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https://github.com/rdkit/rdkit.git
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2b4202867e
* - added gen_rdkit_stubs Python module to generate rdkit-stubs - added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible - added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build - added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF) * fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest * - added missing cmp_func parameter - fixed case with overloads with optional parameters - do not trim params if expected_param_count == -1 - add dummy parameter names if we could not find any - keep into account member functions when making up parameter names - address __init__ and make_constructor __init__ functions - fix incorrectly assigned staticmethods * patched sources * address residual few remarks --------- Co-authored-by: ptosco <paolo.tosco@novartis.com>
109 lines
4.2 KiB
C++
109 lines
4.2 KiB
C++
//
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// Copyright (C) 2020-2021 Brian P Kelley and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDBoost/python.h>
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#include <RDBoost/Wrap.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Deprotect/Deprotect.h>
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namespace python = boost::python;
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namespace RDKit {
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boost::shared_ptr<ROMol> DeprotectWrap(const ROMol &mol,
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const python::object &iterable) {
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if (iterable != python::object()) {
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std::vector<Deprotect::DeprotectData> deprotections;
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pythonObjectToVect<Deprotect::DeprotectData>(iterable, deprotections);
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return Deprotect::deprotect(mol, deprotections);
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} else {
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return Deprotect::deprotect(mol, Deprotect::getDeprotections());
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}
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}
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bool DeprotectInPlaceWrap(ROMol &mol, const python::object &iterable) {
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RWMol &rwmol = static_cast<RWMol &>(mol);
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if (iterable != python::object()) {
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std::vector<Deprotect::DeprotectData> deprotections;
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pythonObjectToVect<Deprotect::DeprotectData>(iterable, deprotections);
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return Deprotect::deprotectInPlace(rwmol, deprotections);
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} else {
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return Deprotect::deprotectInPlace(rwmol, Deprotect::getDeprotections());
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}
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}
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//! Make a copy so we don't try and change a const vector
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std::vector<Deprotect::DeprotectData> GetDeprotectionsWrap() {
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return Deprotect::getDeprotections();
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}
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} // namespace RDKit
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struct deprotect_wrap {
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static void wrap() {
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const char *constructor_doc =
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"Construct a new DeprotectData instance.\n"
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" >>> reaction_class = \"amine\"\n"
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" >>> reaction_smarts = "
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"\"[C;R0][C;R0]([C;R0])([O;R0][C;R0](=[O;R0])[NX3;H0,H1:1])C>>[N:1]\"\n"
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" >>> abbreviation = \"Boc\"\n"
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" >>> full_name = \"tert-butyloxycarbonyl\"\n"
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" >>> data = DeprotectData(reaction_class, reaction_smarts, "
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"abbreviation, full_name)\n"
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" >>> assert data.isValid()\n"
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"\n";
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const char *deprotect_doc_string =
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"DeprotectData class, contains a single deprotection reaction and "
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"information\n"
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"\n"
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" deprotectdata.deprotection_class - functional group being protected\n"
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" deprotectdata.reaction_smarts - reaction smarts used for "
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"deprotection\n"
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" deprotectdata.abbreviation - common abbreviation for the protecting "
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"group\n"
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" deprotectdata.full_name - full name for the protecting group\n"
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"\n"
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"\n";
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RegisterVectorConverter<RDKit::Deprotect::DeprotectData>(
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"DeprotectDataVect");
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python::class_<RDKit::Deprotect::DeprotectData>(
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"DeprotectData", deprotect_doc_string,
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python::init<std::string, std::string, std::string, std::string>(
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constructor_doc,
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python::args("self", "deprotection_class", "reaction_smarts",
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"abbreviation", "full_name")))
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.def_readonly("deprotection_class",
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&RDKit::Deprotect::DeprotectData::deprotection_class)
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.def_readonly("full_name", &RDKit::Deprotect::DeprotectData::full_name)
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.def_readonly("abbreviation",
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&RDKit::Deprotect::DeprotectData::abbreviation)
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.def_readonly("reaction_smarts",
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&RDKit::Deprotect::DeprotectData::reaction_smarts)
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.def_readonly("example", &RDKit::Deprotect::DeprotectData::example)
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.def("isValid", &RDKit::Deprotect::DeprotectData::isValid,
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python::args("self"),
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"Returns True if the DeprotectData has a valid reaction");
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python::def("GetDeprotections", &RDKit::GetDeprotectionsWrap,
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"Return the default list of deprotections");
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python::def(
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"Deprotect", &RDKit::DeprotectWrap,
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(python::arg("mol"), python::arg("deprotections") = python::object()),
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"Return the deprotected version of the molecule.");
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python::def(
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"DeprotectInPlace", &RDKit::DeprotectInPlaceWrap,
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(python::arg("mol"), python::arg("deprotections") = python::object()),
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"Deprotects the molecule in place.");
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}
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};
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void wrap_deprotect() { deprotect_wrap::wrap(); }
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