Index

A

AbsoluteScore (class in drugex.training.scorers.modifiers) addCCToFragments() (drugex.molecules.converters.dummy_molecules.dummyMolsFromFragments static method) addWordsFromSeq() (drugex.data.corpus.interfaces.SequenceVocabulary method) allMethodsExecuted() (drugex.training.tests.TestModelMonitor method) annotate() (drugex.molecules.interfaces.Molecule method) (drugex.molecules.mol.DrExMol method) appendTableToFile() (drugex.training.monitors.FileMonitor static method) apply() (drugex.data.fragments.FragmentCorpusEncoder method) (drugex.data.processing.CorpusEncoder method) (drugex.data.processing.Standardization method) (drugex.parallel.evaluator.ParallelSupplierEvaluator method) (drugex.parallel.interfaces.ParallelProcessor method)

asDataLoader() (drugex.data.interfaces.DataSet method) asRDKit() (drugex.molecules.interfaces.Molecule method) (drugex.molecules.mol.DrExMol method) AtomCounter (class in drugex.training.scorers.properties) AtomLayer (class in drugex.training.generators.graph_transformer) attachToGPUs() (drugex.training.explorers.interfaces.Explorer method) (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.interfaces.FragGenerator method) (drugex.training.generators.sequence_rnn.SequenceRNN method) (drugex.training.interfaces.Model method)

B

backUpFiles() (in module drugex.logs.utils) backUpFilesInFolder() (in module drugex.logs.utils) BaseMolSupplier (class in drugex.molecules.interfaces)

BATCH_SIZE (drugex.training.tests.TrainingTestCase attribute) Block (class in drugex.training.generators.graph_transformer) (class in drugex.training.generators.sequence_transformer) bridgeFragments() (drugex.molecules.converters.dummy_molecules.dummyMolsFromFragments static method)

C

calc_fps() (drugex.training.rewards.ParetoTanimotoDistance static method) calc_voc_fp() (drugex.data.corpus.vocabulary.VocSmiles method) calculateScore() (in module drugex.training.scorers.sascorer) callwarning() (in module drugex.logs.utils) canonicalize() (in module drugex.utils.gcmol) canonicalize_list() (in module drugex.utils.gcmol) Chained (class in drugex.training.scorers.modifiers) check_sha256sum() (in module drugex.utils.download) checkSmiles() (drugex.training.scorers.smiles.SmilesChecker static method) CleanSMILES (class in drugex.molecules.converters.standardizers) ClippedScore (class in drugex.training.scorers.modifiers) close() (drugex.training.interfaces.TrainingMonitor method) (drugex.training.monitors.FileMonitor method) (drugex.training.monitors.NullMonitor method) (drugex.training.tests.TestModelMonitor method)

collate_fn() (drugex.data.datasets.SmilesFragDataSet.TargetCreator.TgtData method) columns (drugex.data.datasets.SmilesDataSet attribute) (drugex.data.datasets.SmilesFragDataSet attribute) config_logger() (in module drugex.logs.config) ConversionException convert() (drugex.data.corpus.interfaces.Corpus method) (drugex.molecules.interfaces.BaseMolSupplier method) (drugex.molecules.interfaces.MolSupplier method) Corpus (class in drugex.data.corpus.interfaces) CorpusEncoder (class in drugex.data.processing) CorpusTest (class in drugex.data.corpus.tests) createLoaders() (drugex.data.datasets.SmilesFragDataSet method) (drugex.data.interfaces.DataSet method)

D

DataSet (class in drugex.data.interfaces) Dataset (class in drugex.dataset) DatasetArgParser() (in module drugex.dataset) DataSplitter (class in drugex.data.interfaces) DataToLoader (class in drugex.data.interfaces) dataToLoader() (drugex.data.datasets.GraphFragDataSet static method) (drugex.data.datasets.SmilesDataSet static method) (drugex.data.datasets.SmilesFragDataSet static method) (drugex.data.interfaces.DataSet static method) decode() (drugex.data.corpus.interfaces.Vocabulary method) (drugex.data.corpus.vocabulary.VocGraph method) (drugex.data.corpus.vocabulary.VocNonGPT method) (drugex.data.corpus.vocabulary.VocSmiles method) decodeLoaders() (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.interfaces.FragGenerator method) (drugex.training.generators.sequence_transformer.SequenceTransformer method) DefaultStandardizer (class in drugex.molecules.converters.standardizers) defaultWords (drugex.data.corpus.vocabulary.VocGraph attribute) (drugex.data.corpus.vocabulary.VocSmiles attribute) download_file() (in module drugex.utils.download) DrExMol (class in drugex.molecules.mol) DrExToSMILES (class in drugex.molecules.converters.default) drugex module drugex.about module drugex.data module drugex.data.corpus module drugex.data.corpus.corpus module drugex.data.corpus.interfaces module drugex.data.corpus.tests module drugex.data.corpus.vocabulary module drugex.data.datasets module drugex.data.fragments module drugex.data.interfaces module drugex.data.processing module drugex.data.tests module drugex.data.utils module drugex.dataset module drugex.logs module drugex.logs.config module drugex.logs.utils module drugex.molecules module drugex.molecules.converters module drugex.molecules.converters.default module drugex.molecules.converters.dummy_molecules module drugex.molecules.converters.fragmenters module drugex.molecules.converters.interfaces module drugex.molecules.converters.standardizers module drugex.molecules.converters.tests module drugex.molecules.interfaces module drugex.molecules.mol module

drugex.molecules.suppliers module drugex.parallel module drugex.parallel.collectors module drugex.parallel.evaluator module drugex.parallel.interfaces module drugex.parallel.tests module drugex.training module drugex.training.environment module drugex.training.explorers module drugex.training.explorers.frag_graph_explorer module drugex.training.explorers.frag_sequence_explorer module drugex.training.explorers.interfaces module drugex.training.explorers.sequence_explorer module drugex.training.generators module drugex.training.generators.graph_transformer module drugex.training.generators.interfaces module drugex.training.generators.sequence_rnn module drugex.training.generators.sequence_transformer module drugex.training.generators.utils module drugex.training.interfaces module drugex.training.monitors module drugex.training.rewards module drugex.training.scorers module drugex.training.scorers.interfaces module drugex.training.scorers.modifiers module drugex.training.scorers.properties module drugex.training.scorers.qsprpred module drugex.training.scorers.sascorer module drugex.training.scorers.similarity module drugex.training.scorers.smiles module drugex.training.tests module drugex.utils module drugex.utils.download module drugex.utils.fingerprints module drugex.utils.gcmol module drugex.utils.optim module drugex.utils.pareto module DrugExEnvironment (class in drugex.training.environment) dummyMolsFromFragments (class in drugex.molecules.converters.dummy_molecules)

E

enable_file_logger() (in module drugex.logs.utils) encode() (drugex.data.corpus.interfaces.Vocabulary method) (drugex.data.corpus.vocabulary.VocGraph method) (drugex.data.corpus.vocabulary.VocNonGPT method) (drugex.data.corpus.vocabulary.VocSmiles method) encodeFrag() (drugex.data.fragments.GraphFragmentEncoder method) (drugex.data.fragments.SequenceFragmentEncoder method) (drugex.data.interfaces.FragmentPairEncoder method) encodeFragments() (drugex.data.fragments.FragmentCorpusEncoder method) encodeMol() (drugex.data.fragments.GraphFragmentEncoder method) (drugex.data.fragments.SequenceFragmentEncoder method) (drugex.data.interfaces.FragmentPairEncoder method)

endStep() (drugex.training.interfaces.TrainingMonitor method) (drugex.training.monitors.FileMonitor method) (drugex.training.monitors.NullMonitor method) (drugex.training.tests.TestModelMonitor method) Environment (class in drugex.training.interfaces) error() (drugex.parallel.evaluator.ParallelSupplierEvaluator method) evaluate() (drugex.training.generators.interfaces.Generator method) evolve() (drugex.training.generators.sequence_rnn.SequenceRNN method) Explorer (class in drugex.training.explorers.interfaces) export_conda_environment() (in module drugex.logs.utils)

F

FileMonitor (class in drugex.training.monitors) filter() (drugex.logs.config.LevelFilter method) filterFragments() (drugex.molecules.converters.fragmenters.Fragmenter method) filterNewMolecules() (drugex.training.generators.interfaces.Generator method) finetuning_file (drugex.training.tests.TrainingTestCase attribute) fit() (drugex.training.explorers.interfaces.Explorer method) (drugex.training.explorers.interfaces.FragExplorer method) (drugex.training.explorers.sequence_explorer.SequenceExplorer method) (drugex.training.generators.interfaces.Generator method) (drugex.training.interfaces.Model method) fitTestModel() (drugex.training.tests.TrainingTestCase method) format() (drugex.logs.config.LevelFormatter method) forward() (drugex.training.explorers.frag_graph_explorer.FragGraphExplorer method) (drugex.training.explorers.frag_sequence_explorer.FragSequenceExplorer method) (drugex.training.explorers.sequence_explorer.SequenceExplorer method) (drugex.training.generators.graph_transformer.AtomLayer method) (drugex.training.generators.graph_transformer.Block method) (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.sequence_rnn.SequenceRNN method) (drugex.training.generators.sequence_transformer.Block method) (drugex.training.generators.sequence_transformer.GPT2Layer method) (drugex.training.generators.sequence_transformer.SequenceTransformer method) (drugex.training.generators.utils.PositionalEmbedding method) (drugex.training.generators.utils.PositionalEncoding method) (drugex.training.generators.utils.PositionwiseFeedForward method) (drugex.training.generators.utils.SublayerConnection method)

FragExplorer (class in drugex.training.explorers.interfaces) FragGenerator (class in drugex.training.generators.interfaces) FraggleSimilarity (class in drugex.training.scorers.similarity) FragGraphDataset (class in drugex.dataset) FragGraphExplorer (class in drugex.training.explorers.frag_graph_explorer) FragmentCorpusEncoder (class in drugex.data.fragments) FragmentCorpusEncoder.FragmentPairsCollector (class in drugex.data.fragments) FragmentDataset (class in drugex.dataset) Fragmenter (class in drugex.molecules.converters.fragmenters) FragmenterWithSelectedFragment (class in drugex.molecules.converters.fragmenters) FragmentPairEncoder (class in drugex.data.interfaces) FragmentPairs (class in drugex.data.tests) FragmentPairsEncodedSupplier (class in drugex.data.fragments) FragmentPairsEncodedSupplier.FragmentEncodingException FragmentPairsEncodedSupplier.MoleculeEncodingException FragmentPairsSplitter (class in drugex.data.fragments) FragmentPairsSupplier (class in drugex.data.fragments) FragSequenceDataset (class in drugex.dataset) FragSequenceExplorer (class in drugex.training.explorers.frag_sequence_explorer) fromDataFrame() (drugex.data.corpus.vocabulary.VocGraph static method) fromFile() (drugex.data.corpus.interfaces.Vocabulary static method) (drugex.data.corpus.vocabulary.VocGraph static method) (drugex.data.corpus.vocabulary.VocNonGPT static method) (drugex.data.corpus.vocabulary.VocSmiles static method) (drugex.data.interfaces.DataSet method)

G

Gaussian (class in drugex.training.scorers.modifiers) generate() (drugex.training.generators.interfaces.FragGenerator method) (drugex.training.generators.interfaces.Generator method) (drugex.training.generators.sequence_rnn.SequenceRNN method) generate_backup_runID() (in module drugex.logs.utils) generateBackupDir() (in module drugex.logs.utils) Generator (class in drugex.training.generators.interfaces) get_atom_tk() (drugex.data.corpus.vocabulary.VocGraph method) get_fingerprint() (in module drugex.utils.fingerprints) get_git_info() (in module drugex.logs.config) get_graph() (drugex.training.scorers.similarity.GraphEditInverseDistance method) get_Pareto_fronts() (in module drugex.utils.pareto) get_runid() (in module drugex.logs.config) getAnnotation() (drugex.molecules.interfaces.Molecule method) (drugex.molecules.mol.DrExMol method) getBatchOutputs() (drugex.training.explorers.frag_graph_explorer.FragGraphExplorer method) (drugex.training.explorers.frag_sequence_explorer.FragSequenceExplorer method) (drugex.training.explorers.interfaces.FragExplorer method) getChunkSize() (drugex.parallel.interfaces.ParallelProcessor method) getColumns() (drugex.data.datasets.GraphFragDataSet method) (drugex.data.datasets.SmilesDataSet method) (drugex.data.datasets.SmilesFragDataSet method) getData() (drugex.data.interfaces.DataSet method) getDataPaths() (in module drugex.data.utils) getFPs() (drugex.training.rewards.ParetoTanimotoDistance method) getFragmentPairs() (drugex.data.fragments.FragmentCorpusEncoder method) getFragments() (drugex.molecules.converters.fragmenters.Fragmenter method) getKey() (drugex.training.scorers.interfaces.Scorer method) (drugex.training.scorers.properties.AtomCounter method) (drugex.training.scorers.properties.Isomer method) (drugex.training.scorers.properties.LigandEfficiency method) (drugex.training.scorers.properties.LipophilicEfficiency method) (drugex.training.scorers.properties.Property method) (drugex.training.scorers.properties.Scaffold method) (drugex.training.scorers.properties.Uniqueness method) (drugex.training.scorers.qsprpred.QSPRPredScorer method) (drugex.training.scorers.similarity.FraggleSimilarity method) (drugex.training.scorers.similarity.GraphEditInverseDistance method) (drugex.training.scorers.similarity.TverskyFingerprintSimilarity method) (drugex.training.scorers.similarity.TverskyGraphSimilarity method) (drugex.training.tests.MockScorer method) getList() (drugex.parallel.collectors.ListExtend method) (drugex.parallel.interfaces.ListCollector method) getMetadata() (drugex.molecules.interfaces.Molecule method) (drugex.molecules.mol.DrExMol method) getModel() (drugex.training.explorers.interfaces.Explorer method) (drugex.training.generators.interfaces.Generator method) (drugex.training.interfaces.ModelProvider method) (drugex.training.monitors.FileMonitor method) (drugex.training.monitors.NullMonitor method) (drugex.training.tests.TestModelMonitor method) getModifiedScores() (drugex.training.scorers.interfaces.Scorer method)

getModifier() (drugex.training.scorers.interfaces.Scorer method) getMoleculeRank() (drugex.training.rewards.ParetoCrowdingDistance method) (drugex.training.rewards.ParetoRewardScheme method) (drugex.training.rewards.ParetoTanimotoDistance method) getMols() (drugex.data.corpus.tests.CorpusTest static method) getNovelMoleculeMetrics() (drugex.training.explorers.interfaces.Explorer method) getPairs() (drugex.data.tests.FragmentPairs method) getParetoFronts() (drugex.training.rewards.ParetoRewardScheme method) getPredictor() (in module drugex.training.tests) getRandomFile() (drugex.data.tests.ProcessingTests static method) (drugex.training.tests.TrainingTestCase static method) getRewards() (drugex.training.interfaces.Environment method) getScorerKeys() (drugex.training.interfaces.Environment method) getScores() (drugex.training.environment.DrugExEnvironment method) (drugex.training.interfaces.Environment method) (drugex.training.scorers.interfaces.Scorer method) (drugex.training.scorers.properties.AtomCounter method) (drugex.training.scorers.properties.Isomer method) (drugex.training.scorers.properties.LigandEfficiency method) (drugex.training.scorers.properties.LipophilicEfficiency method) (drugex.training.scorers.properties.Property method) (drugex.training.scorers.properties.Scaffold method) (drugex.training.scorers.properties.Uniqueness method) (drugex.training.scorers.qsprpred.QSPRPredScorer method) (drugex.training.scorers.similarity.FraggleSimilarity method) (drugex.training.scorers.similarity.GraphEditInverseDistance method) (drugex.training.scorers.similarity.TverskyFingerprintSimilarity method) (drugex.training.scorers.similarity.TverskyGraphSimilarity method) (drugex.training.tests.MockScorer method) getSmiles() (drugex.training.tests.TrainingTestCase method) getStandardizationMols() (drugex.data.tests.ProcessingTests method) getTempFilePath() (drugex.data.corpus.tests.CorpusTest static method) getTestEnvironment() (drugex.training.tests.TrainingTestCase method) getTestFile() (drugex.parallel.tests.TestFileParsers static method) getTestMols() (drugex.data.tests.ProcessingTests method) getUniqueID() (drugex.molecules.interfaces.Molecule method) (drugex.molecules.mol.DrExMol method) getUnmodifiedScores() (drugex.training.environment.DrugExEnvironment method) (drugex.training.interfaces.Environment method) getVoc() (drugex.data.corpus.corpus.SequenceCorpus method) (drugex.data.corpus.interfaces.Corpus method) (drugex.data.fragments.GraphFragmentEncoder method) (drugex.data.fragments.SequenceFragmentEncoder method) (drugex.data.interfaces.DataSet method) (drugex.data.interfaces.FragmentPairEncoder method) getVocPath() (drugex.data.interfaces.DataSet method) getVocPaths() (in module drugex.data.utils) GPT2Layer (class in drugex.training.generators.sequence_transformer) GraphEditInverseDistance (class in drugex.training.scorers.similarity) GraphFragDataSet (class in drugex.data.datasets) GraphFragmentEncoder (class in drugex.data.fragments) GraphTransformer (class in drugex.training.generators.graph_transformer)

I

Identity (class in drugex.molecules.converters.default) init_h() (drugex.training.generators.sequence_rnn.SequenceRNN method) init_logfile() (in module drugex.logs.config) init_states() (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.interfaces.FragGenerator method) InitializationException

initSupplier() (drugex.parallel.evaluator.ParallelSupplierEvaluator method) Isomer (class in drugex.training.scorers.properties) ItemException iterLoader() (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.interfaces.FragGenerator method) (drugex.training.generators.sequence_transformer.SequenceTransformer method)

L

LevelFilter (class in drugex.logs.config) LevelFormatter (class in drugex.logs.config) LigandEfficiency (class in drugex.training.scorers.properties) likelihood() (drugex.training.generators.sequence_rnn.SequenceRNN method) Linear (class in drugex.training.scorers.modifiers) LipophilicEfficiency (class in drugex.training.scorers.properties) ListAppend (class in drugex.parallel.collectors) ListCollector (class in drugex.parallel.interfaces) ListExtend (class in drugex.parallel.collectors)

ListSupplier (class in drugex.molecules.suppliers) load_molecules() (in module drugex.dataset) loaderFromFrags() (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.interfaces.FragGenerator method) (drugex.training.generators.sequence_transformer.SequenceTransformer method) loadStates() (drugex.training.interfaces.Model method) loadStatesFromFile() (drugex.training.interfaces.Model method) LogFileConfig (class in drugex.logs.config) logPerformanceAndCompounds() (drugex.training.explorers.interfaces.Explorer method) (drugex.training.generators.interfaces.Generator method)

M

MAX_SMILES (drugex.training.tests.TrainingTestCase attribute) MinMaxGaussian (class in drugex.training.scorers.modifiers) MockScorer (class in drugex.training.tests) Model (class in drugex.training.interfaces) ModelEvaluator (class in drugex.training.interfaces) ModelProvider (class in drugex.training.interfaces) module drugex drugex.about drugex.data drugex.data.corpus drugex.data.corpus.corpus drugex.data.corpus.interfaces drugex.data.corpus.tests drugex.data.corpus.vocabulary drugex.data.datasets drugex.data.fragments drugex.data.interfaces drugex.data.processing drugex.data.tests drugex.data.utils drugex.dataset drugex.logs drugex.logs.config drugex.logs.utils drugex.molecules drugex.molecules.converters drugex.molecules.converters.default drugex.molecules.converters.dummy_molecules drugex.molecules.converters.fragmenters drugex.molecules.converters.interfaces drugex.molecules.converters.standardizers drugex.molecules.converters.tests drugex.molecules.interfaces drugex.molecules.mol drugex.molecules.suppliers drugex.parallel drugex.parallel.collectors drugex.parallel.evaluator drugex.parallel.interfaces drugex.parallel.tests drugex.training drugex.training.environment drugex.training.explorers drugex.training.explorers.frag_graph_explorer drugex.training.explorers.frag_sequence_explorer drugex.training.explorers.interfaces drugex.training.explorers.sequence_explorer drugex.training.generators drugex.training.generators.graph_transformer drugex.training.generators.interfaces drugex.training.generators.sequence_rnn drugex.training.generators.sequence_transformer drugex.training.generators.utils drugex.training.interfaces drugex.training.monitors drugex.training.rewards drugex.training.scorers drugex.training.scorers.interfaces drugex.training.scorers.modifiers drugex.training.scorers.properties drugex.training.scorers.qsprpred drugex.training.scorers.sascorer drugex.training.scorers.similarity drugex.training.scorers.smiles drugex.training.tests drugex.utils drugex.utils.download drugex.utils.fingerprints drugex.utils.gcmol drugex.utils.optim drugex.utils.pareto

MolConverter (class in drugex.molecules.converters.interfaces) Molecule (class in drugex.molecules.interfaces) MolSupplier (class in drugex.molecules.interfaces)

N

N_EPOCHS (drugex.training.tests.TrainingTestCase attribute) N_PROC (drugex.training.tests.TrainingTestCase attribute) next() (drugex.data.corpus.interfaces.Corpus method) (drugex.data.fragments.FragmentPairsEncodedSupplier method) (drugex.data.fragments.FragmentPairsSupplier method) (drugex.molecules.interfaces.MolSupplier method) (drugex.molecules.suppliers.ListSupplier method) (drugex.molecules.suppliers.StandardizedSupplier method)

NullMonitor (class in drugex.training.monitors) numBridgeheadsAndSpiro() (in module drugex.training.scorers.sascorer)

P

pad_mask() (in module drugex.training.generators.utils) ParallelException ParallelProcessor (class in drugex.parallel.interfaces) ParallelSupplierEvaluator (class in drugex.parallel.evaluator) ParetoCrowdingDistance (class in drugex.training.rewards) ParetoRewardScheme (class in drugex.training.rewards) ParetoTanimotoDistance (class in drugex.training.rewards) parse_molecular_formula() (drugex.training.scorers.properties.Isomer static method) parseDecoded() (drugex.data.corpus.vocabulary.VocSmiles method) parseWord() (drugex.data.corpus.vocabulary.VocGraph static method) passToSubmonitors() (drugex.training.tests.TestModelMonitor method)

policy_gradient() (drugex.training.explorers.interfaces.Explorer method) (drugex.training.explorers.interfaces.FragExplorer method) (drugex.training.explorers.sequence_explorer.SequenceExplorer method) PositionalEmbedding (class in drugex.training.generators.utils) PositionalEncoding (class in drugex.training.generators.utils) PositionwiseFeedForward (class in drugex.training.generators.utils) pretraining_file (drugex.training.tests.TrainingTestCase attribute) ProcessingTests (class in drugex.data.tests) processMolecule() (drugex.data.corpus.corpus.SequenceCorpus method) (drugex.data.corpus.interfaces.Corpus method) Property (class in drugex.training.scorers.properties)

Q

QSPRPredScorer (class in drugex.training.scorers.qsprpred)

R

RandomTrainTestSplitter (class in drugex.data.processing) RDKitToDrEx (class in drugex.molecules.converters.default) readFragmentScores() (in module drugex.training.scorers.sascorer) readVocs() (drugex.data.datasets.SmilesDataSet method) (drugex.data.datasets.SmilesFragDataSet method) (drugex.data.interfaces.DataSet method)

remove_duplicates() (in module drugex.utils.gcmol) removeIfNew() (drugex.data.corpus.interfaces.SequenceVocabulary method) reset() (drugex.data.interfaces.DataSet method) ResultCollector (class in drugex.parallel.interfaces) RewardScheme (class in drugex.training.interfaces) RewardScheme.RewardException run() (drugex.parallel.evaluator.ParallelSupplierEvaluator method)

S

sample() (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.interfaces.Generator method) (drugex.training.generators.sequence_rnn.SequenceRNN method) (drugex.training.generators.sequence_transformer.SequenceTransformer method) sample_input() (drugex.training.explorers.frag_graph_explorer.FragGraphExplorer method) (drugex.training.explorers.frag_sequence_explorer.FragSequenceExplorer method) (drugex.training.explorers.interfaces.FragExplorer method) sampleEncodedPairsToLoader() (drugex.training.explorers.frag_graph_explorer.FragGraphExplorer method) (drugex.training.explorers.frag_sequence_explorer.FragSequenceExplorer method) (drugex.training.explorers.interfaces.FragExplorer method) saveBestState() (drugex.training.explorers.interfaces.Explorer method) saveEpochData() (drugex.training.monitors.FileMonitor method) saveModel() (drugex.training.interfaces.TrainingMonitor method) (drugex.training.monitors.FileMonitor method) (drugex.training.monitors.NullMonitor method) (drugex.training.tests.TestModelMonitor method) saveMolecules() (drugex.training.monitors.FileMonitor method) savePerformanceInfo() (drugex.training.interfaces.TrainingMonitor method) (drugex.training.monitors.FileMonitor method) (drugex.training.monitors.NullMonitor method) (drugex.training.tests.TestModelMonitor method) saveProgress() (drugex.training.interfaces.TrainingMonitor method) (drugex.training.monitors.FileMonitor method) (drugex.training.monitors.NullMonitor method) (drugex.training.tests.TestModelMonitor method) saveVoc() (drugex.data.corpus.corpus.SequenceCorpus method) Scaffold (class in drugex.training.scorers.properties) ScheduledOptim (class in drugex.utils.optim) ScoreModifier (class in drugex.training.scorers.interfaces) Scorer (class in drugex.training.scorers.interfaces) scorers (drugex.training.tests.TrainingTestCase attribute) scoring_functions() (drugex.training.scorers.properties.Isomer method) SEED (drugex.training.tests.TrainingTestCase attribute) sendDataToFile() (drugex.data.interfaces.DataSet method)

SequenceCorpus (class in drugex.data.corpus.corpus) SequenceDataset (class in drugex.dataset) SequenceExplorer (class in drugex.training.explorers.sequence_explorer) SequenceFragmentEncoder (class in drugex.data.fragments) SequenceRNN (class in drugex.training.generators.sequence_rnn) SequenceTransformer (class in drugex.training.generators.sequence_transformer) SequenceVocabulary (class in drugex.data.corpus.interfaces) setLogger() (in module drugex.logs) setModifier() (drugex.training.scorers.interfaces.Scorer method) setPairCollectors() (drugex.dataset.FragmentDataset method) setUp() (drugex.training.tests.TrainingTestCase method) setUpSmilesFragData() (drugex.training.tests.TrainingTestCase method) setVoc() (drugex.data.interfaces.DataSet method) setVocabulary() (drugex.dataset.Dataset method) sha256sum() (in module drugex.utils.download) smiles (drugex.molecules.mol.DrExMol property) SmilesChecker (class in drugex.training.scorers.smiles) SmilesDataSet (class in drugex.data.datasets) SmilesFragDataSet (class in drugex.data.datasets) SmilesFragDataSet.TargetCreator (class in drugex.data.datasets) SmilesFragDataSet.TargetCreator.TgtData (class in drugex.data.datasets) SmilesToDrEx (class in drugex.molecules.converters.default) SmoothClippedScore (class in drugex.training.scorers.modifiers) SmoothHump (class in drugex.training.scorers.modifiers) splitFragmentPairs() (drugex.data.fragments.FragmentCorpusEncoder method) splitSequence() (drugex.data.corpus.interfaces.SequenceVocabulary method) (drugex.data.corpus.vocabulary.VocSmiles method) Squared (class in drugex.training.scorers.modifiers) Standardization (class in drugex.data.processing) Standardization.Collector (class in drugex.data.processing) StandardizationException standardize() (drugex.training.tests.TrainingTestCase method) StandardizedSupplier (class in drugex.molecules.suppliers) step() (drugex.utils.optim.ScheduledOptim method) SublayerConnection (class in drugex.training.generators.utils)

T

test_data_dir (drugex.training.tests.TrainingTestCase attribute) test_default() (drugex.molecules.converters.tests.TestStandardizer method) test_frag_suppliers() (drugex.data.tests.ProcessingTests method) test_fragmentation_with_selected_fragment() (drugex.data.tests.ProcessingTests method) test_getScores() (drugex.training.tests.TestScorer method) test_gragh_scaffold_encoding() (drugex.data.tests.ProcessingTests method) test_graph_frag_encoder() (drugex.data.tests.ProcessingTests method) test_graph_transformer() (drugex.training.tests.TrainingTestCase method) test_graph_transformer_scaffold() (drugex.training.tests.TrainingTestCase method) test_graph_voc() (drugex.data.corpus.tests.CorpusTest method) test_pair_encode_graph() (drugex.data.tests.FragmentPairs method) test_pair_encode_smiles() (drugex.data.tests.FragmentPairs method) test_pair_encode_smiles_parallel() (drugex.data.tests.FragmentPairs method) test_parallel() (drugex.parallel.tests.TestFileParsers method) test_parallel_with_suppliers() (drugex.parallel.tests.TestFileParsers method) test_sequence_corpus_file() (drugex.data.corpus.tests.CorpusTest method) test_sequence_rnn() (drugex.training.tests.TrainingTestCase method) test_sequence_transformer() (drugex.training.tests.TrainingTestCase method) test_sequence_transformer_scaffold() (drugex.training.tests.TrainingTestCase method) test_smiles_encoder() (drugex.data.tests.ProcessingTests method) test_smiles_frag_encoder() (drugex.data.tests.ProcessingTests method)

test_smiles_scaffold_encoding() (drugex.data.tests.ProcessingTests method) test_standardization() (drugex.data.tests.ProcessingTests method) TestFileParsers (class in drugex.parallel.tests) TestModelMonitor (class in drugex.training.tests) TestScorer (class in drugex.training.tests) TestStandardizer (class in drugex.molecules.converters.tests) ThresholdedLinear (class in drugex.training.scorers.modifiers) thresholds (drugex.training.tests.TrainingTestCase attribute) toDataFrame() (drugex.data.corpus.vocabulary.VocGraph method) toFile() (drugex.data.corpus.interfaces.SequenceVocabulary method) (drugex.data.corpus.interfaces.Vocabulary method) (drugex.data.corpus.vocabulary.VocGraph method) toList() (drugex.molecules.interfaces.MolSupplier method) TrainingMonitor (class in drugex.training.interfaces) TrainingTestCase (class in drugex.training.tests) trainNet() (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.interfaces.Generator method) (drugex.training.generators.sequence_rnn.SequenceRNN method) (drugex.training.generators.sequence_transformer.SequenceTransformer method) tri_mask() (in module drugex.training.generators.utils) TverskyFingerprintSimilarity (class in drugex.training.scorers.similarity) TverskyGraphSimilarity (class in drugex.training.scorers.similarity)

U

unique() (in module drugex.training.generators.utils) Uniqueness (class in drugex.training.scorers.properties)

updateDevices() (drugex.training.interfaces.Model method) updateIndex() (drugex.data.corpus.interfaces.SequenceVocabulary method) updateVoc() (drugex.data.interfaces.DataSet method)

V

validateNet() (drugex.training.generators.graph_transformer.GraphTransformer method) (drugex.training.generators.interfaces.Generator method) (drugex.training.generators.sequence_rnn.SequenceRNN method) (drugex.training.generators.sequence_transformer.SequenceTransformer method)

Vocabulary (class in drugex.data.corpus.interfaces) VocGraph (class in drugex.data.corpus.vocabulary) VocNonGPT (class in drugex.data.corpus.vocabulary) VocSmiles (class in drugex.data.corpus.vocabulary)

W

WeightedSum (class in drugex.training.rewards)

Z

zero_grad() (drugex.utils.optim.ScheduledOptim method)