1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
|
/**********************************************************************
RDKitConv.cpp - Convert OpenBabel OBMol to RGKit molecules
Copyright (C) 2007 by Chris Morley
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
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.
**********************************************************************
This code calls C++ routines in RDKit which are
Copyright (C) 2003-2006 Rational Discovery LLC
BSD license
***********************************************************************/
#include <openbabel/babelconfig.h>
#include <RDKitConv.h>
using OpenBabel::OBMolAtomIter;
using OpenBabel::OBMolBondIter;
RDKit::RWMol OBMolToRWMol(OpenBabel::OBMol* pOBMol);
RDKit::RWMol OBMolToRWMol(OpenBabel::OBMol* pOBMol)
{
RDKit::RWMol RDMol;
FOR_ATOMS_OF_MOL(a,pOBMol)
{
RDMol.addAtom();
RDKit::Atom* pRDAtom = RDMol.getActiveAtom();
pRDAtom->setAtomicNum(a->GetAtomicNum());
pRDAtom->setFormalCharge(a->GetFormalCharge());
}
FOR_BONDS_OF_MOL(b,pOBMol)
{
//bond order >3 needs doing properly
//assume RDKit atom indices start at 0
RDMol.addBond(b->GetBeginAtomIdx()-1, b->GetEndAtomIdx()-1, (RDKit::Bond::BondType)b->GetBO());
}
std::string msg("RWMol made from ");
if(pOBMol->GetTitle())
msg += pOBMol->GetTitle();
else
msg += "OBMol";
OpenBabel::obErrorLog.ThrowError(__FUNCTION__, msg, OpenBabel::obInfo);
return RDMol;
}
|
