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//
//
// Copyright (C) 2020 Schrödinger, LLC
//
// @@ 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.
//
#include <string>
#include <RDBoost/Wrap.h>
#include <RDBoost/python.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/CIPLabeler/CIPLabeler.h>
#include <GraphMol/FileParsers/FileParsers.h>
namespace python = boost::python;
using RDKit::CIPLabeler::assignCIPLabels;
void rdMaxIterationsExceededTranslator(
RDKit::CIPLabeler::MaxIterationsExceeded const &x) {
std::ostringstream ss;
ss << x.what();
PyErr_SetString(PyExc_RuntimeError, ss.str().c_str());
}
void assignCIPLabelsWrapHelper(RDKit::ROMol &mol,
const python::object &atomsToLabel,
const python::object &bondsToLabel,
unsigned int maxRecursiveIterations) {
auto atoms = pythonObjectToDynBitset(atomsToLabel, mol.getNumAtoms());
auto bonds = pythonObjectToDynBitset(bondsToLabel, mol.getNumBonds());
// If both atoms and bonds are None, assign all the mol.
if (!atomsToLabel && !bondsToLabel) {
atoms.set();
bonds.set();
}
assignCIPLabels(mol, atoms, bonds, maxRecursiveIterations);
}
BOOST_PYTHON_MODULE(rdCIPLabeler) {
python::scope().attr("__doc__") =
"Module containing a function to assign stereochemical labels based "
"on an accurate CIP rules implementation. This algoritm is a port "
"of https://github.com/SiMolecule/centres, which was originally "
"written by John Mayfield. The original algorithm is described in:\n\n"
"Hanson, R. M., Musacchio, S., Mayfield, J. W., Vainio, M. J., Yerin, "
"A., Redkin, D.\nAlgorithmic Analysis of Cahn--Ingold--Prelog Rules of "
"Stereochemistry:\nProposals for Revised Rules and a Guide for Machine "
"Implementation.\nJ. Chem. Inf. Model. 2018, 58, 1755-1765.\n";
python::register_exception_translator<
RDKit::CIPLabeler::MaxIterationsExceeded>(
&rdMaxIterationsExceededTranslator);
std::string docString =
"New implementation of Stereo assignment using a true CIP ranking.\n"
"On return: The molecule to contains CIP flags\n"
"Errors: when maxRecursiveIterations is exceeded, throws a "
"MaxIterationsExceeded error\nARGUMENTS:\n\n"
" - mol: the molecule\n"
" - atomsToLabel: (optional) list of atoms to label\n"
" - bondsToLabel: (optional) list of bonds to label\n"
" - maxRecursiveIterations: (optional) protects against pseudo-infinite\n"
"recursion for highly symmetrical structures.\n A value of 1,250,000 take"
" about 1 second. Most structures requires less than 10,000"
"iterations.\n A peptide with MW~3000 took about 100 iterations, and a "
"20,000 mw protein took about 600 iterations\n(0 = default - no limit)\n";
python::def(
"AssignCIPLabels", assignCIPLabelsWrapHelper,
(python::arg("mol"), python::arg("atomsToLabel") = python::object(),
python::arg("bondsToLabel") = python::object(),
python::arg("maxRecursiveIterations") = 0),
docString.c_str());
}
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