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//
// Copyright (C) 2007-2021 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.
//
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#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() noexcept { 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, bool updateLabels,
bool preserveProps) {
PRECONDITION(dp_mol, "no molecule");
PRECONDITION(atom, "bad atom");
dp_mol->replaceAtom(idx, atom, updateLabels, preserveProps);
};
void ReplaceBond(unsigned int idx, Bond *bond, bool preserveProps) {
PRECONDITION(dp_mol, "no molecule");
PRECONDITION(bond, "bad bond");
dp_mol->replaceBond(idx, bond, preserveProps);
};
void BeginBatchEdit() {
PRECONDITION(dp_mol, "no molecule");
dp_mol->beginBatchEdit();
};
void RollbackBatchEdit() {
PRECONDITION(dp_mol, "no molecule");
dp_mol->rollbackBatchEdit();
};
void CommitBatchEdit() {
PRECONDITION(dp_mol, "no molecule");
dp_mol->commitBatchEdit();
};
ROMol *GetMol() const {
PRECONDITION(dp_mol, "no molecule");
auto *res = new ROMol(*dp_mol);
return res;
};
private:
RWMol *dp_mol;
};
} // namespace
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\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 &>(python::args("self", "m"),
"Construct from a Mol"))
.def("RemoveAtom", &EditableMol::RemoveAtom,
python::args("self", "idx"),
"Remove the specified atom from the molecule")
.def("RemoveBond", &EditableMol::RemoveBond,
python::args("self", "idx1", "idx2"),
"Remove the specified bond from the molecule")
.def("AddBond", &EditableMol::AddBond,
((python::arg("self"), python::arg("beginAtomIdx")),
python::arg("endAtomIdx"),
python::arg("order") = Bond::UNSPECIFIED),
"add a bond, returns the total number of bonds")
.def("AddAtom", &EditableMol::AddAtom,
((python::arg("self"), python::arg("atom"))),
"add an atom, returns the index of the newly added atom")
.def("ReplaceAtom", &EditableMol::ReplaceAtom,
((python::arg("self"), python::arg("index")),
python::arg("newAtom"), python::arg("updateLabel") = false,
python::arg("preserveProps") = false),
"replaces the specified atom with the provided one\n"
"If updateLabel is True, the new atom becomes the active atom\n"
"If preserveProps is True preserve keep the existing props unless "
"explicit set on the new atom")
.def("ReplaceBond", &EditableMol::ReplaceBond,
((python::arg("self"), python::arg("index")),
python::arg("newBond"), python::arg("preserveProps") = false),
"replaces the specified bond with the provided one.\n"
"If preserveProps is True preserve keep the existing props unless "
"explicit set on the new bond")
.def("BeginBatchEdit", &EditableMol::BeginBatchEdit,
python::args("self"), "starts batch editing")
.def("RollbackBatchEdit", &EditableMol::RollbackBatchEdit,
python::args("self"), "cancels batch editing")
.def("CommitBatchEdit", &EditableMol::CommitBatchEdit,
python::args("self"),
"finishes batch editing and makes the actual edits")
.def("GetMol", &EditableMol::GetMol,
"Returns a Mol (a normal molecule)",
python::return_value_policy<python::manage_new_object>(),
python::args("self"));
};
};
} // namespace RDKit
void wrap_EditableMol() { RDKit::EditableMol_wrapper::wrap(); }
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