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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
106 lines
4.1 KiB
C++
106 lines
4.1 KiB
C++
//
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// Copyright (c) 2016, 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 "PreprocessRxn.h"
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#include "ReactionParser.h"
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/shared_ptr.hpp>
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#include <boost/thread/once.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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#include <GraphMol/FilterCatalog/FunctionalGroupHierarchy.h>
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namespace RDKit {
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bool preprocessReaction(ChemicalReaction &rxn,
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const std::string &propName)
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{
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const bool normalized=true;
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return preprocessReaction(rxn,
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GetFlattenedFunctionalGroupHierarchy(normalized),
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propName);
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}
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bool preprocessReaction(ChemicalReaction &rxn,
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unsigned int &numWarnings,
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unsigned int &numErrors,
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std::vector<
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std::vector<std::pair<unsigned int,std::string> > >&reactantLabels,
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const std::string &propName)
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{
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const bool normalized = true;
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return preprocessReaction(rxn,
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numWarnings,
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numErrors,
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reactantLabels,
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GetFlattenedFunctionalGroupHierarchy(normalized),
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propName);
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}
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bool preprocessReaction(ChemicalReaction &rxn,
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const std::map<std::string, ROMOL_SPTR> &queries,
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const std::string &propName) {
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unsigned int numWarnings, numErrors;
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std::vector<
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std::vector<std::pair<unsigned int,std::string> > >reactantLabels;
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return preprocessReaction(rxn,
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numWarnings,
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numErrors,
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reactantLabels,
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queries,
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propName);
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}
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bool preprocessReaction(ChemicalReaction &rxn,
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unsigned int &numWarnings,
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unsigned int &numErrors,
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std::vector<
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std::vector<std::pair<unsigned int,std::string> > >&reactantLabels,
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const std::map<std::string, ROMOL_SPTR> &queries,
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const std::string &propName) {
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rxn.setImplicitPropertiesFlag(true);
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rxn.initReactantMatchers();
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if (rxn.validate(numWarnings, numErrors)) {
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addRecursiveQueriesToReaction(rxn,
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queries,
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propName,
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&reactantLabels);
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return true;
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}
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return false;
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}
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}
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