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510 lines
13 KiB
C++
510 lines
13 KiB
C++
// $Id$
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//
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// Copyright (C) 2006 Greg Landrum
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// All Rights Reserved
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//
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// The tests in this file demonstrate the use of RDKit with
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// the boost iostreams library. Particularly the compression pieces
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// of that library.
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//
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Depictor/RDDepictor.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <fstream>
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#include <iostream>
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#ifdef SUPPORT_COMPRESSED_IO
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#include <boost/iostreams/device/file.hpp>
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#include <boost/iostreams/filtering_stream.hpp>
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#include <boost/iostreams/filter/gzip.hpp>
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#include <boost/iostreams/filter/bzip2.hpp>
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#include <boost/iostreams/operations.hpp>
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#include <boost/range/iterator_range.hpp>
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#endif
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#include <string>
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using namespace RDKit;
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namespace io = boost::iostreams;
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void test1() {
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#ifdef SUPPORT_COMPRESSED_IO
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BOOST_LOG(rdInfoLog) << "testing basic reading from compressed streams"
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<< std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fname2 =
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rdbase + "/Code/Demos/RDKit/BinaryIO/test_data/triazine.mol.gz";
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RWMol *m;
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io::filtering_istream inStrm;
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inStrm.push(io::gzip_decompressor());
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inStrm.push(io::file_source(fname2));
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TEST_ASSERT(inStrm.is_complete());
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unsigned int lineNo = 0;
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m = MolDataStreamToMol(inStrm, lineNo);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(6));
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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#else
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BOOST_LOG(rdInfoLog) << "Compressed IO disabled; test skipped" << std::endl;
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#endif
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}
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void test2() {
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#ifdef SUPPORT_COMPRESSED_IO
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BOOST_LOG(rdInfoLog)
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<< "testing writing to, then reading from compressed streams"
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<< std::endl;
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std::string smiles = "C1CCCC1";
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std::string buff, molBlock;
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RWMol *m;
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(5));
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m->setProp(common_properties::_Name, "monkey");
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io::filtering_ostream outStrm;
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outStrm.push(io::gzip_compressor());
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outStrm.push(io::back_inserter(buff));
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TEST_ASSERT(outStrm.is_complete());
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molBlock = MolToMolBlock(*m);
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outStrm << molBlock;
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outStrm.reset();
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delete m;
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io::filtering_istream inStrm;
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inStrm.push(io::gzip_decompressor());
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inStrm.push(boost::make_iterator_range(buff));
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TEST_ASSERT(inStrm.is_complete());
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unsigned int lineNo = 0;
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m = MolDataStreamToMol(inStrm, lineNo);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(5));
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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#else
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BOOST_LOG(rdInfoLog) << "Compressed IO disabled; test skipped" << std::endl;
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#endif
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}
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void test3() {
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#ifdef SUPPORT_COMPRESSED_IO
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BOOST_LOG(rdInfoLog)
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<< "testing writing pickles to a file then reading them back"
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<< std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fname2 = rdbase + "/Code/Demos/RDKit/BinaryIO/test_data/mols.rdb";
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std::string smiles, buff;
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RWMol *m;
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std::vector<unsigned int> filePs;
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io::filtering_ostream outStrm;
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outStrm.push(
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io::file_sink(fname2, std::ios_base::out | std::ios_base::binary));
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TEST_ASSERT(outStrm.is_complete());
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smiles = "C1CCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(4));
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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smiles = "C1CCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(4));
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RDDepict::compute2DCoords(*m);
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filePs.push_back(0);
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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smiles = "C1CCCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(5));
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RDDepict::compute2DCoords(*m);
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filePs.push_back(outStrm.tellp());
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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smiles = "c1ccccc1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(6));
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RDDepict::compute2DCoords(*m);
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filePs.push_back(outStrm.tellp());
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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smiles = "c1ccccc1CC(=O)O";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(9));
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RDDepict::compute2DCoords(*m);
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filePs.push_back(outStrm.tellp());
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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outStrm.flush();
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outStrm.reset();
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io::filtering_istream inStrm;
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inStrm.push(
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io::file_source(fname2, std::ios_base::in | std::ios_base::binary));
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TEST_ASSERT(inStrm.is_complete());
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(4));
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delete m;
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(4));
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delete m;
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(5));
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delete m;
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(6));
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delete m;
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(9));
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delete m;
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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#else
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BOOST_LOG(rdInfoLog) << "Compressed IO disabled; test skipped" << std::endl;
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#endif
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}
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void test4() {
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#ifdef SUPPORT_COMPRESSED_IO
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BOOST_LOG(rdInfoLog) << "testing writing pickles to a single compressed file "
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"then reading them back" << std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fname2 = rdbase + "/Code/Demos/RDKit/BinaryIO/test_data/mols.rdz";
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std::string smiles;
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RWMol *m;
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io::filtering_ostream outStrm;
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outStrm.push(io::gzip_compressor());
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outStrm.push(
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io::file_sink(fname2, std::ios_base::out | std::ios_base::binary));
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TEST_ASSERT(outStrm.is_complete());
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smiles = "C1CCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(4));
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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smiles = "C1CCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(4));
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RDDepict::compute2DCoords(*m);
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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smiles = "C1CCCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(5));
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RDDepict::compute2DCoords(*m);
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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smiles = "c1ccccc1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(6));
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RDDepict::compute2DCoords(*m);
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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smiles = "c1ccccc1CC(=O)O";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(9));
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RDDepict::compute2DCoords(*m);
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MolPickler::pickleMol(*m, outStrm);
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delete m;
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io::flush(outStrm);
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outStrm.pop();
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io::filtering_istream inStrm;
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inStrm.push(io::gzip_decompressor());
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inStrm.push(
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io::file_source(fname2, std::ios_base::in | std::ios_base::binary));
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TEST_ASSERT(inStrm.is_complete());
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(4));
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delete m;
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(4));
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delete m;
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(5));
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delete m;
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(6));
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delete m;
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(inStrm, *m);
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TEST_ASSERT(m->getNumAtoms(9));
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delete m;
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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#else
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BOOST_LOG(rdInfoLog) << "Compressed IO disabled; test skipped" << std::endl;
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#endif
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}
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void test5() {
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#ifdef SUPPORT_COMPRESSED_IO
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BOOST_LOG(rdInfoLog) << "testing writing compressed pickles to a single file "
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"then reading them back" << std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fname2 = rdbase + "/Code/Demos/RDKit/BinaryIO/test_data/tmp.rdz";
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std::string smiles, buff;
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RWMol *m;
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std::vector<unsigned int> filePs;
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io::filtering_ostream outStrm;
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outStrm.push(
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io::file_sink(fname2, std::ios_base::out | std::ios_base::binary));
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TEST_ASSERT(outStrm.is_complete());
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smiles = "C1CCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(4));
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io::filtering_ostream *tmpStrm;
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tmpStrm = new io::filtering_ostream();
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tmpStrm->push(io::gzip_compressor());
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tmpStrm->push(io::back_inserter(buff));
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filePs.push_back(0);
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MolPickler::pickleMol(*m, *tmpStrm);
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delete m;
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tmpStrm->reset();
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outStrm << buff.size();
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outStrm << buff;
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std::cerr << "sz: " << buff.size() << " " << outStrm.tellp() << std::endl;
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buff = "";
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tmpStrm->push(io::gzip_compressor());
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tmpStrm->push(io::back_inserter(buff));
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smiles = "C1CCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(4));
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RDDepict::compute2DCoords(*m);
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filePs.push_back(outStrm.tellp());
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MolPickler::pickleMol(*m, *tmpStrm);
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delete m;
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tmpStrm->reset();
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outStrm << buff.size();
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outStrm << buff;
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std::cerr << "sz: " << buff.size() << " " << outStrm.tellp() << std::endl;
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buff = "";
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tmpStrm->push(io::gzip_compressor());
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tmpStrm->push(io::back_inserter(buff));
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smiles = "C1CCCC1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(5));
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RDDepict::compute2DCoords(*m);
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filePs.push_back(outStrm.tellp());
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MolPickler::pickleMol(*m, *tmpStrm);
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delete m;
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tmpStrm->reset();
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outStrm << buff.size();
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outStrm << buff;
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std::cerr << "sz: " << buff.size() << " " << outStrm.tellp() << std::endl;
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buff = "";
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tmpStrm->push(io::gzip_compressor());
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tmpStrm->push(io::back_inserter(buff));
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smiles = "c1ccccc1";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(6));
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RDDepict::compute2DCoords(*m);
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filePs.push_back(outStrm.tellp());
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MolPickler::pickleMol(*m, *tmpStrm);
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delete m;
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tmpStrm->reset();
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outStrm << buff.size();
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outStrm << buff;
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std::cerr << "sz: " << buff.size() << " " << outStrm.tellp() << std::endl;
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buff = "";
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tmpStrm->push(io::gzip_compressor());
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tmpStrm->push(io::back_inserter(buff));
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smiles = "c1ccccc1CC(=O)O";
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m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms(9));
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RDDepict::compute2DCoords(*m);
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filePs.push_back(outStrm.tellp());
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MolPickler::pickleMol(*m, *tmpStrm);
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delete m;
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tmpStrm->reset();
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outStrm << buff.size();
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outStrm << buff;
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std::cerr << "sz: " << buff.size() << " " << outStrm.tellp() << std::endl;
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delete tmpStrm;
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io::flush(outStrm);
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outStrm.pop();
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io::filtering_istream tmpIStrm;
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io::filtering_istream inStrm;
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unsigned int sz;
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char *charArr;
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inStrm.push(
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io::file_source(fname2, std::ios_base::in | std::ios_base::binary));
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TEST_ASSERT(inStrm.is_complete());
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inStrm >> sz;
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charArr = new char[sz];
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inStrm.read(charArr, sz);
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buff = "";
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buff.append(charArr, sz);
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tmpIStrm.push(io::gzip_decompressor());
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tmpIStrm.push(boost::make_iterator_range(buff));
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(tmpIStrm, *m);
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TEST_ASSERT(m->getNumAtoms(4));
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delete m;
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inStrm >> sz;
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delete[] charArr;
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charArr = new char[sz];
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inStrm.read(charArr, sz);
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buff = "";
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buff.append(charArr, sz);
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tmpIStrm.reset();
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tmpIStrm.push(io::gzip_decompressor());
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tmpIStrm.push(boost::make_iterator_range(buff));
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(tmpIStrm, *m);
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TEST_ASSERT(m->getNumAtoms(4));
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delete m;
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inStrm >> sz;
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delete[] charArr;
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charArr = new char[sz];
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inStrm.read(charArr, sz);
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buff = "";
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buff.append(charArr, sz);
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tmpIStrm.reset();
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tmpIStrm.push(io::gzip_decompressor());
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tmpIStrm.push(boost::make_iterator_range(buff));
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(tmpIStrm, *m);
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TEST_ASSERT(m->getNumAtoms(5));
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delete m;
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inStrm >> sz;
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delete[] charArr;
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charArr = new char[sz];
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inStrm.read(charArr, sz);
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buff = "";
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buff.append(charArr, sz);
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tmpIStrm.reset();
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tmpIStrm.push(io::gzip_decompressor());
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tmpIStrm.push(boost::make_iterator_range(buff));
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(tmpIStrm, *m);
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TEST_ASSERT(m->getNumAtoms(6));
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delete m;
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inStrm >> sz;
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delete[] charArr;
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charArr = new char[sz];
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inStrm.read(charArr, sz);
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buff = "";
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buff.append(charArr, sz);
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tmpIStrm.reset();
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tmpIStrm.push(io::gzip_decompressor());
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tmpIStrm.push(boost::make_iterator_range(buff));
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m = new RWMol();
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TEST_ASSERT(m);
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MolPickler::molFromPickle(tmpIStrm, *m);
|
|
TEST_ASSERT(m->getNumAtoms(9));
|
|
delete m;
|
|
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
#else
|
|
BOOST_LOG(rdInfoLog) << "Compressed IO disabled; test skipped" << std::endl;
|
|
#endif
|
|
}
|
|
|
|
int main(int argc, char *argv[]) {
|
|
RDLog::InitLogs();
|
|
#if 1
|
|
test1();
|
|
test2();
|
|
test3();
|
|
test4();
|
|
test5();
|
|
#endif
|
|
return 0;
|
|
}
|