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>
126 lines
5.0 KiB
C++
126 lines
5.0 KiB
C++
//
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// Copyright (C) 2003-2019 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 <RDBoost/PySequenceHolder.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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void setDataHelper(SDMolSupplier &self, const std::string &text, bool sanitize,
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bool removeHs, bool strictParsing) {
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self.setData(text, sanitize, removeHs, strictParsing);
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}
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void setStreamIndices(SDMolSupplier &self, python::object arg) {
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std::vector<std::streampos> loc;
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PySequenceHolder<int> seq(arg);
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loc.reserve(seq.size());
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for (unsigned int i = 0; i < seq.size(); ++i) {
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loc.push_back(static_cast<std::streampos>(seq[i]));
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}
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self.setStreamIndices(loc);
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}
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std::string sdMolSupplierClassDoc =
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"A class which supplies molecules from an SD 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 = SDMolSupplier('in.sdf')\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 = SDMolSupplier('in.sdf')\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:\n\n\
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>>> suppl = SDMolSupplier('in.sdf')\n\
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>>> mol1 = suppl[0] \n\
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>>> mol2 = suppl[1] \n\
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# NOTE: this will generate an IndexError if the supplier doesn't have that many\n\
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molecules.\n\
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\n\
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4) Random Access 2: looping over all molecules \n\n\
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>>> suppl = SDMolSupplier('in.sdf')\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 SD 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 sdmolsup_wrap {
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static void wrap() {
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python::class_<SDMolSupplier, boost::noncopyable>(
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"SDMolSupplier", sdMolSupplierClassDoc.c_str(),
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python::init<>(python::args("self")))
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.def(python::init<std::string, bool, bool, bool>(
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(python::arg("self"), python::arg("fileName"),
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python::arg("sanitize") = true, python::arg("removeHs") = true,
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python::arg("strictParsing") = true)))
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.def("__enter__", &MolIOEnter<SDMolSupplier>,
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python::return_internal_reference<>())
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.def("__exit__", &MolIOExit<SDMolSupplier>)
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.def("__iter__", &MolSupplIter<SDMolSupplier>,
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python::return_internal_reference<1>(), python::args("self"))
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.def("__next__", &MolSupplNext<SDMolSupplier>,
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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<SDMolSupplier>,
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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", &SDMolSupplier::reset, python::args("self"),
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"Resets our position in the file to the beginning.\n")
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.def("__len__", &SDMolSupplier::length, python::args("self"))
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.def("SetData", setDataHelper, "Sets the text to be parsed",
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(python::arg("self"), python::arg("data"),
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python::arg("sanitize") = true, python::arg("removeHs") = true,
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python::arg("strictParsing") = true))
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.def("_SetStreamIndices", setStreamIndices,
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"Sets the locations of mol beginnings in the input stream. Be "
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"*very* careful with this method.",
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(python::arg("self"), python::arg("locs")))
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.def("GetItemText", &SDMolSupplier::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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.def("atEnd", &SDMolSupplier::atEnd, python::args("self"),
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"Returns whether or not we have hit EOF.\n")
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.def("GetProcessPropertyLists", &SDMolSupplier::getProcessPropertyLists,
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python::args("self"),
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"returns whether or not any property lists that are present will "
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"be processed when reading molecules")
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.def("SetProcessPropertyLists", &SDMolSupplier::setProcessPropertyLists,
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python::args("self", "val"),
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"sets whether or not any property lists that are present will be "
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"processed when reading molecules");
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};
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};
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} // namespace RDKit
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void wrap_sdsupplier() { RDKit::sdmolsup_wrap::wrap(); }
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