mirror of
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>
90 lines
3.5 KiB
C++
90 lines
3.5 KiB
C++
//
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// Copyright (C) 2005-2021 Greg Landrum and Rational Discovery LLC
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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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#define NO_IMPORT_ARRAY
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#include <RDBoost/python.h>
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#include <string>
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// ours
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/RDKitBase.h>
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#include "MolSupplier.h"
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#include "ContextManagers.h"
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namespace python = boost::python;
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namespace RDKit {
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std::string tdtMolSupplierClassDoc =
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"A class which supplies molecules from a TDT file.\n\
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\n\
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Usage examples:\n\
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\n\
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1) Lazy evaluation: the molecules are not constructed until we ask for them:\n\n\
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>>> suppl = TDTMolSupplier('in.smi')\n\
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>>> for mol in suppl:\n\
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... mol.GetNumAtoms()\n\
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\n\
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2) Lazy evaluation 2:\n\n\
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>>> suppl = TDTMolSupplier('in.smi')\n\
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>>> mol1 = next(suppl)\n\
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>>> mol2 = next(suppl)\n\
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>>> suppl.reset()\n\
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>>> mol3 = next(suppl)\n\n\
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# mol3 and mol1 are the same:\
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>>> MolToSmiles(mol3)==MolToSmiles(mol1)\n\
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\n\
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3) Random Access: all molecules are constructed as soon as we ask for the\n\
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length:\n\n\
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>>> suppl = TDTMolSupplier('in.smi')\n\
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>>> nMols = len(suppl)\n\
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>>> for i in range(nMols):\n\
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... suppl[i].GetNumAtoms()\n\
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\n\
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Properties in the file are used to set properties on each molecule.\n\
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The properties are accessible using the mol.GetProp(propName) method.\n\
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\n";
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struct tdtmolsup_wrap {
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static void wrap() {
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python::class_<TDTMolSupplier, boost::noncopyable>(
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"TDTMolSupplier", tdtMolSupplierClassDoc.c_str(),
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python::init<>(python::args("self")))
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.def(python::init<std::string, std::string, int, int, bool>(
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(python::arg("self"), python::arg("fileName"),
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python::arg("nameRecord") = "", python::arg("confId2D") = -1,
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python::arg("confId3D") = -1, python::arg("sanitize") = true)))
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.def("__enter__", &MolIOEnter<TDTMolSupplier>,
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python::return_internal_reference<>())
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.def("__exit__", &MolIOExit<TDTMolSupplier>)
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.def("__iter__", &MolSupplIter<TDTMolSupplier>,
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python::return_internal_reference<1>(), python::args("self"))
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.def("__next__", &MolSupplNext<TDTMolSupplier>,
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"Returns the next molecule in the file. Raises _StopIteration_ "
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"on EOF.\n",
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python::return_value_policy<python::manage_new_object>(),
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python::args("self"))
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.def("__getitem__", &MolSupplGetItem<TDTMolSupplier>,
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python::return_value_policy<python::manage_new_object>(),
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python::args("self", "idx"))
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.def("reset", &TDTMolSupplier::reset, python::args("self"),
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"Resets our position in the file to the beginning.\n")
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.def("__len__", &TDTMolSupplier::length, python::args("self"))
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.def("SetData", &TDTMolSupplier::setData, "Sets the text to be parsed",
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(python::arg("self"), python::arg("data"),
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python::arg("nameRecord") = "", python::arg("confId2D") = -1,
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python::arg("confId3D") = -1, python::arg("sanitize") = true))
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.def("GetItemText", &TDTMolSupplier::getItemText,
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"returns the text for an item",
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(python::arg("self"), python::arg("index")));
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};
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};
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} // namespace RDKit
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void wrap_tdtsupplier() { RDKit::tdtmolsup_wrap::wrap(); }
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