8.4f 0.0000",
i,
(char*)str1.c_str(),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
switch(bond->GetBO())
{
case 1 : strcpy(bond_string,"SINGLE"); break;
case 2 : strcpy(bond_string,"DOUBLE"); break;
case 3 : strcpy(bond_string,"TRIPLE"); break;
case 5 : strcpy(bond_string,"AROMATIC"); break;
default : strcpy(bond_string,"SINGLE");
}
snprintf(buffer, BUFF_SIZE, "%5d %4d %4d %s",
bond->GetIdx()+1,
bond->GetBeginAtomIdx(),
bond->GetEndAtomIdx(),
bond_string);
ofs << buffer << endl;
}
return(true);
}
}
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