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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 ReadHIN(istream &ifs,OBMol &mol,char *title)
{
// Right now only read in the first molecule
int i;
int max, bo;
char buffer[BUFF_SIZE];
string str,str1;
float x,y,z;
OBAtom *atom;
vector<string> vs;
while (strstr(buffer,"mol") == NULL)
ifs.getline(buffer, BUFF_SIZE);
ifs.getline(buffer, BUFF_SIZE);
mol.BeginModify();
while (strstr(buffer,"endmol") == NULL)
{
tokenize(vs,buffer); // Don't really know how long it'll be
if (vs.size() <= 11) break;
atom = mol.NewAtom();
atom->SetAtomicNum(etab.GetAtomicNum(vs[3].c_str()));
x = atof((char*)vs[7].c_str());
y = atof((char*)vs[8].c_str());
z = atof((char*)vs[9].c_str());
atom->SetVector(x,y,z);
max = 11 + 2 * atoi((char *)vs[10].c_str());
for (i = 11; i < max; i+=2)
{
switch(((char*)vs[i+1].c_str())[0]) // First char in next token
{
case 's': bo = 1; break;
case 'd': bo = 2; break;
case 't': bo = 3; break;
case 'a': bo = 5; break;
default : bo = 1; break;
}
mol.AddBond(mol.NumAtoms(), atoi((char *)vs[i].c_str()), bo);
}
ifs.getline(buffer, BUFF_SIZE);
}
mol.EndModify();
mol.SetTitle(title);
return(true);
}
bool WriteHIN(ostream &ofs,OBMol &mol)
{
unsigned int i, file_num = 1;
string str,str1;
char buffer[BUFF_SIZE];
OBAtom *atom;
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
char bond_char;
ofs << "mol " << file_num << " " << mol.GetTitle() << endl;;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"atom %d - %-3s ** - %8.5f %8.5f %8.5f %8.5f %d ",
i,
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetPartialCharge(),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atom->GetValence());
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
switch(bond->GetBO())
{
case 1 : bond_char = 's'; break;
case 2 : bond_char = 'd'; break;
case 3 : bond_char = 't'; break;
case 5 : bond_char = 'a'; break;
default: bond_char = 's'; break;
}
sprintf(buffer,"%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);
ofs << buffer;
}
ofs << endl;
}
ofs << "endmol " << file_num << endl;
return(true);
}
}
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