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// $Id: EditableMol.cpp 2000 2012-03-23 04:47:22Z glandrum $
//
// Copyright (C) 2007 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
// there's a compiler bug in some versions of g++ that causes this file to not compile unless
// we skip the docstrings:
//#define BOOST_PYTHON_NO_PY_SIGNATURES
#define NO_IMPORT_ARRAY
#include <boost/python.hpp>
#include <string>
#include "rdchem.h"
// ours
#include <GraphMol/RDKitBase.h>
namespace python = boost::python;
namespace RDKit {
namespace {
class EditableMol : boost::noncopyable {
public:
EditableMol(const ROMol &m) {
dp_mol= new RWMol(m);
};
~EditableMol() {
PRECONDITION(dp_mol,"no molecule");
delete dp_mol;
};
void RemoveAtom(unsigned int idx){
PRECONDITION(dp_mol,"no molecule");
dp_mol->removeAtom(idx);
};
void RemoveBond(unsigned int idx1,unsigned int idx2){
PRECONDITION(dp_mol,"no molecule");
dp_mol->removeBond(idx1,idx2);
};
int AddBond(unsigned int begAtomIdx,
unsigned int endAtomIdx,
Bond::BondType order=Bond::UNSPECIFIED)
{
PRECONDITION(dp_mol,"no molecule");
return dp_mol->addBond(begAtomIdx,endAtomIdx,order);
};
int AddAtom(Atom *atom){
PRECONDITION(dp_mol,"no molecule");
PRECONDITION(atom,"bad atom");
return dp_mol->addAtom(atom,true,false);
};
void ReplaceAtom(unsigned int idx,Atom *atom){
PRECONDITION(dp_mol,"no molecule");
PRECONDITION(atom,"bad atom");
dp_mol->replaceAtom(idx,atom);
};
ROMol *GetMol() const{
PRECONDITION(dp_mol,"no molecule");
ROMol *res=new ROMol(*dp_mol);
return res;
};
private:
RWMol *dp_mol;
};
}
struct EditableMol_wrapper {
static void wrap(){
std::string molClassDoc = "The EditableMol class.\n\n\
This class can be used to add/remove bonds and atoms to\n\
a molecule.\n\
In order to use it, you need to first construct an EditableMol\n\
from a standard Mol:\n\
>>> m = Chem.MolFromSmiles('CCC')\n\
>>> em = Chem.EditableMol(m)\n\
>>> em.AddAtom(Chem.Atom(8))\n\
>>> em.AddBond(0,3,Chem.BondType.SINGLE)\n\
>>> m2 = em.GetMol()\n\
>>> Chem.SanitizeMol(m2)\n\
>>> Chem.MolToSmiles(m2)\n\
'CCCO'\n\
\n\
*Note*: It is very, very easy to shoot yourself in the foot with\n\
this class by constructing an unreasonable molecule.\n\
";
python::class_<EditableMol,boost::noncopyable >("EditableMol",
"an editable molecule class",
python::init<const ROMol &>("Construct from a Mol"))
.def("RemoveAtom",&EditableMol::RemoveAtom,
"Remove the specified atom from the molecule")
.def("RemoveBond",&EditableMol::RemoveBond,
"Remove the specified bond from the molecule")
.def("AddBond",&EditableMol::AddBond,
(python::arg("mol"),python::arg("beginAtomIdx"),python::arg("endAtomIdx"),
python::arg("order")=Bond::UNSPECIFIED),
"add a bond, returns the index of the newly added bond")
.def("AddAtom",&EditableMol::AddAtom,
(python::arg("mol"),python::arg("atom")),
"add an atom, returns the index of the newly added atom")
.def("ReplaceAtom",&EditableMol::ReplaceAtom,
(python::arg("mol"),python::arg("index"),python::arg("newAtom")),
"replaces the specified atom with the provided one")
.def("GetMol",&EditableMol::GetMol,
"Returns a Mol (a normal molecule)",
python::return_value_policy<python::manage_new_object>())
;
};
};
}// end of namespace
void wrap_EditableMol() {
RDKit::EditableMol_wrapper::wrap();
}
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