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4c1ea25fda
* Fix a hang when trying to read mols from a directory not a file on linux * thrown an exception at construction time * clarify the readme * update release notes * Refactor the stream opening and checking code to a common method Co-authored-by: Brian Kelley <bkelley@relaytx.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
133 lines
4.5 KiB
C++
133 lines
4.5 KiB
C++
// Copyright (C) 2018 Lorton
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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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#include <fstream>
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// ours
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#include <RDGeneral/BadFileException.h>
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#include <RDGeneral/FileParseException.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/RDKitBase.h>
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#include <RDBoost/python_streambuf.h>
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#include <RDBoost/iterator_next.h>
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#include <maeparser/MaeConstants.hpp>
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#include <maeparser/Reader.hpp>
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#include "MolSupplier.h"
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namespace python = boost::python;
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using namespace schrodinger;
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using boost_adaptbx::python::streambuf;
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namespace {
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bool streamIsGoodOrExhausted(std::istream *stream) {
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PRECONDITION(stream, "bad stream");
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return stream->good() || (stream->eof() && stream->fail() && !stream->bad());
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}
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class LocalMaeMolSupplier : public RDKit::MaeMolSupplier {
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public:
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LocalMaeMolSupplier(python::object &input, bool sanitize, bool removeHs) {
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// FIX: minor leak here
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auto *sb = new streambuf(input);
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dp_inStream = new streambuf::istream(*sb);
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dp_sInStream.reset(dp_inStream);
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df_owner = true;
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df_sanitize = sanitize;
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df_removeHs = removeHs;
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d_reader.reset(new mae::Reader(dp_sInStream));
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CHECK_INVARIANT(streamIsGoodOrExhausted(dp_inStream), "bad instream");
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try {
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d_next_struct = d_reader->next(mae::CT_BLOCK);
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} catch (const mae::read_exception &e) {
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throw RDKit::FileParseException(e.what());
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}
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}
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LocalMaeMolSupplier(streambuf &input, bool sanitize, bool removeHs) {
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dp_inStream = new streambuf::istream(input);
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dp_sInStream.reset(dp_inStream);
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df_owner = true;
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df_sanitize = sanitize;
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df_removeHs = removeHs;
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d_reader.reset(new mae::Reader(dp_sInStream));
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CHECK_INVARIANT(streamIsGoodOrExhausted(dp_inStream), "bad instream");
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try {
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d_next_struct = d_reader->next(mae::CT_BLOCK);
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} catch (const mae::read_exception &e) {
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throw RDKit::FileParseException(e.what());
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}
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}
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LocalMaeMolSupplier(const std::string &fname, bool sanitize = true,
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bool removeHs = true)
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: RDKit::MaeMolSupplier(fname, sanitize, removeHs) {}
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}; // namespace
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LocalMaeMolSupplier *FwdMolSupplIter(LocalMaeMolSupplier *self) { return self; }
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} // namespace
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namespace RDKit {
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std::string maeMolSupplierClassDoc =
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"A class which supplies molecules from file-like object containing Maestro data.\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 = MaeMolSupplier(file('in.mae'))\n\
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>>> for mol in suppl:\n\
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... if mol is not None: mol.GetNumAtoms()\n\
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\n\
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2) we can also read from compressed files: \n\n\
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>>> import gzip\n\
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>>> suppl = MaeMolSupplier(gzip.open('in.maegz'))\n\
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>>> for mol in suppl:\n\
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... if mol is not None: print mol.GetNumAtoms()\n\
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\n\
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Properties in the Maestro 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 maemolsup_wrap {
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static void wrap() {
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python::class_<LocalMaeMolSupplier, boost::noncopyable>(
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"MaeMolSupplier", maeMolSupplierClassDoc.c_str(), python::no_init)
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.def(python::init<python::object &, bool, bool>(
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(python::arg("fileobj"), python::arg("sanitize") = true,
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python::arg("removeHs") =
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true))[python::with_custodian_and_ward_postcall<0, 2>()])
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.def(python::init<streambuf &, bool, bool>(
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(python::arg("streambuf"), python::arg("sanitize") = true,
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python::arg("removeHs") =
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true))[python::with_custodian_and_ward_postcall<0, 2>()])
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.def(python::init<std::string, 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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.def(NEXT_METHOD, (ROMol * (*)(LocalMaeMolSupplier *)) & MolSupplNext,
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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("atEnd", &MaeMolSupplier::atEnd,
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"Returns whether or not we have hit EOF.\n")
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.def("__iter__", &FwdMolSupplIter,
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python::return_internal_reference<1>());
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};
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};
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} // namespace RDKit
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void wrap_maesupplier() { RDKit::maemolsup_wrap::wrap(); }
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