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>
133 lines
5.1 KiB
C++
133 lines
5.1 KiB
C++
//
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// Copyright (C) 2003-2021 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 <RDGeneral/FileParseException.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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SmilesMolSupplier *SmilesSupplierFromText(
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std::string text, std::string delimiter = " ", int smilesColumn = 0,
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int nameColumn = 1, bool titleLine = true, bool sanitize = true) {
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auto *res = new SmilesMolSupplier();
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res->setData(text, delimiter, smilesColumn, nameColumn, titleLine, sanitize);
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return res;
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}
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std::string smilesMolSupplierClassDoc =
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"A class which supplies molecules from a text 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 = SmilesMolSupplier('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 = SmilesMolSupplier('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\
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# mol3 and mol1 are the same:\n\
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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 = SmilesMolSupplier('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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If the input file has a title line and more than two columns (smiles and id), the\n\
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additional columns will be used to set properties on each molecule. The properties\n\
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are accessible using the mol.GetProp(propName) method.\n\
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\n";
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std::string smsDocStr =
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"Constructor\n\n\
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ARGUMENTS: \n\
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\n\
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- fileName: name of the file to be read\n\
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\n\
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- delimiter: (optional) text delimiter (a string). Defauts to ' '.\n\
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\n\
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- smilesColumn: (optional) index of the column containing the SMILES\n\
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data. Defaults to 0.\n\
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\n\
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- nameColumn: (optional) index of the column containing molecule names.\n\
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Defaults to 1.\n\
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\n\
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- titleLine: (optional) set this toggle if the file contains a title line.\n\
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Defaults to 1.\n\
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\n\
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- sanitize: (optional) toggles sanitization of molecules as they are read.\n\
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Defaults to 1.\n\
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\n";
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struct smimolsup_wrap {
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static void wrap() {
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python::class_<SmilesMolSupplier, boost::noncopyable>(
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"SmilesMolSupplier", smilesMolSupplierClassDoc.c_str(),
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python::init<std::string, std::string, int, int, bool, bool>(
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(python::arg("self"), python::arg("data"),
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python::arg("delimiter") = " ", python::arg("smilesColumn") = 0,
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python::arg("nameColumn") = 1, python::arg("titleLine") = true,
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python::arg("sanitize") = true),
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smsDocStr.c_str()))
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.def(python::init<>(python::args("self")))
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.def("__enter__", &MolIOEnter<SmilesMolSupplier>,
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python::return_internal_reference<>())
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.def("__exit__", &MolIOExit<SmilesMolSupplier>)
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.def("__iter__", &MolSupplIter<SmilesMolSupplier>,
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python::return_internal_reference<1>(), python::args("self"))
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.def("__next__", &MolSupplNext<SmilesMolSupplier>,
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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<SmilesMolSupplier>,
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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", &SmilesMolSupplier::reset, python::args("self"),
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"Resets our position in the file to the beginning.\n")
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.def("__len__", &SmilesMolSupplier::length, python::args("self"))
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.def("SetData", &SmilesMolSupplier::setData,
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"Sets the text to be parsed",
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(python::arg("self"), python::arg("data"),
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python::arg("delimiter") = " ", python::arg("smilesColumn") = 0,
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python::arg("nameColumn") = 1, python::arg("titleLine") = true,
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python::arg("sanitize") = true))
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.def("GetItemText", &SmilesMolSupplier::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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python::def(
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"SmilesMolSupplierFromText", SmilesSupplierFromText,
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(python::arg("text"), python::arg("delimiter") = " ",
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python::arg("smilesColumn") = 0, python::arg("nameColumn") = 1,
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python::arg("titleLine") = true, python::arg("sanitize") = true),
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python::return_value_policy<python::manage_new_object>());
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}
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};
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} // namespace RDKit
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void wrap_smisupplier() { RDKit::smimolsup_wrap::wrap(); }
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