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3f7caf0147
* Extend RDKit::MolStandardize with a validation and standardization Pipeline * suggested changes * apply clang-format * apply yapf * MolStandardize::FeaturesValidation optionally disallow dative bonds * add allowDativeBondType to MolStandardize::PipelineOptions * apply clang-format * make the API of other validation classes more consistent with MolStandardize::FeaturesValidation * apply clang-format * PipelineStage to enum class remove virtual functions from Pipeline class be explicit about enums * light refactoring to avoid what I think is an unnecessary call to `parse` * a bit of modernization * make the pipeline configurable * make parse and serialize configurable too * switch to storing pipeline stages using uints * add a simple test for providing a pipeline * update pointer alignment for clang-format * test modifying the parser and serializer * update swig requirement * changes in response to review * changes in response to review * rename PipelineResult's *MolBlock members to *MolData * upgrade swig to 4.2 in the CI environments * add a few missing export directives --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
144 lines
7.0 KiB
C++
144 lines
7.0 KiB
C++
//
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// Copyright (C) 2023 Novartis Biomedical Research
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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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#include <RDBoost/Wrap.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/MolStandardize/Pipeline.h>
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namespace RDKit {
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namespace MolStandardize {
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bool operator==(const PipelineLogEntry &lhs, const PipelineLogEntry &rhs) {
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return (lhs.status == rhs.status) && (lhs.detail == rhs.detail);
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}
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} // namespace MolStandardize
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} // namespace RDKit
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namespace python = boost::python;
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using namespace RDKit;
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void wrap_pipeline() {
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python::class_<MolStandardize::PipelineOptions>("PipelineOptions")
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.def_readwrite("strictParsing",
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&MolStandardize::PipelineOptions::strictParsing)
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.def_readwrite("reportAllFailures",
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&MolStandardize::PipelineOptions::reportAllFailures)
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.def_readwrite("allowEmptyMolecules",
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&MolStandardize::PipelineOptions::allowEmptyMolecules)
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.def_readwrite("allowEnhancedStereo",
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&MolStandardize::PipelineOptions::allowEnhancedStereo)
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.def_readwrite("allowAromaticBondType",
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&MolStandardize::PipelineOptions::allowAromaticBondType)
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.def_readwrite("allowDativeBondType",
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&MolStandardize::PipelineOptions::allowDativeBondType)
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.def_readwrite("is2DZeroThreshold",
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&MolStandardize::PipelineOptions::is2DZeroThreshold)
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.def_readwrite("atomClashLimit",
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&MolStandardize::PipelineOptions::atomClashLimit)
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.def_readwrite("minMedianBondLength",
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&MolStandardize::PipelineOptions::minMedianBondLength)
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.def_readwrite("bondLengthLimit",
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&MolStandardize::PipelineOptions::bondLengthLimit)
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.def_readwrite("allowLongBondsInRings",
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&MolStandardize::PipelineOptions::allowLongBondsInRings)
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.def_readwrite(
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"allowAtomBondClashExemption",
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&MolStandardize::PipelineOptions::allowAtomBondClashExemption)
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.def_readwrite("metalNof", &MolStandardize::PipelineOptions::metalNof)
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.def_readwrite("metalNon", &MolStandardize::PipelineOptions::metalNon)
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.def_readwrite("normalizerData",
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&MolStandardize::PipelineOptions::normalizerData)
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.def_readwrite("normalizerMaxRestarts",
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&MolStandardize::PipelineOptions::normalizerMaxRestarts)
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.def_readwrite("scaledMedianBondLength",
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&MolStandardize::PipelineOptions::scaledMedianBondLength)
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.def_readwrite("outputV2000",
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&MolStandardize::PipelineOptions::outputV2000);
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python::enum_<MolStandardize::PipelineStatus>("PipelineStatus")
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.value("NO_EVENT", MolStandardize::PipelineStatus::NO_EVENT)
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.value("INPUT_ERROR", MolStandardize::PipelineStatus::INPUT_ERROR)
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.value("PREPARE_FOR_VALIDATION_ERROR",
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MolStandardize::PipelineStatus::PREPARE_FOR_VALIDATION_ERROR)
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.value("FEATURES_VALIDATION_ERROR",
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MolStandardize::PipelineStatus::FEATURES_VALIDATION_ERROR)
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.value("BASIC_VALIDATION_ERROR",
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MolStandardize::PipelineStatus::BASIC_VALIDATION_ERROR)
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.value("IS2D_VALIDATION_ERROR",
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MolStandardize::PipelineStatus::IS2D_VALIDATION_ERROR)
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.value("LAYOUT2D_VALIDATION_ERROR",
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MolStandardize::PipelineStatus::LAYOUT2D_VALIDATION_ERROR)
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.value("STEREO_VALIDATION_ERROR",
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MolStandardize::PipelineStatus::STEREO_VALIDATION_ERROR)
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.value("VALIDATION_ERROR",
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MolStandardize::PipelineStatus::VALIDATION_ERROR)
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.value("PREPARE_FOR_STANDARDIZATION_ERROR",
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MolStandardize::PipelineStatus::PREPARE_FOR_STANDARDIZATION_ERROR)
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.value("METAL_STANDARDIZATION_ERROR",
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MolStandardize::PipelineStatus::METAL_STANDARDIZATION_ERROR)
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.value("NORMALIZER_STANDARDIZATION_ERROR",
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MolStandardize::PipelineStatus::NORMALIZER_STANDARDIZATION_ERROR)
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.value("FRAGMENT_STANDARDIZATION_ERROR",
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MolStandardize::PipelineStatus::FRAGMENT_STANDARDIZATION_ERROR)
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.value("CHARGE_STANDARDIZATION_ERROR",
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MolStandardize::PipelineStatus::CHARGE_STANDARDIZATION_ERROR)
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.value("STANDARDIZATION_ERROR",
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MolStandardize::PipelineStatus::STANDARDIZATION_ERROR)
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.value("OUTPUT_ERROR", MolStandardize::PipelineStatus::OUTPUT_ERROR)
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.value("PIPELINE_ERROR", MolStandardize::PipelineStatus::PIPELINE_ERROR)
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.value("METALS_DISCONNECTED",
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MolStandardize::PipelineStatus::METALS_DISCONNECTED)
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.value("NORMALIZATION_APPLIED",
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MolStandardize::PipelineStatus::NORMALIZATION_APPLIED)
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.value("FRAGMENTS_REMOVED",
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MolStandardize::PipelineStatus::FRAGMENTS_REMOVED)
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.value("PROTONATION_CHANGED",
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MolStandardize::PipelineStatus::PROTONATION_CHANGED)
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.value("STRUCTURE_MODIFICATION",
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MolStandardize::PipelineStatus::STRUCTURE_MODIFICATION);
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python::enum_<MolStandardize::PipelineStage>("PipelineStage")
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.value("PARSING_INPUT", MolStandardize::PipelineStage::PARSING_INPUT)
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.value("PREPARE_FOR_VALIDATION",
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MolStandardize::PipelineStage::PREPARE_FOR_VALIDATION)
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.value("VALIDATION", MolStandardize::PipelineStage::VALIDATION)
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.value("PREPARE_FOR_STANDARDIZATION",
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MolStandardize::PipelineStage::PREPARE_FOR_STANDARDIZATION)
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.value("STANDARDIZATION", MolStandardize::PipelineStage::STANDARDIZATION)
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.value("SERIALIZING_OUTPUT",
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MolStandardize::PipelineStage::SERIALIZING_OUTPUT)
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.value("COMPLETED", MolStandardize::PipelineStage::COMPLETED);
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python::class_<MolStandardize::PipelineLogEntry>("PipelineLogEntry",
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python::no_init)
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.def_readonly("status", &MolStandardize::PipelineLogEntry::status)
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.def_readonly("detail", &MolStandardize::PipelineLogEntry::detail);
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python::class_<MolStandardize::PipelineLog>("PipelineLog", python::no_init)
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.def(python::vector_indexing_suite<MolStandardize::PipelineLog>());
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python::class_<MolStandardize::PipelineResult>("PipelineResult",
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python::no_init)
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.def_readonly("status", &MolStandardize::PipelineResult::status)
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.def_readonly("stage", &MolStandardize::PipelineResult::stage)
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.def_readonly("log", &MolStandardize::PipelineResult::log)
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.def_readonly("inputMolData",
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&MolStandardize::PipelineResult::inputMolData)
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.def_readonly("outputMolData",
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&MolStandardize::PipelineResult::outputMolData)
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.def_readonly("parentMolData",
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&MolStandardize::PipelineResult::parentMolData);
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python::class_<MolStandardize::Pipeline>("Pipeline")
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.def(python::init<const MolStandardize::PipelineOptions &>())
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.def("run", &MolStandardize::Pipeline::run);
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}
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