mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
fa89438358
* Adds C++ Enumeration Engine to the RDKit * Adds Sanitization helpers, wrappers and tests * Clang format * Remove unused enumerationStateOnly flag * Fixes docStrings to current API * Adds doc strings * Removes RGroupPosition, adds getPosition to EnumerationBase * Fixes readability. * Adds EnumerateLibraryBase::reset and getReaction * Added getReagents method to EnumerateLibrary * Make the tests have the same naming * Need to save the initial state for resetting. * Stupid case-insensitive file systems * Moves ResetState to EnumerateLibraryBase * Adds removeNonmatchingReagents helper * Renames currentPosition to getPosition * Adds Enumeration Toolkit tutorial * Fixes Python3 serialization and enumerators * Verified to run on python2 and 3 * Fixes integer issues on windows * The number of enumeration should be unsigned. * Adds deserialization constructor * Moves boost_serialization to the end * Deprecates Clone in favor of copy * Update tests to use copy.copy not Clone * Move RGROUPS and BBS into an EnumerationTypes namespace * Make sure old pickles work * Adds pickle for backwards compatibility * Moves to uint64_t from size_t for public api * Whups, accidentally used the binary archiver. * Commits boost 1.55 serialization * Makes serialization turnoffable Like Filter Catalog * Fixes tests when serialization not available. Adds more enumeration strategy tests * Fixes a syntax error on some versions of python * Fixes sanitizeRxn to actually make proper RGroup atoms * Updates SanitizeRXN python API * Updates Enumeration API to a parameter class - fixes reagent removal * Adds a mess of tests * Change stats to return a string. * Exposes EvenPairSamplingStrategy Stats to python * Fixes a crash bug in SanitizeRxn * Adds better testing of the even pair sampling * Fixes namespace * One more try to fix gcc * Enum classes are c++11 and a microsoft extension. * Fix typo * Fixes np.median for python3 * Fixes atom iterators * Adds virtual tags to derived virtual functions (for clarity) * Fixes size comparison issues * Adds doc string * Small cleanup (has no effect since flags aren’t used) * fixes crash bug on windows * get the tests working on windows * Updates tutorial * Adds Glare implementation to Contrib
300 lines
12 KiB
C++
300 lines
12 KiB
C++
//
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// Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#include <RDGeneral/utils.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/ChemReactions/Enumerate/CartesianProduct.h>
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#include <GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h>
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#include <GraphMol/ChemReactions/Enumerate/RandomSample.h>
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#include <GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h>
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#include <GraphMol/ChemReactions/Enumerate/Enumerate.h>
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#include <GraphMol/ChemReactions/ReactionParser.h>
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#include <GraphMol/ChemReactions/ReactionUtils.h>
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#include <GraphMol/ChemReactions/SanitizeRxn.h>
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#ifdef RDK_USE_BOOST_SERIALIZATION
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/archive/text_oarchive.hpp>
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#include <boost/archive/text_iarchive.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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#endif
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using namespace RDKit;
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#ifdef RDK_USE_BOOST_SERIALIZATION
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// for each starting point check to see that the archive
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// starts at the same point
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void pickleTest(EnumerationStrategyBase &en, size_t len) {
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boost::shared_ptr<EnumerationStrategyBase> base(en.copy());
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TEST_ASSERT(std::string(base->type()) == std::string(en.type()));
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for (size_t i = 0; i < len; ++i) {
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std::stringstream ss;
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{
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boost::archive::text_oarchive ar(ss);
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ar &base;
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}
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boost::shared_ptr<EnumerationStrategyBase> copy;
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{
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boost::archive::text_iarchive ar(ss);
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ar ©
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}
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TEST_ASSERT(std::string(base->type()) == std::string(copy->type()));
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TEST_ASSERT(base->next() == copy->next());
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TEST_ASSERT(base->getPosition() == en.next());
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}
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}
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#endif
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void testSamplers() {
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EnumerationTypes::BBS bbs;
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bbs.resize(3);
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for (int i = 0; i < 10; ++i)
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bbs[0].push_back(boost::shared_ptr<ROMol>(SmilesToMol("C=CCN=C=S")));
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for (int i = 0; i < 5; ++i)
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bbs[1].push_back(boost::shared_ptr<ROMol>(SmilesToMol("NCc1ncc(Cl)cc1Br")));
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for (int i = 0; i < 6; ++i)
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bbs[2].push_back(
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boost::shared_ptr<ROMol>(SmilesToMol("NCCCc1ncc(Cl)cc1Br")));
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ChemicalReaction rxn;
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CartesianProductStrategy cart;
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cart.initialize(rxn, bbs);
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RandomSampleStrategy rand;
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rand.initialize(rxn, bbs);
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RandomSampleAllBBsStrategy randBBs;
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randBBs.initialize(rxn, bbs);
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EvenSamplePairsStrategy even;
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even.initialize(rxn, bbs);
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std::vector<boost::shared_ptr<EnumerationStrategyBase> > enumerators;
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enumerators.push_back(
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boost::shared_ptr<EnumerationStrategyBase>(cart.copy()));
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enumerators.push_back(
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boost::shared_ptr<EnumerationStrategyBase>(rand.copy()));
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enumerators.push_back(
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boost::shared_ptr<EnumerationStrategyBase>(randBBs.copy()));
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enumerators.push_back(
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boost::shared_ptr<EnumerationStrategyBase>(even.copy()));
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#ifdef RDK_USE_BOOST_SERIALIZATION
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for (size_t i = 0; i < enumerators.size(); ++i) {
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TEST_ASSERT(enumerators[i]->getNumPermutations() == 10 * 5 * 6);
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pickleTest(*enumerators[i], 10 * 5 * 6);
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}
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#endif
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// for(auto&& i: enumerators) {
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// TEST_ASSERT(i->getNumPermutations() == 10*5*6);
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//}
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}
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void testEvenSamplers() {
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EnumerationTypes::BBS bbs;
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bbs.resize(3);
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unsigned long R1 = 6000;
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unsigned long R2 = 500;
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unsigned long R3 = 10000;
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for (unsigned long i = 0; i < R1; ++i)
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bbs[0].push_back(boost::shared_ptr<ROMol>(SmilesToMol("C=CCN=C=S")));
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for (unsigned long i = 0; i < R2; ++i)
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bbs[1].push_back(boost::shared_ptr<ROMol>(SmilesToMol("NCc1ncc(Cl)cc1Br")));
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for (unsigned long i = 0; i < R3; ++i)
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bbs[2].push_back(
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boost::shared_ptr<ROMol>(SmilesToMol("NCCCc1ncc(Cl)cc1Br")));
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ChemicalReaction rxn;
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EvenSamplePairsStrategy even;
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even.initialize(rxn, bbs);
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std::cout << even.getNumPermutations() << " " << R1 * R2 * R3 << std::endl;
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TEST_ASSERT(even.getNumPermutations() == R1 * R2 * R3);
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for (size_t i = 0; i < 5000; ++i) {
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even.next();
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}
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even.stats();
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}
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const char *smiresults[] = {
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"C=CCNC(=S)NCc1ncc(Cl)cc1Br", "CC=CCNC(=S)NCc1ncc(Cl)cc1Br",
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"C=CCNC(=S)NCCc1ncc(Cl)cc1Br", "CC=CCNC(=S)NCCc1ncc(Cl)cc1Br",
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"C=CCNC(=S)NCCCc1ncc(Cl)cc1Br", "CC=CCNC(=S)NCCCc1ncc(Cl)cc1Br"};
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void testEnumerations() {
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EnumerationTypes::BBS bbs;
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bbs.resize(2);
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bbs[0].push_back(boost::shared_ptr<ROMol>(SmilesToMol("C=CCN=C=S")));
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bbs[0].push_back(boost::shared_ptr<ROMol>(SmilesToMol("CC=CCN=C=S")));
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bbs[1].push_back(boost::shared_ptr<ROMol>(SmilesToMol("NCc1ncc(Cl)cc1Br")));
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bbs[1].push_back(boost::shared_ptr<ROMol>(SmilesToMol("NCCc1ncc(Cl)cc1Br")));
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bbs[1].push_back(boost::shared_ptr<ROMol>(SmilesToMol("NCCCc1ncc(Cl)cc1Br")));
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ChemicalReaction *rxn = RxnSmartsToChemicalReaction(
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"[N;$(N-[#6]):3]=[C;$(C=S):1].[N;$(N[#6]);!$(N=*);!$([N-]);!$(N#*);"
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"!$([ND3]);!$([ND4]);!$(N[O,N]);!$(N[C,S]=[S,O,N]):2]>>[N:3]-[C:1]-[N+0:"
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"2]");
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{
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EnumerateLibrary en(*rxn, bbs);
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size_t i = 0;
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for (; (bool)en; ++i) {
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std::vector<std::vector<std::string> > res = en.nextSmiles();
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TEST_ASSERT(res.size() == 1);
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TEST_ASSERT(res[0].size() == 1);
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TEST_ASSERT(res[0][0] == smiresults[i]);
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TEST_ASSERT(i<=6);
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}
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TEST_ASSERT(i == 6);
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// tests reset
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en.resetState();
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i = 0;
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for (; (bool)en; ++i) {
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std::vector<std::vector<std::string> > res = en.nextSmiles();
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TEST_ASSERT(res.size() == 1);
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TEST_ASSERT(res[0].size() == 1);
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TEST_ASSERT(res[0][0] == smiresults[i]);
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TEST_ASSERT(i<=6);
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}
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TEST_ASSERT(i == 6);
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}
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#ifdef RDK_USE_BOOST_SERIALIZATION
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{
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boost::shared_ptr<EnumerateLibrary> en(
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new EnumerateLibrary(*rxn, bbs, RandomSampleStrategy()));
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std::vector<std::vector<std::vector<std::string> > >smir;
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for (size_t j = 0; j < 10; ++j) {
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std::vector<std::vector<std::string> > smiles = en->nextSmiles();
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smir.push_back(smiles);
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}
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en->resetState();
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for (size_t i = 0; i < 1000; ++i) {
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// pickle and unpickle
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std::stringstream ss;
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{
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boost::archive::text_oarchive ar(ss);
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ar &en;
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}
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boost::shared_ptr<EnumerateLibrary> copy;
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{
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boost::archive::text_iarchive ar(ss);
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ar ©
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}
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for (size_t j = 0; j < 10; ++j) {
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TEST_ASSERT(en->nextSmiles() == copy->nextSmiles());
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}
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copy->resetState();
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for (size_t j = 0; j < 10; ++j) {
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TEST_ASSERT(smir[j] == copy->nextSmiles());
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}
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}
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}
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#endif
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delete rxn;
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}
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const char *rxndata = "$RXN\nUntitled Document-1\n ChemDraw10291618492D\n\n 3 1\n$MOL\n\n\n\n 2 1 0 0 0 0 0 0 0 0999 V2000\n 0.4125 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0\n -0.4125 0.0000 0.0000 R2 0 0 0 0 0 0 0 0 0 2 0 0\n 1 2 1 0 0\nM END\n$MOL\n\n\n\n 2 1 0 0 0 0 0 0 0 0999 V2000\n -0.4125 0.0000 0.0000 R1 0 0 0 0 0 0 0 0 0 1 0 0\n 0.4125 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0\nM END\n$MOL\n\n\n\n 2 1 0 0 0 0 0 0 0 0999 V2000\n 0.4125 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 5 0 0\n -0.4125 0.0000 0.0000 R4 0 0 0 0 0 0 0 0 0 4 0 0\n 1 2 1 0 0\nM END\n$MOL\n\n\n\n 14 15 0 0 0 0 0 0 0 0999 V2000\n 0.5072 -0.5166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5072 0.3084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2949 -0.7616 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7817 -0.0880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2967 0.5794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5558 -1.5443 0.0000 R1 0 0 0 0 0 0 0 0 0 1 0 0\n -0.2073 0.7208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.9218 0.3083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.9217 -0.5167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.2073 -0.9292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.6362 0.7208 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0\n 1.5452 1.3661 0.0000 N 0 0 0 0 0 0 0 0 0 5 0 0\n 2.3507 1.5443 0.0000 R4 0 0 0 0 0 0 0 0 0 4 0 0\n -2.3507 0.3083 0.0000 R2 0 0 0 0 0 0 0 0 0 2 0 0\n 1 2 2 0 0\n 1 3 1 0 0\n 3 4 1 0 0\n 4 5 1 0 0\n 5 2 1 0 0\n 3 6 1 0 0\n 2 7 1 0 0\n 7 8 2 0 0\n 8 9 1 0 0\n 9 10 2 0 0\n 10 1 1 0 0\n 8 11 1 0 0\n 12 13 1 0 0\n 11 14 1 0 0\n 12 5 1 0 0\nM END\n";
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void testInsaneEnumerations() {
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EnumerationTypes::BBS bbs;
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bbs.resize(3);
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ChemicalReaction *rxn2 = RxnBlockToChemicalReaction(rxndata);
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//RxnOps::sanitizeRxn(*rxn2, MolOps::AdjustQueryParameters());
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MatchVectType tvect;
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bbs[0].push_back(boost::shared_ptr<ROMol>(SmilesToMol("CCNCC")));
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bbs[0].push_back(boost::shared_ptr<ROMol>(SmilesToMol("NCC")));
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std::cerr << "0,0 " << (int)SubstructMatch(*bbs[0][0].get(), *rxn2->getReactants()[0].get(), tvect) << std::endl;
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std::cerr << "0,1 " << (int)SubstructMatch(*bbs[0][1].get(), *rxn2->getReactants()[0].get(), tvect) << std::endl;
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bbs[1].push_back(boost::shared_ptr<ROMol>(SmilesToMol("ClC1CCC1")));
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bbs[1].push_back(boost::shared_ptr<ROMol>(SmilesToMol("ClC1CCC1Cl")));
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std::cerr << "1,0 " << (int)SubstructMatch(*bbs[1][0].get(), *rxn2->getReactants()[1].get(), tvect) << std::endl;
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std::cerr << "1,1 " << (int)SubstructMatch(*bbs[1][1].get(), *rxn2->getReactants()[1].get(), tvect) << std::endl;
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bbs[2].push_back(boost::shared_ptr<ROMol>(SmilesToMol("CCNCC")));
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bbs[2].push_back(boost::shared_ptr<ROMol>(SmilesToMol("NCC")));
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std::cerr << "2,0 " << (int)SubstructMatch(*bbs[2][0].get(), *rxn2->getReactants()[2].get(), tvect) << std::endl;
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std::cerr << "2,1 " << (int)SubstructMatch(*bbs[2][1].get(), *rxn2->getReactants()[2].get(), tvect) << std::endl;
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{
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ChemicalReaction *rxn = RxnBlockToChemicalReaction(rxndata);
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RxnOps::sanitizeRxn(*rxn, MolOps::AdjustQueryParameters());
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std::cerr << ChemicalReactionToRxnBlock(*rxn) << std::endl;
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EnumerationParams ThereCanBeOnlyOne;
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ThereCanBeOnlyOne.reagentMaxMatchCount = 1;
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EnumerationTypes::BBS bbs2 = removeNonmatchingReagents(
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*rxn, bbs,
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ThereCanBeOnlyOne);
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TEST_ASSERT(bbs2[0].size() == 1);
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TEST_ASSERT(bbs2[1].size() == 1);
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TEST_ASSERT(bbs2[2].size() == 1);
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delete rxn;
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}
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delete rxn2;
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}
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int main(int argc, char *argv[]) {
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RDLog::InitLogs();
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bool doLong = false;
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if (argc > 1) {
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if (!strncmp(argv[1], "-l", 2)) {
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doLong = true;
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}
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}
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/*
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testSamplers();
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testEvenSamplers();
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testEnumerations();
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*/
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testInsaneEnumerations();
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}
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