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Replace awful enum reflection macros with Better Enums (rdkit#7913)
* - moved SMILES and RGroupDecomp JSON parsers to their own translation units - added missing DLL export decorators that had been previously forgotten - changed the signatures of MolToCXSmiles and updateCXSmilesFieldsFromJSON to replace enum parameters with the underlying types - updated ReleaseNotes.md * make sure cxSmilesFields is only updated if the JSON string contains keys belonging to the CXSmilesFields enum * added missing copyright notices --------- Co-authored-by: ptosco <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,33 +1,35 @@ | ||
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| rdkit_library(RGroupDecomposition RGroupDecomp.cpp RGroupDecompData.cpp RGroupData.cpp RGroupUtils.cpp RGroupCore.cpp | ||
| RGroupDecompParams.cpp RGroupScore.cpp RGroupFingerprintScore.cpp RGroupGa.cpp | ||
| rdkit_library(RGroupDecomposition RGroupDecomp.cpp RGroupDecompData.cpp | ||
| RGroupData.cpp RGroupUtils.cpp RGroupCore.cpp | ||
| RGroupDecompParams.cpp RGroupScore.cpp RGroupFingerprintScore.cpp | ||
| RGroupGa.cpp RGroupDecompJSONParsers.cpp | ||
| LINK_LIBRARIES | ||
| FMCS ChemTransforms SubstructMatch SmilesParse Fingerprints | ||
| GraphMol RDGeneral ga MolEnumerator TautomerQuery ) | ||
| GraphMol RDGeneral ga MolEnumerator TautomerQuery) | ||
| target_compile_definitions(RGroupDecomposition PRIVATE RDKIT_RGROUPDECOMPOSITION_BUILD) | ||
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| rdkit_headers( | ||
| RGroupDecomp.h RGroupDecompParams.h | ||
| DEST GraphMol/RGroupDecomposition) | ||
| RGroupDecomp.h RGroupDecompParams.h RGroupDecompJSONParsers.h | ||
| DEST GraphMol/RGroupDecomposition) | ||
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| if(RDK_BUILD_PYTHON_WRAPPERS) | ||
| add_subdirectory(Wrap) | ||
| add_subdirectory(Wrap) | ||
| endif() | ||
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| rdkit_test(testRGroupDecomp testRGroupDecomp.cpp | ||
| LINK_LIBRARIES RGroupDecomposition ) | ||
| LINK_LIBRARIES RGroupDecomposition) | ||
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| rdkit_test(testRGroupDecompInternals testRGroupInternals.cpp | ||
| LINK_LIBRARIES RGroupDecomposition ) | ||
| LINK_LIBRARIES RGroupDecomposition) | ||
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| rdkit_catch_test(rgroupCatchTests catch_rgd.cpp | ||
| LINK_LIBRARIES RGroupDecomposition ) | ||
| LINK_LIBRARIES RGroupDecomposition) | ||
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| find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS program_options CONFIG) | ||
| if(RDK_BUILD_CPP_TESTS AND Boost_FOUND) | ||
| add_executable(gaExample GaExample.cpp) | ||
| if(NOT Boost_USE_STATIC_LIBS) | ||
| target_compile_definitions(gaExample PUBLIC -DBOOST_PROGRAM_OPTIONS_DYN_LINK) | ||
| endif() | ||
| target_link_libraries(gaExample RGroupDecomposition ${Boost_PROGRAM_OPTIONS_LIBRARY}) | ||
| endif() | ||
| add_executable(gaExample GaExample.cpp) | ||
| if(NOT Boost_USE_STATIC_LIBS) | ||
| target_compile_definitions(gaExample PUBLIC -DBOOST_PROGRAM_OPTIONS_DYN_LINK) | ||
| endif() | ||
| target_link_libraries(gaExample RGroupDecomposition ${Boost_PROGRAM_OPTIONS_LIBRARY}) | ||
| endif() |
89 changes: 89 additions & 0 deletions
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Code/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.cpp
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| // | ||
| // Copyright (C) 2024 Novartis Biomedical Research and other RDKit contributors | ||
| // | ||
| // @@ All Rights Reserved @@ | ||
| // This file is part of the RDKit. | ||
| // The contents are covered by the terms of the BSD license | ||
| // which is included in the file license.txt, found at the root | ||
| // of the RDKit source tree. | ||
| // | ||
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| #define USE_BETTER_ENUMS | ||
| #include "RGroupDecompJSONParsers.h" | ||
| #include <RDGeneral/BoostStartInclude.h> | ||
| #include <boost/property_tree/ptree.hpp> | ||
| #include <boost/property_tree/json_parser.hpp> | ||
| #include <RDGeneral/BoostEndInclude.h> | ||
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| namespace RDKit { | ||
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| void updateRGroupDecompositionParametersFromJSON( | ||
| RGroupDecompositionParameters ¶ms, const std::string &details_json) { | ||
| updateRGroupDecompositionParametersFromJSON(params, details_json.c_str()); | ||
| } | ||
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| void updateRGroupDecompositionParametersFromJSON( | ||
| RGroupDecompositionParameters ¶ms, const char *details_json) { | ||
| if (details_json && strlen(details_json)) { | ||
| std::istringstream ss; | ||
| boost::property_tree::ptree pt; | ||
| ss.str(details_json); | ||
| boost::property_tree::read_json(ss, pt); | ||
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| std::string labels; | ||
| labels = pt.get<std::string>("labels", labels); | ||
| if (RGroupLabels::_is_valid(labels.c_str())) { | ||
| params.labels = RGroupLabels::_from_string(labels.c_str()); | ||
| } | ||
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| std::string matchingStrategy; | ||
| matchingStrategy = | ||
| pt.get<std::string>("matchingStrategy", matchingStrategy); | ||
| if (RGroupMatching::_is_valid(matchingStrategy.c_str())) { | ||
| params.matchingStrategy = | ||
| RGroupMatching::_from_string(matchingStrategy.c_str()); | ||
| } | ||
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| std::string scoreMethod; | ||
| scoreMethod = pt.get<std::string>("scoreMethod", scoreMethod); | ||
| if (RGroupScore::_is_valid(scoreMethod.c_str())) { | ||
| params.scoreMethod = RGroupScore::_from_string(scoreMethod.c_str()); | ||
| } | ||
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| std::string rgroupLabelling; | ||
| rgroupLabelling = pt.get<std::string>("rgroupLabelling", rgroupLabelling); | ||
| if (RGroupLabelling::_is_valid(rgroupLabelling.c_str())) { | ||
| params.rgroupLabelling = | ||
| RGroupLabelling::_from_string(rgroupLabelling.c_str()); | ||
| } | ||
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| std::string alignment; | ||
| alignment = pt.get<std::string>("alignment", alignment); | ||
| if (RGroupCoreAlignment::_is_valid(alignment.c_str())) { | ||
| params.alignment = RGroupCoreAlignment::_from_string(alignment.c_str()); | ||
| } | ||
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| params.chunkSize = pt.get<unsigned int>("chunkSize", params.chunkSize); | ||
| params.onlyMatchAtRGroups = | ||
| pt.get<bool>("onlyMatchAtRGroups", params.onlyMatchAtRGroups); | ||
| params.removeAllHydrogenRGroups = pt.get<bool>( | ||
| "removeAllHydrogenRGroups", params.removeAllHydrogenRGroups); | ||
| params.removeAllHydrogenRGroupsAndLabels = | ||
| pt.get<bool>("removeAllHydrogenRGroupsAndLabels", | ||
| params.removeAllHydrogenRGroupsAndLabels); | ||
| params.removeHydrogensPostMatch = pt.get<bool>( | ||
| "removeHydrogensPostMatch", params.removeHydrogensPostMatch); | ||
| params.allowNonTerminalRGroups = | ||
| pt.get<bool>("allowNonTerminalRGroups", params.allowNonTerminalRGroups); | ||
| params.allowMultipleRGroupsOnUnlabelled = | ||
| pt.get<bool>("allowMultipleRGroupsOnUnlabelled", | ||
| params.allowMultipleRGroupsOnUnlabelled); | ||
| params.doTautomers = pt.get<bool>("doTautomers", params.doTautomers); | ||
| params.doEnumeration = pt.get<bool>("doEnumeration", params.doEnumeration); | ||
| params.includeTargetMolInResults = pt.get<bool>( | ||
| "includeTargetMolInResults", params.includeTargetMolInResults); | ||
| params.timeout = pt.get<double>("timeout", params.timeout); | ||
| } | ||
| } | ||
|
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| } // end namespace RDKit |
24 changes: 24 additions & 0 deletions
24
Code/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.h
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| // | ||
| // Copyright (C) 2024 Novartis Biomedical Research and other RDKit contributors | ||
| // | ||
| // @@ All Rights Reserved @@ | ||
| // This file is part of the RDKit. | ||
| // The contents are covered by the terms of the BSD license | ||
| // which is included in the file license.txt, found at the root | ||
| // of the RDKit source tree. | ||
| // | ||
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| #pragma once | ||
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| #include "RGroupDecompParams.h" | ||
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| namespace RDKit { | ||
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| RDKIT_RGROUPDECOMPOSITION_EXPORT void | ||
| updateRGroupDecompositionParametersFromJSON( | ||
| RGroupDecompositionParameters ¶ms, const std::string &details_json); | ||
| RDKIT_RGROUPDECOMPOSITION_EXPORT void | ||
| updateRGroupDecompositionParametersFromJSON( | ||
| RGroupDecompositionParameters ¶ms, const char *details_json); | ||
|
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| } // end namespace RDKit |
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