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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"
#include "obutil.h"
#include "molvector.h"
using namespace std;
namespace OpenBabel {
//Functions for dealing with groups of molecules. MolVec will read either all
//molecules from a file or a set of conformers.
OBMolVector::~OBMolVector()
{
for (unsigned int i = 0; i < _molvec.size(); i++)
{
delete _molvec[i];
_molvec[i] = NULL;
}
}
// Read all molecules from a file into a OBMolVector. Input and output types
// default to SDF
void OBMolVector::Read(ifstream &ifs, const io_type in_type, const io_type out_type, int nToRead)
{
int nRead= 0;
OBFileFormat ff;
while (1)
{
if (nRead == nToRead) break;
OBMol *mol;
mol = new OBMol;
(*mol).SetInputType(in_type);
(*mol).SetOutputType(out_type);
ff.ReadMolecule(ifs,*mol);
nRead++;
if (!(*mol).NumAtoms())
{
delete mol;
mol = NULL;
break;
}
_molvec.push_back(mol);
}
}
// Write a OBMolVector to a file. Output type defaults to SDF
void OBMolVector::Write(ofstream &ofs)
{
vector<OBMol *>::iterator mol_i;
OBFileFormat ff;
for (mol_i = _molvec.begin(); mol_i != _molvec.end(); mol_i++)
{
ff.WriteMolecule(ofs,(**mol_i));
}
}
// Get a specific molecule from a OBMolVector. Index starts at zero.
OBMol *OBMolVector::GetMol(int i)
{
if (i >= 0 && i < (signed)_molvec.size())
return(_molvec[i]);
else
{
cerr << "Index " << i << " out of range in OBMolVector::GetMol " << endl;
return(NULL);
}
}
// Read a set of conformers from an input file and put them into a MolVec.
// This function read the first molecule and sets the current title (held
// int the variable master) to be the current title. It continues to read
// molecules and push them into the vector util it reads a molecule with a
// different name. At this point it rewinds the file stream to the beginning
// of the current molecule and returns
bool OBMolVector::ReadConfs(ifstream &ifs, const io_type in_type, const io_type out_type)
{
OBMol *mol;
OBFileFormat ff;
string title,master;
_molvec.resize(0);
int i = 1;
while (1)
{
mol = new OBMol;
(*mol).SetInputType(in_type);
(*mol).SetOutputType(out_type);
streampos sp = ifs.tellg();
ff.ReadMolecule(ifs,*mol);
if (mol->NumAtoms() == 0)
{
delete mol; mol = NULL;
return(false);
}
title = mol->GetTitle();
if (i == 1)
{
master = title;
_molvec.push_back(mol);
}
else
{
if (title == master)
_molvec.push_back(mol);
else
{
ifs.seekg(sp);
delete mol; mol = NULL;
break;
}
}
i++;
}
return(true);
}
} // namespace OpenBabel
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