mirror of
https://github.com/rdkit/rdkit.git
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121 lines
4.7 KiB
C++
121 lines
4.7 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 <RDBoost/iterator_next.h>
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#include "MolSupplier.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(), python::init<>())
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.def(python::init<std::string, bool, bool, bool>(
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(python::arg("fileName"), python::arg("sanitize") = true,
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python::arg("removeHs") = true,
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python::arg("strictParsing") = true)))
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.def("__iter__", (SDMolSupplier * (*)(SDMolSupplier *)) & MolSupplIter,
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python::return_internal_reference<1>())
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.def(
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NEXT_METHOD,
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(ROMol * (*)(SDMolSupplier *)) & MolSupplNextAcceptNullLastMolecule,
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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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.def("__getitem__",
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(ROMol * (*)(SDMolSupplier *, int)) & MolSupplGetItem,
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python::return_value_policy<python::manage_new_object>())
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.def("reset", &SDMolSupplier::reset,
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"Resets our position in the file to the beginning.\n")
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.def("__len__", &SDMolSupplier::length)
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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,
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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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"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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"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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