mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
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
4.8 KiB
C++
133 lines
4.8 KiB
C++
//
|
|
// Copyright (C) 2020 Shrey Aryan
|
|
//
|
|
// @@ 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.
|
|
//
|
|
#ifdef RDK_BUILD_THREADSAFE_SSS
|
|
|
|
#define NO_IMPORT_ARRAY
|
|
#include <RDBoost/python.h>
|
|
|
|
#include <string>
|
|
|
|
// ours
|
|
#include <GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <RDGeneral/FileParseException.h>
|
|
#include <GraphMol/Wrap/ContextManagers.h>
|
|
|
|
#include "MolSupplier.h"
|
|
#include "MultithreadedMolSupplier.h"
|
|
|
|
namespace python = boost::python;
|
|
|
|
namespace RDKit {
|
|
std::string multiSmilesMolSupplierClassDoc =
|
|
"A class which concurrently supplies molecules from a text file.\n\
|
|
Please note that this class is still a bit experimental and the API may\n\
|
|
change in future releases.\n\
|
|
\n\
|
|
Usage examples:\n\
|
|
\n\
|
|
1) Lazy evaluation: the molecules might not be constructed until we ask for them:\n\n\
|
|
>>> suppl = MultithreadedSmilesMolSupplier('in.smi')\n\
|
|
>>> for mol in suppl:\n\
|
|
... if(mol):\n\
|
|
... mol.GetNumAtoms()\n\
|
|
\n\
|
|
2) Lazy evaluation 2:\n\n\
|
|
>>> suppl = MultithreadedSmilesMolSupplier('in.smi')\n\
|
|
>>> while (!suppl.atEnd()):\n\
|
|
... mol = next(mol)\n\
|
|
... if(mol):\n\
|
|
... mol.GetNumAtoms()\n\
|
|
\n";
|
|
|
|
std::string multiSmsDocStr =
|
|
"Constructor\n\n\
|
|
ARGUMENTS: \n\
|
|
\n\
|
|
- fileName: name of the file to be read\n\
|
|
\n\
|
|
- delimiter: (optional) text delimiter (a string). Defauts to ' \t'.\n\
|
|
\n\
|
|
- smilesColumn: (optional) index of the column containing the SMILES\n\
|
|
data. Defaults to 0.\n\
|
|
\n\
|
|
- nameColumn: (optional) index of the column containing molecule names.\n\
|
|
Defaults to 1.\n\
|
|
\n\
|
|
- titleLine: (optional) set this toggle if the file contains a title line.\n\
|
|
Defaults to true.\n\
|
|
\n\
|
|
- sanitize: (optional) toggles sanitization of molecules as they are read.\n\
|
|
Defaults to true.\n\
|
|
\n\
|
|
- numWriterThreads: (optional) number of writer threads. Defaults to 1.\n\
|
|
\n\
|
|
- sizeInputQueue: (optional) size of input/reader queue. Defaults to 5.\n\
|
|
\n\
|
|
- sizeOutputQueue: (optional) size of output/writer queue. Defaults to 5.\n\
|
|
\n";
|
|
|
|
struct multiSmiMolSup_wrap {
|
|
static void wrap() {
|
|
python::class_<MultithreadedSmilesMolSupplier, boost::noncopyable>(
|
|
"MultithreadedSmilesMolSupplier",
|
|
multiSmilesMolSupplierClassDoc.c_str(),
|
|
python::init<>(python::args("self")))
|
|
.def(python::init<std::string, std::string, int, int, bool, bool,
|
|
unsigned int, size_t, size_t>(
|
|
(python::arg("self"), python::arg("fileName"),
|
|
python::arg("delimiter") = " \t", python::arg("smilesColumn") = 0,
|
|
python::arg("nameColumn") = 1, python::arg("titleLine") = true,
|
|
python::arg("sanitize") = true,
|
|
python::arg("numWriterThreads") = 1,
|
|
python::arg("sizeInputQueue") = 5,
|
|
python::arg("sizeOutputQueue") = 5),
|
|
multiSmsDocStr.c_str()))
|
|
.def("__iter__",
|
|
(MultithreadedSmilesMolSupplier *
|
|
(*)(MultithreadedSmilesMolSupplier *)) &
|
|
MTMolSupplIter,
|
|
python::return_internal_reference<1>(), python::args("self"))
|
|
.def("__enter__",
|
|
(MultithreadedSmilesMolSupplier *
|
|
(*)(MultithreadedSmilesMolSupplier *)) &
|
|
MolIOEnter,
|
|
python::return_internal_reference<>())
|
|
.def("__exit__",
|
|
(bool (*)(MultithreadedSmilesMolSupplier *, python::object,
|
|
python::object, python::object)) &
|
|
MolIOExit)
|
|
.def("__next__",
|
|
(ROMol * (*)(MultithreadedSmilesMolSupplier *)) &
|
|
MolForwardSupplNext,
|
|
"Returns the next molecule in the file. Raises _StopIteration_ "
|
|
"on EOF.\n",
|
|
python::return_value_policy<python::manage_new_object>(),
|
|
python::args("self"))
|
|
.def("atEnd", &MultithreadedSmilesMolSupplier::atEnd,
|
|
python::args("self"),
|
|
"Returns true if we have read all records else false.\n")
|
|
.def("GetLastRecordId",
|
|
(unsigned int (*)(MultithreadedSmilesMolSupplier *)) &
|
|
MTMolSupplLastId,
|
|
python::args("self"),
|
|
"Returns the record id for the last extracted item.\n")
|
|
.def("GetLastItemText",
|
|
(std::string(*)(MultithreadedSmilesMolSupplier *)) &
|
|
MTMolSupplLastItem,
|
|
python::args("self"),
|
|
"Returns the text for the last extracted item.\n");
|
|
};
|
|
};
|
|
} // namespace RDKit
|
|
|
|
void wrap_multiSmiSupplier() { RDKit::multiSmiMolSup_wrap::wrap(); }
|
|
#endif
|