Index

_

__init__() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleFailure method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleSettings method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork method) (asapdiscovery.alchemy.schema.fec.SolventSettings method) (asapdiscovery.alchemy.schema.fec.TransformationResult method) (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams method) (asapdiscovery.alchemy.schema.network.MaximalPlanner method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner method) (asapdiscovery.alchemy.schema.network.NetworkPlanner method) (asapdiscovery.alchemy.schema.network.PlannedNetwork method) (asapdiscovery.alchemy.schema.network.RadialPlanner method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) (asapdiscovery.data.operators.deduplicator.LigandDeDuplicator method) (asapdiscovery.data.operators.selectors.mcs_selector.MCSSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveOneOutSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveSimilarOutSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.PairwiseSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.SelfDockingSelector method) (asapdiscovery.data.operators.selectors.selector.SelectorBase method) (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (asapdiscovery.data.operators.state_expanders.protomer_expander.EpikExpander method) (asapdiscovery.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpanderBase method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansion method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansionSet method) (asapdiscovery.data.operators.state_expanders.stereo_expander.StereoExpander method) (asapdiscovery.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (asapdiscovery.data.readers.meta_ligand_factory.MetaLigandFactory method) (asapdiscovery.data.readers.meta_structure_factory.MetaStructureFactory method) (asapdiscovery.data.readers.molfile.MolFileFactory method) (asapdiscovery.data.readers.structure_dir.StructureDirFactory method) (asapdiscovery.data.schema.complex.Complex method) (asapdiscovery.data.schema.complex.ComplexBase method) (asapdiscovery.data.schema.complex.PreppedComplex method) (asapdiscovery.data.schema.experimental.ExperimentalCompoundData method) (asapdiscovery.data.schema.identifiers.LigandIdentifiers method) (asapdiscovery.data.schema.identifiers.LigandProvenance method) (asapdiscovery.data.schema.identifiers.TargetIdentifiers method) (asapdiscovery.data.schema.legacy.CrystalCompoundData method) (asapdiscovery.data.schema.legacy.EnantiomerPair method) (asapdiscovery.data.schema.legacy.EnantiomerPairList method) (asapdiscovery.data.schema.ligand.ChemicalRelationship method) (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) (asapdiscovery.data.schema.pairs.CompoundStructurePair method) (asapdiscovery.data.schema.pairs.PairBase method) (asapdiscovery.data.schema.schema_base.DataModelAbstractBase method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.schema.sets.CompoundMultiStructure method) (asapdiscovery.data.schema.sets.MultiStructureBase method) (asapdiscovery.data.schema.target.PreppedTarget method) (asapdiscovery.data.schema.target.Target method) (asapdiscovery.data.services.aws.cloudfront.CloudFront method) (asapdiscovery.data.services.aws.s3.S3 method) (asapdiscovery.data.services.cdd.cdd_api.CDDAPI method) (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory method) (asapdiscovery.data.services.postera.manifold_artifacts.ArtifactType method) (asapdiscovery.data.services.postera.manifold_artifacts.ManifoldArtifactUploader method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) (asapdiscovery.data.services.postera.postera_factory.PosteraFactory method) (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader method) (asapdiscovery.data.services.services_config.CDDSettings method) (asapdiscovery.data.services.services_config.CloudfrontSettings method) (asapdiscovery.data.services.services_config.PosteraSettings method) (asapdiscovery.data.services.services_config.S3Settings method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.logging.FileLogger method) (asapdiscovery.data.util.logging.HiddenPrint method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.gif_viz.GIFVisualizer method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.dataviz.html_viz.HTMLVisualizer method) (asapdiscovery.dataviz.visualizer.VisualizerBase method) (asapdiscovery.docking.analysis.DockingDataset method) (asapdiscovery.docking.analysis.DockingResults method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking.DockingBase method) (asapdiscovery.docking.docking.DockingInputBase method) (asapdiscovery.docking.docking.DockingInputMultiStructure method) (asapdiscovery.docking.docking.DockingInputPair method) (asapdiscovery.docking.docking.DockingResult method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.openeye.POSIT_METHOD method) (asapdiscovery.docking.openeye.POSIT_RELAX_MODE method) (asapdiscovery.docking.openeye.POSITDocker method) (asapdiscovery.docking.openeye.POSITDockingResults method) (asapdiscovery.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (asapdiscovery.docking.schema.pose_generation.PosedLigands method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (asapdiscovery.docking.scorer.ChemGauss4Scorer method) (asapdiscovery.docking.scorer.E3MLModelScorer method) (asapdiscovery.docking.scorer.E3NNScorer method) (asapdiscovery.docking.scorer.FINTScorer method) (asapdiscovery.docking.scorer.GATScorer method) (asapdiscovery.docking.scorer.MetaScorer method) (asapdiscovery.docking.scorer.MLModelScorer method) (asapdiscovery.docking.scorer.SchnetScorer method) (asapdiscovery.docking.scorer.Score method) (asapdiscovery.docking.scorer.ScorerBase method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.genetics.blast.PDBEntry method) (asapdiscovery.genetics.blast.PDBRecord method) (asapdiscovery.genetics.seq_alignment.Alignment method) (asapdiscovery.ml.config.ConfigBase method) (asapdiscovery.ml.config.DataAugConfig method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetConfig method) (asapdiscovery.ml.config.DatasetSplitterConfig method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingConfig method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionConfig method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerConfig method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.ml.data_augmentation.JitterFixed method) (asapdiscovery.ml.dataset.DockedDataset method) (asapdiscovery.ml.dataset.GraphDataset method) (asapdiscovery.ml.dataset.GroupedDockedDataset method) (asapdiscovery.ml.es.BestEarlyStopping method) (asapdiscovery.ml.es.ConvergedEarlyStopping method) (asapdiscovery.ml.es.PatientConvergedEarlyStopping method) (asapdiscovery.ml.inference.E3nnInference method) (asapdiscovery.ml.inference.GATInference method) (asapdiscovery.ml.inference.InferenceBase method) (asapdiscovery.ml.inference.SchnetInference method) (asapdiscovery.ml.inference.StructuralInference method) (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) (asapdiscovery.ml.models.LocalMLModelSpec method) (asapdiscovery.ml.models.MLModelBase method) (asapdiscovery.ml.models.MLModelRegistry method) (asapdiscovery.ml.models.MLModelSpec method) (asapdiscovery.ml.sweep.Sweeper method) (asapdiscovery.ml.trainer.Trainer method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.protein_prep.ProteinPrepper method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.modeling.schema.MoleculeFilter method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) (asapdiscovery.simulation.simulate.SimulationResult method) (asapdiscovery.simulation.simulate.SimulatorBase method) (asapdiscovery.simulation.simulate.VanillaMDSimulator method) (asapdiscovery.simulation.szybki.SzybkiFreeformConformerAnalyzer method) (asapdiscovery.simulation.szybki.SzybkiFreeformResult method) (asapdiscovery.simulation.szybki.SzybkiResultCols method) (asapdiscovery.workflows.docking_workflows.cross_docking.CrossDockingWorkflowInputs method) (asapdiscovery.workflows.docking_workflows.large_scale_docking.LargeScaleDockingInputs method) (asapdiscovery.workflows.docking_workflows.small_scale_docking.SmallScaleDockingInputs method) (asapdiscovery.workflows.docking_workflows.workflows.DockingWorkflowInputsBase method) (asapdiscovery.workflows.docking_workflows.workflows.PosteraDockingWorkflowInputs method) (asapdiscovery.workflows.prep_workflows.protein_prep.ProteinPrepInputs method)

A

action_network() (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) actualise_dask_delayed_iterable() (in module asapdiscovery.data.util.dask_utils) add_absolute_expt() (in module asapdiscovery.alchemy.predict) add_command() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) add_gif_progress_bar() (in module asapdiscovery.dataviz.gif_viz) add_identifiers_to_df() (in module asapdiscovery.alchemy.predict) add_module() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) add_molecules() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) add_relative_expt() (in module asapdiscovery.alchemy.predict) add_seqres_to_openeye_protein() (in module asapdiscovery.modeling.modeling) agg_modes() (in module asapdiscovery.ml.cli_args) AlchemiscaleFailure (class in asapdiscovery.alchemy.schema.fec) AlchemiscaleFailure.Config (class in asapdiscovery.alchemy.schema.fec) AlchemiscaleHelper (class in asapdiscovery.alchemy.utils) AlchemiscaleResults (class in asapdiscovery.alchemy.schema.fec) AlchemiscaleResults.Config (class in asapdiscovery.alchemy.schema.fec) AlchemiscaleSettings (class in asapdiscovery.alchemy.schema.fec) AlchemyDataSet (class in asapdiscovery.alchemy.schema.prep_workflow) AlchemyDataSet.Config (class in asapdiscovery.alchemy.schema.prep_workflow) AlchemyPrepWorkflow (class in asapdiscovery.alchemy.schema.prep_workflow) AlchemyPrepWorkflow.Config (class in asapdiscovery.alchemy.schema.prep_workflow) align_all_pdbs() (in module asapdiscovery.data.services.rcsb.rcsb_download) Alignment (class in asapdiscovery.genetics.seq_alignment) allow_extra_args (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) allow_interspersed_args (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) allow_zero_in_degree() (in module asapdiscovery.ml.cli_args) alphas() (in module asapdiscovery.ml.cli_args) append() (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) apply() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) apply_bloom_abstraction() (in module asapdiscovery.genetics.fitness) ArtifactType (class in asapdiscovery.data.services.postera.manifold_artifacts) asapdiscovery module asapdiscovery.alchemy module asapdiscovery.alchemy.cli module asapdiscovery.alchemy.cli.alchemy module asapdiscovery.alchemy.cli.cli module asapdiscovery.alchemy.cli.prep module asapdiscovery.alchemy.cli.utils module asapdiscovery.alchemy.predict module asapdiscovery.alchemy.schema module asapdiscovery.alchemy.schema.atom_mapping module asapdiscovery.alchemy.schema.base module asapdiscovery.alchemy.schema.fec module asapdiscovery.alchemy.schema.forcefield module asapdiscovery.alchemy.schema.network module asapdiscovery.alchemy.schema.prep_workflow module asapdiscovery.alchemy.utils module asapdiscovery.cli module asapdiscovery.cli.cli module asapdiscovery.cli.cli_args module asapdiscovery.data module asapdiscovery.data.backend module asapdiscovery.data.backend.openeye module asapdiscovery.data.backend.plip module asapdiscovery.data.backend.rdkit module asapdiscovery.data.metadata module asapdiscovery.data.metadata.master_seqres module asapdiscovery.data.metadata.master_seqres.fasta_to_seqres module asapdiscovery.data.metadata.resources module asapdiscovery.data.operators module asapdiscovery.data.operators.deduplicator module asapdiscovery.data.operators.selectors module asapdiscovery.data.operators.selectors.mcs_selector module asapdiscovery.data.operators.selectors.pairwise_selector module asapdiscovery.data.operators.selectors.selector module asapdiscovery.data.operators.selectors.selector_list module asapdiscovery.data.operators.state_expanders module asapdiscovery.data.operators.state_expanders.expansion_tag module asapdiscovery.data.operators.state_expanders.protomer_expander module asapdiscovery.data.operators.state_expanders.state_expander module asapdiscovery.data.operators.state_expanders.stereo_expander module asapdiscovery.data.operators.state_expanders.tautomer_expander module asapdiscovery.data.readers module asapdiscovery.data.readers.meta_ligand_factory module asapdiscovery.data.readers.meta_structure_factory module asapdiscovery.data.readers.molfile module asapdiscovery.data.readers.structure_dir module asapdiscovery.data.schema module asapdiscovery.data.schema.complex module asapdiscovery.data.schema.experimental module asapdiscovery.data.schema.identifiers module asapdiscovery.data.schema.legacy module asapdiscovery.data.schema.ligand module asapdiscovery.data.schema.pairs module asapdiscovery.data.schema.schema_base module asapdiscovery.data.schema.sets module asapdiscovery.data.schema.target module asapdiscovery.data.sequence module asapdiscovery.data.services module asapdiscovery.data.services.aws module asapdiscovery.data.services.aws.cloudfront module asapdiscovery.data.services.aws.s3 module asapdiscovery.data.services.cdd module

asapdiscovery.data.services.cdd.cdd_api module asapdiscovery.data.services.cdd.cdd_download module asapdiscovery.data.services.fragalysis module asapdiscovery.data.services.fragalysis.fragalysis_download module asapdiscovery.data.services.fragalysis.fragalysis_reader module asapdiscovery.data.services.postera module asapdiscovery.data.services.postera.manifold_artifacts module asapdiscovery.data.services.postera.manifold_data_validation module asapdiscovery.data.services.postera.molecule_set module asapdiscovery.data.services.postera.postera_api module asapdiscovery.data.services.postera.postera_factory module asapdiscovery.data.services.postera.postera_uploader module asapdiscovery.data.services.rcsb module asapdiscovery.data.services.rcsb.rcsb_download module asapdiscovery.data.services.services_config module asapdiscovery.data.services.web_utils module asapdiscovery.data.testing module asapdiscovery.data.testing.test_resources module asapdiscovery.data.util module asapdiscovery.data.util.dask_utils module asapdiscovery.data.util.data_conversion module asapdiscovery.data.util.execution_utils module asapdiscovery.data.util.logging module asapdiscovery.data.util.stringenum module asapdiscovery.data.util.utils module asapdiscovery.dataviz module asapdiscovery.dataviz.gif_viz module asapdiscovery.dataviz.html_viz module asapdiscovery.dataviz.resources module asapdiscovery.dataviz.resources.fonts module asapdiscovery.dataviz.show_contacts module asapdiscovery.dataviz.visualizer module asapdiscovery.docking module asapdiscovery.docking.analysis module asapdiscovery.docking.docking module asapdiscovery.docking.docking_data_validation module asapdiscovery.docking.openeye module asapdiscovery.docking.schema module asapdiscovery.docking.schema.pose_generation module asapdiscovery.docking.scorer module asapdiscovery.genetics module asapdiscovery.genetics.blast module asapdiscovery.genetics.calculate_rmsd module asapdiscovery.genetics.cli module asapdiscovery.genetics.cli_args module asapdiscovery.genetics.example module asapdiscovery.genetics.fitness module asapdiscovery.genetics.seq_alignment module asapdiscovery.ml module asapdiscovery.ml.cli module asapdiscovery.ml.cli_args module asapdiscovery.ml.cli_sweep module asapdiscovery.ml.config module asapdiscovery.ml.data_augmentation module asapdiscovery.ml.dataset module asapdiscovery.ml.es module asapdiscovery.ml.inference module asapdiscovery.ml.loss module asapdiscovery.ml.models module asapdiscovery.ml.pretrained_models module asapdiscovery.ml.sweep module asapdiscovery.ml.trainer module asapdiscovery.modeling module asapdiscovery.modeling.modeling module asapdiscovery.modeling.protein_prep module asapdiscovery.modeling.schema module asapdiscovery.simulation module asapdiscovery.simulation.simulate module asapdiscovery.simulation.szybki module asapdiscovery.workflows module asapdiscovery.workflows.docking_workflows module asapdiscovery.workflows.docking_workflows.cli module asapdiscovery.workflows.docking_workflows.cross_docking module asapdiscovery.workflows.docking_workflows.large_scale_docking module asapdiscovery.workflows.docking_workflows.small_scale_docking module asapdiscovery.workflows.docking_workflows.workflows module asapdiscovery.workflows.prep_workflows module asapdiscovery.workflows.prep_workflows.cli module asapdiscovery.workflows.prep_workflows.protein_prep module attn_drops() (in module asapdiscovery.ml.cli_args)

B

b1() (in module asapdiscovery.ml.cli_args) b2() (in module asapdiscovery.ml.cli_args) backend_wrapper() (in module asapdiscovery.data.util.dask_utils) BackendType (class in asapdiscovery.data.util.dask_utils) batch_size() (in module asapdiscovery.ml.cli_args) BestEarlyStopping (class in asapdiscovery.ml.es) bfloat16() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method)

biases() (in module asapdiscovery.ml.cli_args) blast_json() (in module asapdiscovery.genetics.cli_args) bloom_abstraction() (in module asapdiscovery.genetics.fitness) buffers() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) build() (asapdiscovery.ml.config.OptimizerConfig method) build_dimer_from_monomer() (in module asapdiscovery.modeling.modeling) build_interaction_dict() (in module asapdiscovery.data.backend.plip) bytes64_to_oedu() (in module asapdiscovery.data.backend.openeye)

C

cache() (asapdiscovery.modeling.protein_prep.ProteinPrepper static method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase static method) cache_dir() (in module asapdiscovery.cli.cli_args) CacheType (class in asapdiscovery.modeling.protein_prep) calculate_rmsd_openeye() (in module asapdiscovery.docking.analysis) calculate_tanimoto_oe() (in module asapdiscovery.docking.analysis) callback (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) cancel_actioned_tasks() (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) canonical_tautomer (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) capitalize() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) casefold() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) cast_uuids() (asapdiscovery.data.schema.identifiers.LigandIdentifiers class method) cast_versions() (asapdiscovery.ml.models.LocalMLModelSpec class method) (asapdiscovery.ml.models.MLModelBase class method) (asapdiscovery.ml.models.MLModelSpec class method) cdd_to_schema() (in module asapdiscovery.data.util.utils) cdd_to_schema_pair() (in module asapdiscovery.data.util.utils) CDDAPI (class in asapdiscovery.data.services.cdd.cdd_api) CDDSettings (class in asapdiscovery.data.services.services_config) center() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) check() (asapdiscovery.ml.es.BestEarlyStopping method) (asapdiscovery.ml.es.ConvergedEarlyStopping method) (asapdiscovery.ml.es.PatientConvergedEarlyStopping method) check_and_apply_truncation() (asapdiscovery.simulation.simulate.VanillaMDSimulator class method) check_and_build_ds() (asapdiscovery.ml.sweep.Sweeper class method) (asapdiscovery.ml.trainer.Trainer class method) check_empty_dataframe() (in module asapdiscovery.data.util.utils) check_filelist_has_elements() (in module asapdiscovery.data.util.utils) check_inputs() (asapdiscovery.workflows.docking_workflows.cross_docking.CrossDockingWorkflowInputs class method) (asapdiscovery.workflows.docking_workflows.large_scale_docking.LargeScaleDockingInputs class method) (asapdiscovery.workflows.docking_workflows.small_scale_docking.SmallScaleDockingInputs class method) (asapdiscovery.workflows.docking_workflows.workflows.DockingWorkflowInputsBase class method) (asapdiscovery.workflows.docking_workflows.workflows.PosteraDockingWorkflowInputs class method) (asapdiscovery.workflows.prep_workflows.protein_prep.ProteinPrepInputs class method) check_mtenn_version() (asapdiscovery.ml.models.LocalMLModelSpec method) (asapdiscovery.ml.models.MLModelBase method) (asapdiscovery.ml.models.MLModelSpec method) check_name_length_and_truncate() (in module asapdiscovery.data.util.utils) check_restraint_setup() (asapdiscovery.simulation.simulate.VanillaMDSimulator class method) check_steps() (asapdiscovery.simulation.simulate.VanillaMDSimulator class method) check_strings_for_equality_with_exclusion() (in module asapdiscovery.data.schema.schema_base) ChemGauss4Scorer (class in asapdiscovery.docking.scorer) ChemicalRelationship (class in asapdiscovery.data.schema.ligand) children() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) choose_best_pdb_entry() (asapdiscovery.genetics.blast.PDBEntry class method) clear() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) clear_SD_data() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) (in module asapdiscovery.data.backend.openeye) CloudFront (class in asapdiscovery.data.services.aws.cloudfront) CloudfrontSettings (class in asapdiscovery.data.services.services_config) collect_errors() (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) collect_results() (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) collect_usage_pieces() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) ColorMethod (class in asapdiscovery.dataviz.html_viz) comb_km() (in module asapdiscovery.ml.cli_args) comb_readout() (in module asapdiscovery.ml.cli_args) comb_substrate() (in module asapdiscovery.ml.cli_args) combination() (in module asapdiscovery.ml.cli_args) combine_files() (in module asapdiscovery.data.util.utils) combine_protein_ligand() (in module asapdiscovery.data.backend.openeye) command() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) command_class (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) commands (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) compile() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) Complex (class in asapdiscovery.data.schema.complex) ComplexBase (class in asapdiscovery.data.schema.complex) CompoundMultiStructure (class in asapdiscovery.data.schema.sets) CompoundStructurePair (class in asapdiscovery.data.schema.pairs) compute_fint_score() (in module asapdiscovery.data.backend.plip) ConfigBase (class in asapdiscovery.ml.config) constraints (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) construct() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper class method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper class method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper class method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleFailure class method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults class method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleSettings class method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory class method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork class method) (asapdiscovery.alchemy.schema.fec.SolventSettings class method) (asapdiscovery.alchemy.schema.fec.TransformationResult class method) (asapdiscovery.alchemy.schema.network.MaximalPlanner class method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner class method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner class method) (asapdiscovery.alchemy.schema.network.NetworkPlanner class method) (asapdiscovery.alchemy.schema.network.PlannedNetwork class method) (asapdiscovery.alchemy.schema.network.RadialPlanner class method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet class method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (asapdiscovery.data.operators.deduplicator.LigandDeDuplicator class method) (asapdiscovery.data.operators.selectors.mcs_selector.MCSSelector class method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveOneOutSelector class method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveSimilarOutSelector class method) (asapdiscovery.data.operators.selectors.pairwise_selector.PairwiseSelector class method) (asapdiscovery.data.operators.selectors.pairwise_selector.SelfDockingSelector class method) (asapdiscovery.data.operators.selectors.selector.SelectorBase class method) (asapdiscovery.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (asapdiscovery.data.operators.state_expanders.protomer_expander.EpikExpander class method) (asapdiscovery.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpanderBase class method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansion class method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansionSet class method) (asapdiscovery.data.operators.state_expanders.stereo_expander.StereoExpander class method) (asapdiscovery.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (asapdiscovery.data.readers.meta_ligand_factory.MetaLigandFactory class method) (asapdiscovery.data.readers.meta_structure_factory.MetaStructureFactory class method) (asapdiscovery.data.readers.molfile.MolFileFactory class method) (asapdiscovery.data.readers.structure_dir.StructureDirFactory class method) (asapdiscovery.data.schema.complex.Complex class method) (asapdiscovery.data.schema.complex.ComplexBase class method) (asapdiscovery.data.schema.complex.PreppedComplex class method) (asapdiscovery.data.schema.experimental.ExperimentalCompoundData class method) (asapdiscovery.data.schema.identifiers.LigandIdentifiers class method) (asapdiscovery.data.schema.identifiers.LigandProvenance class method) (asapdiscovery.data.schema.identifiers.TargetIdentifiers class method) (asapdiscovery.data.schema.legacy.CrystalCompoundData class method) (asapdiscovery.data.schema.legacy.EnantiomerPair class method) (asapdiscovery.data.schema.legacy.EnantiomerPairList class method) (asapdiscovery.data.schema.ligand.Ligand class method) (asapdiscovery.data.schema.ligand.ReferenceLigand class method) (asapdiscovery.data.schema.pairs.CompoundStructurePair class method) (asapdiscovery.data.schema.pairs.PairBase class method) (asapdiscovery.data.schema.schema_base.DataModelAbstractBase class method) (asapdiscovery.data.schema.sets.CompoundMultiStructure class method) (asapdiscovery.data.schema.sets.MultiStructureBase class method) (asapdiscovery.data.schema.target.PreppedTarget class method) (asapdiscovery.data.schema.target.Target class method) (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory class method) (asapdiscovery.data.services.postera.manifold_artifacts.ManifoldArtifactUploader class method) (asapdiscovery.data.services.postera.postera_factory.PosteraFactory class method) (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader class method) (asapdiscovery.data.services.services_config.CDDSettings class method) (asapdiscovery.data.services.services_config.CloudfrontSettings class method) (asapdiscovery.data.services.services_config.PosteraSettings class method) (asapdiscovery.data.services.services_config.S3Settings class method) (asapdiscovery.dataviz.gif_viz.GIFVisualizer class method) (asapdiscovery.dataviz.html_viz.HTMLVisualizer class method) (asapdiscovery.dataviz.visualizer.VisualizerBase class method) (asapdiscovery.docking.docking.DockingBase class method) (asapdiscovery.docking.docking.DockingInputBase class method) (asapdiscovery.docking.docking.DockingInputMultiStructure class method) (asapdiscovery.docking.docking.DockingInputPair class method) (asapdiscovery.docking.docking.DockingResult class method) (asapdiscovery.docking.openeye.POSITDocker class method) (asapdiscovery.docking.openeye.POSITDockingResults class method) (asapdiscovery.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (asapdiscovery.docking.schema.pose_generation.PosedLigands class method) (asapdiscovery.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (asapdiscovery.docking.scorer.ChemGauss4Scorer class method) (asapdiscovery.docking.scorer.E3MLModelScorer class method) (asapdiscovery.docking.scorer.E3NNScorer class method) (asapdiscovery.docking.scorer.FINTScorer class method) (asapdiscovery.docking.scorer.GATScorer class method) (asapdiscovery.docking.scorer.MetaScorer class method) (asapdiscovery.docking.scorer.MLModelScorer class method) (asapdiscovery.docking.scorer.SchnetScorer class method) (asapdiscovery.docking.scorer.Score class method) (asapdiscovery.docking.scorer.ScorerBase class method) (asapdiscovery.genetics.blast.PDBEntry class method) (asapdiscovery.genetics.blast.PDBRecord class method) (asapdiscovery.ml.config.ConfigBase class method) (asapdiscovery.ml.config.DataAugConfig class method) (asapdiscovery.ml.config.DatasetConfig class method) (asapdiscovery.ml.config.DatasetSplitterConfig class method) (asapdiscovery.ml.config.EarlyStoppingConfig class method) (asapdiscovery.ml.config.LossFunctionConfig class method) (asapdiscovery.ml.config.OptimizerConfig class method) (asapdiscovery.ml.inference.E3nnInference class method) (asapdiscovery.ml.inference.GATInference class method) (asapdiscovery.ml.inference.InferenceBase class method) (asapdiscovery.ml.inference.SchnetInference class method) (asapdiscovery.ml.inference.StructuralInference class method) (asapdiscovery.ml.models.LocalMLModelSpec class method) (asapdiscovery.ml.models.MLModelBase class method) (asapdiscovery.ml.models.MLModelRegistry class method) (asapdiscovery.ml.models.MLModelSpec class method) (asapdiscovery.ml.sweep.Sweeper class method) (asapdiscovery.ml.trainer.Trainer class method) (asapdiscovery.modeling.protein_prep.ProteinPrepper class method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase class method) (asapdiscovery.modeling.schema.MoleculeFilter class method) (asapdiscovery.simulation.simulate.SimulationResult class method) (asapdiscovery.simulation.simulate.SimulatorBase class method) (asapdiscovery.simulation.simulate.VanillaMDSimulator class method) (asapdiscovery.simulation.szybki.SzybkiFreeformResult class method) (asapdiscovery.workflows.docking_workflows.cross_docking.CrossDockingWorkflowInputs class method) (asapdiscovery.workflows.docking_workflows.large_scale_docking.LargeScaleDockingInputs class method) (asapdiscovery.workflows.docking_workflows.small_scale_docking.SmallScaleDockingInputs class method) (asapdiscovery.workflows.docking_workflows.workflows.DockingWorkflowInputsBase class method) (asapdiscovery.workflows.docking_workflows.workflows.PosteraDockingWorkflowInputs class method) (asapdiscovery.workflows.prep_workflows.protein_prep.ProteinPrepInputs class method)

construct_regex_function() (in module asapdiscovery.data.util.utils) cont() (in module asapdiscovery.ml.cli_args) context_class (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) context_settings (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) ConvergedEarlyStopping (class in asapdiscovery.ml.es) copy() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleFailure method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleSettings method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork method) (asapdiscovery.alchemy.schema.fec.SolventSettings method) (asapdiscovery.alchemy.schema.fec.TransformationResult method) (asapdiscovery.alchemy.schema.network.MaximalPlanner method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner method) (asapdiscovery.alchemy.schema.network.NetworkPlanner method) (asapdiscovery.alchemy.schema.network.PlannedNetwork method) (asapdiscovery.alchemy.schema.network.RadialPlanner method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (asapdiscovery.data.operators.deduplicator.LigandDeDuplicator method) (asapdiscovery.data.operators.selectors.mcs_selector.MCSSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveOneOutSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveSimilarOutSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.PairwiseSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.SelfDockingSelector method) (asapdiscovery.data.operators.selectors.selector.SelectorBase method) (asapdiscovery.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (asapdiscovery.data.operators.state_expanders.protomer_expander.EpikExpander method) (asapdiscovery.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpanderBase method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansion method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansionSet method) (asapdiscovery.data.operators.state_expanders.stereo_expander.StereoExpander method) (asapdiscovery.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (asapdiscovery.data.readers.meta_ligand_factory.MetaLigandFactory method) (asapdiscovery.data.readers.meta_structure_factory.MetaStructureFactory method) (asapdiscovery.data.readers.molfile.MolFileFactory method) (asapdiscovery.data.readers.structure_dir.StructureDirFactory method) (asapdiscovery.data.schema.complex.Complex method) (asapdiscovery.data.schema.complex.ComplexBase method) (asapdiscovery.data.schema.complex.PreppedComplex method) (asapdiscovery.data.schema.experimental.ExperimentalCompoundData method) (asapdiscovery.data.schema.identifiers.LigandIdentifiers method) (asapdiscovery.data.schema.identifiers.LigandProvenance method) (asapdiscovery.data.schema.identifiers.TargetIdentifiers method) (asapdiscovery.data.schema.legacy.CrystalCompoundData method) (asapdiscovery.data.schema.legacy.EnantiomerPair method) (asapdiscovery.data.schema.legacy.EnantiomerPairList method) (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) (asapdiscovery.data.schema.pairs.CompoundStructurePair method) (asapdiscovery.data.schema.pairs.PairBase method) (asapdiscovery.data.schema.schema_base.DataModelAbstractBase method) (asapdiscovery.data.schema.sets.CompoundMultiStructure method) (asapdiscovery.data.schema.sets.MultiStructureBase method) (asapdiscovery.data.schema.target.PreppedTarget method) (asapdiscovery.data.schema.target.Target method) (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory method) (asapdiscovery.data.services.postera.manifold_artifacts.ManifoldArtifactUploader method) (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) (asapdiscovery.data.services.postera.postera_factory.PosteraFactory method) (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader method) (asapdiscovery.data.services.services_config.CDDSettings method) (asapdiscovery.data.services.services_config.CloudfrontSettings method) (asapdiscovery.data.services.services_config.PosteraSettings method) (asapdiscovery.data.services.services_config.S3Settings method) (asapdiscovery.dataviz.gif_viz.GIFVisualizer method) (asapdiscovery.dataviz.html_viz.HTMLVisualizer method) (asapdiscovery.dataviz.visualizer.VisualizerBase method) (asapdiscovery.docking.docking.DockingBase method) (asapdiscovery.docking.docking.DockingInputBase method) (asapdiscovery.docking.docking.DockingInputMultiStructure method) (asapdiscovery.docking.docking.DockingInputPair method) (asapdiscovery.docking.docking.DockingResult method) (asapdiscovery.docking.openeye.POSITDocker method) (asapdiscovery.docking.openeye.POSITDockingResults method) (asapdiscovery.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (asapdiscovery.docking.schema.pose_generation.PosedLigands method) (asapdiscovery.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (asapdiscovery.docking.scorer.ChemGauss4Scorer method) (asapdiscovery.docking.scorer.E3MLModelScorer method) (asapdiscovery.docking.scorer.E3NNScorer method) (asapdiscovery.docking.scorer.FINTScorer method) (asapdiscovery.docking.scorer.GATScorer method) (asapdiscovery.docking.scorer.MetaScorer method) (asapdiscovery.docking.scorer.MLModelScorer method) (asapdiscovery.docking.scorer.SchnetScorer method) (asapdiscovery.docking.scorer.Score method) (asapdiscovery.docking.scorer.ScorerBase method) (asapdiscovery.genetics.blast.PDBEntry method) (asapdiscovery.genetics.blast.PDBRecord method) (asapdiscovery.ml.config.ConfigBase method) (asapdiscovery.ml.config.DataAugConfig method) (asapdiscovery.ml.config.DatasetConfig method) (asapdiscovery.ml.config.DatasetSplitterConfig method) (asapdiscovery.ml.config.EarlyStoppingConfig method) (asapdiscovery.ml.config.LossFunctionConfig method) (asapdiscovery.ml.config.OptimizerConfig method) (asapdiscovery.ml.inference.E3nnInference method) (asapdiscovery.ml.inference.GATInference method) (asapdiscovery.ml.inference.InferenceBase method) (asapdiscovery.ml.inference.SchnetInference method) (asapdiscovery.ml.inference.StructuralInference method) (asapdiscovery.ml.models.LocalMLModelSpec method) (asapdiscovery.ml.models.MLModelBase method) (asapdiscovery.ml.models.MLModelRegistry method) (asapdiscovery.ml.models.MLModelSpec method) (asapdiscovery.ml.sweep.Sweeper method) (asapdiscovery.ml.trainer.Trainer method) (asapdiscovery.modeling.protein_prep.ProteinPrepper method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase method) (asapdiscovery.modeling.schema.MoleculeFilter method) (asapdiscovery.simulation.simulate.SimulationResult method) (asapdiscovery.simulation.simulate.SimulatorBase method) (asapdiscovery.simulation.simulate.VanillaMDSimulator method) (asapdiscovery.simulation.szybki.SzybkiFreeformResult method) (asapdiscovery.workflows.docking_workflows.cross_docking.CrossDockingWorkflowInputs method) (asapdiscovery.workflows.docking_workflows.large_scale_docking.LargeScaleDockingInputs method) (asapdiscovery.workflows.docking_workflows.small_scale_docking.SmallScaleDockingInputs method) (asapdiscovery.workflows.docking_workflows.workflows.DockingWorkflowInputsBase method) (asapdiscovery.workflows.docking_workflows.workflows.PosteraDockingWorkflowInputs method) (asapdiscovery.workflows.prep_workflows.protein_prep.ProteinPrepInputs method) core_smarts() (in module asapdiscovery.cli.cli_args) count() (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams method) (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) cpu() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) create() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) create_absolute_report() (in module asapdiscovery.alchemy.predict) create_alchemy_dataset() (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) create_fec_dataset() (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory method) create_network() (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) create_protein_only_system() (in module asapdiscovery.alchemy.utils) create_relative_report() (in module asapdiscovery.alchemy.predict) cross_docking_workflow() (in module asapdiscovery.workflows.docking_workflows.cross_docking) CrossDockingWorkflowInputs (class in asapdiscovery.workflows.docking_workflows.cross_docking) CrystalCompoundData (class in asapdiscovery.data.schema.legacy) cuda() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) cutoff() (in module asapdiscovery.ml.cli_args)

D

dampening() (in module asapdiscovery.ml.cli_args) dask_args() (in module asapdiscovery.cli.cli_args) dask_cluster_from_type() (in module asapdiscovery.data.util.dask_utils) dask_n_workers() (in module asapdiscovery.cli.cli_args) dask_time_delta_diff() (in module asapdiscovery.data.util.dask_utils) dask_timedelta_to_hh_mm() (in module asapdiscovery.data.util.dask_utils) dask_type() (in module asapdiscovery.cli.cli_args) dask_vmap() (in module asapdiscovery.data.util.dask_utils) DaskType (class in asapdiscovery.data.util.dask_utils) data_aug() (in module asapdiscovery.ml.cli_args) DataAugConfig (class in asapdiscovery.ml.config) DataAugType (class in asapdiscovery.ml.config) DataModelAbstractBase (class in asapdiscovery.data.schema.schema_base) DatasetConfig (class in asapdiscovery.ml.config) DatasetSplitterConfig (class in asapdiscovery.ml.config) DatasetSplitterType (class in asapdiscovery.ml.config) DatasetType (class in asapdiscovery.ml.config) DataStorageType (class in asapdiscovery.data.schema.schema_base) derivative() (in module asapdiscovery.ml.cli_args) destroy() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) device() (in module asapdiscovery.ml.cli_args) dG_to_pIC50() (in module asapdiscovery.alchemy.predict) dg_to_postera_dataframe() (in module asapdiscovery.alchemy.predict) dict() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleFailure method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleSettings method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork method) (asapdiscovery.alchemy.schema.fec.SolventSettings method) (asapdiscovery.alchemy.schema.fec.TransformationResult method) (asapdiscovery.alchemy.schema.network.MaximalPlanner method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner method) (asapdiscovery.alchemy.schema.network.NetworkPlanner method) (asapdiscovery.alchemy.schema.network.PlannedNetwork method) (asapdiscovery.alchemy.schema.network.RadialPlanner method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (asapdiscovery.data.operators.deduplicator.LigandDeDuplicator method) (asapdiscovery.data.operators.selectors.mcs_selector.MCSSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveOneOutSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveSimilarOutSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.PairwiseSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.SelfDockingSelector method) (asapdiscovery.data.operators.selectors.selector.SelectorBase method) (asapdiscovery.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (asapdiscovery.data.operators.state_expanders.protomer_expander.EpikExpander method) (asapdiscovery.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpanderBase method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansion method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansionSet method) (asapdiscovery.data.operators.state_expanders.stereo_expander.StereoExpander method) (asapdiscovery.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (asapdiscovery.data.readers.meta_ligand_factory.MetaLigandFactory method) (asapdiscovery.data.readers.meta_structure_factory.MetaStructureFactory method) (asapdiscovery.data.readers.molfile.MolFileFactory method) (asapdiscovery.data.readers.structure_dir.StructureDirFactory method) (asapdiscovery.data.schema.complex.Complex method) (asapdiscovery.data.schema.complex.ComplexBase method) (asapdiscovery.data.schema.complex.PreppedComplex method) (asapdiscovery.data.schema.experimental.ExperimentalCompoundData method) (asapdiscovery.data.schema.identifiers.LigandIdentifiers method) (asapdiscovery.data.schema.identifiers.LigandProvenance method) (asapdiscovery.data.schema.identifiers.TargetIdentifiers method) (asapdiscovery.data.schema.legacy.CrystalCompoundData method) (asapdiscovery.data.schema.legacy.EnantiomerPair method) (asapdiscovery.data.schema.legacy.EnantiomerPairList method) (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) (asapdiscovery.data.schema.pairs.CompoundStructurePair method) (asapdiscovery.data.schema.pairs.PairBase method) (asapdiscovery.data.schema.schema_base.DataModelAbstractBase method) (asapdiscovery.data.schema.sets.CompoundMultiStructure method) (asapdiscovery.data.schema.sets.MultiStructureBase method) (asapdiscovery.data.schema.target.PreppedTarget method) (asapdiscovery.data.schema.target.Target method) (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory method) (asapdiscovery.data.services.postera.manifold_artifacts.ManifoldArtifactUploader method) (asapdiscovery.data.services.postera.postera_factory.PosteraFactory method) (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader method) (asapdiscovery.data.services.services_config.CDDSettings method) (asapdiscovery.data.services.services_config.CloudfrontSettings method) (asapdiscovery.data.services.services_config.PosteraSettings method) (asapdiscovery.data.services.services_config.S3Settings method) (asapdiscovery.dataviz.gif_viz.GIFVisualizer method) (asapdiscovery.dataviz.html_viz.HTMLVisualizer method) (asapdiscovery.dataviz.visualizer.VisualizerBase method) (asapdiscovery.docking.docking.DockingBase method) (asapdiscovery.docking.docking.DockingInputBase method) (asapdiscovery.docking.docking.DockingInputMultiStructure method) (asapdiscovery.docking.docking.DockingInputPair method) (asapdiscovery.docking.docking.DockingResult method) (asapdiscovery.docking.openeye.POSITDocker method) (asapdiscovery.docking.openeye.POSITDockingResults method) (asapdiscovery.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (asapdiscovery.docking.schema.pose_generation.PosedLigands method) (asapdiscovery.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (asapdiscovery.docking.scorer.ChemGauss4Scorer method) (asapdiscovery.docking.scorer.E3MLModelScorer method) (asapdiscovery.docking.scorer.E3NNScorer method) (asapdiscovery.docking.scorer.FINTScorer method) (asapdiscovery.docking.scorer.GATScorer method) (asapdiscovery.docking.scorer.MetaScorer method) (asapdiscovery.docking.scorer.MLModelScorer method) (asapdiscovery.docking.scorer.SchnetScorer method) (asapdiscovery.docking.scorer.Score method) (asapdiscovery.docking.scorer.ScorerBase method) (asapdiscovery.genetics.blast.PDBEntry method) (asapdiscovery.genetics.blast.PDBRecord method) (asapdiscovery.ml.config.ConfigBase method) (asapdiscovery.ml.config.DataAugConfig method) (asapdiscovery.ml.config.DatasetConfig method) (asapdiscovery.ml.config.DatasetSplitterConfig method) (asapdiscovery.ml.config.EarlyStoppingConfig method) (asapdiscovery.ml.config.LossFunctionConfig method) (asapdiscovery.ml.config.OptimizerConfig method) (asapdiscovery.ml.inference.E3nnInference method) (asapdiscovery.ml.inference.GATInference method) (asapdiscovery.ml.inference.InferenceBase method) (asapdiscovery.ml.inference.SchnetInference method) (asapdiscovery.ml.inference.StructuralInference method) (asapdiscovery.ml.models.LocalMLModelSpec method) (asapdiscovery.ml.models.MLModelBase method) (asapdiscovery.ml.models.MLModelRegistry method) (asapdiscovery.ml.models.MLModelSpec method) (asapdiscovery.ml.sweep.Sweeper method) (asapdiscovery.ml.trainer.Trainer method) (asapdiscovery.modeling.protein_prep.ProteinPrepper method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase method) (asapdiscovery.modeling.schema.MoleculeFilter method) (asapdiscovery.simulation.simulate.SimulationResult method) (asapdiscovery.simulation.simulate.SimulatorBase method) (asapdiscovery.simulation.simulate.VanillaMDSimulator method) (asapdiscovery.simulation.szybki.SzybkiFreeformResult method) (asapdiscovery.workflows.docking_workflows.cross_docking.CrossDockingWorkflowInputs method) (asapdiscovery.workflows.docking_workflows.large_scale_docking.LargeScaleDockingInputs method) (asapdiscovery.workflows.docking_workflows.small_scale_docking.SmallScaleDockingInputs method) (asapdiscovery.workflows.docking_workflows.workflows.DockingWorkflowInputsBase method) (asapdiscovery.workflows.docking_workflows.workflows.PosteraDockingWorkflowInputs method) (asapdiscovery.workflows.prep_workflows.protein_prep.ProteinPrepInputs method)

dipole() (in module asapdiscovery.ml.cli_args) do_MSA() (in module asapdiscovery.genetics.seq_alignment) dock() (asapdiscovery.docking.docking.DockingBase method) (asapdiscovery.docking.openeye.POSITDocker method) DockedDataset (class in asapdiscovery.ml.dataset) DockingBase (class in asapdiscovery.docking.docking) DockingDataset (class in asapdiscovery.docking.analysis) DockingInputBase (class in asapdiscovery.docking.docking) DockingInputMultiStructure (class in asapdiscovery.docking.docking) DockingInputPair (class in asapdiscovery.docking.docking) DockingResult (class in asapdiscovery.docking.docking) DockingResultCols (class in asapdiscovery.docking.docking_data_validation) DockingResults (class in asapdiscovery.docking.analysis) DockingWorkflowInputsBase (class in asapdiscovery.workflows.docking_workflows.workflows) double() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) download() (in module asapdiscovery.data.services.fragalysis.fragalysis_download) download_cdd_data() (in module asapdiscovery.alchemy.predict) download_file() (in module asapdiscovery.data.util.utils) download_molecules() (in module asapdiscovery.data.services.cdd.cdd_download) download_pdb_structure() (in module asapdiscovery.data.services.rcsb.rcsb_download) download_PDBs() (in module asapdiscovery.data.services.rcsb.rcsb_download) download_url() (in module asapdiscovery.data.services.cdd.cdd_download) draw_mol() (in module asapdiscovery.alchemy.predict) drop_non_output_columns() (in module asapdiscovery.data.services.postera.manifold_data_validation) ds_cache() (in module asapdiscovery.ml.cli_args) ds_cache_overwrite() (in module asapdiscovery.ml.cli_args) ds_config_cache() (in module asapdiscovery.ml.cli_args) ds_config_cache_overwrite() (in module asapdiscovery.ml.cli_args) ds_rand_seed() (in module asapdiscovery.ml.cli_args) ds_split_args() (in module asapdiscovery.ml.cli_args) ds_split_config_cache() (in module asapdiscovery.ml.cli_args) ds_split_config_cache_overwrite() (in module asapdiscovery.ml.cli_args) ds_split_type() (in module asapdiscovery.ml.cli_args) du_to_complex() (in module asapdiscovery.modeling.modeling)

E

E3MLModelScorer (class in asapdiscovery.docking.scorer) e3nn_args() (in module asapdiscovery.ml.cli_args) E3nnInference (class in asapdiscovery.ml.inference) E3NNScorer (class in asapdiscovery.docking.scorer) EarlyStoppingConfig (class in asapdiscovery.ml.config) EarlyStoppingType (class in asapdiscovery.ml.config) email() (in module asapdiscovery.genetics.cli_args) EnantiomerPair (class in asapdiscovery.data.schema.legacy) EnantiomerPairList (class in asapdiscovery.data.schema.legacy) encode() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) endswith() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method)

enforce_one() (in module asapdiscovery.ml.cli_args) EpikExpander (class in asapdiscovery.data.operators.state_expanders.protomer_expander) eps() (in module asapdiscovery.ml.cli_args) es_args() (in module asapdiscovery.ml.cli_args) es_burnin() (in module asapdiscovery.ml.cli_args) es_config_cache() (in module asapdiscovery.ml.cli_args) es_config_cache_overwrite() (in module asapdiscovery.ml.cli_args) es_divergence() (in module asapdiscovery.ml.cli_args) es_n_check() (in module asapdiscovery.ml.cli_args) es_patience() (in module asapdiscovery.ml.cli_args) es_type() (in module asapdiscovery.ml.cli_args) estimate_n_workers() (in module asapdiscovery.data.util.execution_utils) eval() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) ewaldErrorTolerance (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) example() (in module asapdiscovery.genetics.example) exists() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) exp_file() (in module asapdiscovery.ml.cli_args) expandtabs() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) ExperimentalCompoundData (class in asapdiscovery.data.schema.experimental) extend() (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) extra_config() (in module asapdiscovery.ml.cli_args) extra_repr() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) extract_compounds_from_filenames() (in module asapdiscovery.data.util.utils) extract_experimental_data() (in module asapdiscovery.alchemy.predict) extract_zip() (in module asapdiscovery.data.services.fragalysis.fragalysis_download)

F

failure_mode() (in module asapdiscovery.cli.cli_args) FailureMode (class in asapdiscovery.data.util.dask_utils) fasta_align_data() (asapdiscovery.genetics.seq_alignment.Alignment static method) feat_drops() (in module asapdiscovery.ml.cli_args) fetch_test_file() (in module asapdiscovery.data.testing.test_resources) ff_xmls (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) FileLogger (class in asapdiscovery.data.util.logging) filter_molecules_dataframe() (in module asapdiscovery.data.util.utils) find() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) find_component_chains() (in module asapdiscovery.modeling.modeling) FINTScorer (class in asapdiscovery.docking.scorer) fix_device() (asapdiscovery.ml.sweep.Sweeper class method) (asapdiscovery.ml.trainer.Trainer class method) fixed_inchi (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) fixed_inchikey (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) flattened (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) float() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) force_new_sweep() (in module asapdiscovery.ml.cli_args) ForceFieldParams (class in asapdiscovery.alchemy.schema.forcefield) format() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) format_commands() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) format_epilog() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) format_help() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) format_help_text() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) format_map() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method)

format_options() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) format_usage() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) forward() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) fragalysis_dir() (in module asapdiscovery.cli.cli_args) FragalysisFactory (class in asapdiscovery.data.services.fragalysis.fragalysis_reader) FreeEnergyCalculationFactory (class in asapdiscovery.alchemy.schema.fec) FreeEnergyCalculationFactory.Config (class in asapdiscovery.alchemy.schema.fec) FreeEnergyCalculationNetwork (class in asapdiscovery.alchemy.schema.fec) FreeEnergyCalculationNetwork.Config (class in asapdiscovery.alchemy.schema.fec) from_complex() (asapdiscovery.data.schema.complex.PreppedComplex class method) from_complexes() (asapdiscovery.ml.dataset.DockedDataset class method) (asapdiscovery.ml.dataset.GroupedDockedDataset class method) from_dir() (asapdiscovery.data.readers.structure_dir.StructureDirFactory class method) (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory class method) from_exp_compounds() (asapdiscovery.ml.dataset.GraphDataset class method) from_exp_file() (asapdiscovery.ml.config.DatasetConfig class method) from_file() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper class method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper class method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper class method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleFailure class method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults class method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory class method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork class method) (asapdiscovery.alchemy.schema.fec.SolventSettings class method) (asapdiscovery.alchemy.schema.fec.TransformationResult class method) (asapdiscovery.alchemy.schema.network.MaximalPlanner class method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner class method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner class method) (asapdiscovery.alchemy.schema.network.NetworkPlanner class method) (asapdiscovery.alchemy.schema.network.PlannedNetwork class method) (asapdiscovery.alchemy.schema.network.RadialPlanner class method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet class method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) from_files() (asapdiscovery.ml.dataset.DockedDataset class method) (asapdiscovery.ml.dataset.GroupedDockedDataset class method) from_inchi() (asapdiscovery.data.schema.ligand.Ligand class method) (asapdiscovery.data.schema.ligand.ReferenceLigand class method) from_iterable() (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags class method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags class method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase class method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags class method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags class method) from_latest_by_target() (asapdiscovery.ml.inference.E3nnInference class method) (asapdiscovery.ml.inference.GATInference class method) (asapdiscovery.ml.inference.InferenceBase class method) (asapdiscovery.ml.inference.SchnetInference class method) (asapdiscovery.ml.inference.StructuralInference class method) from_latest_by_target_and_type() (asapdiscovery.docking.scorer.E3MLModelScorer static method) (asapdiscovery.docking.scorer.E3NNScorer static method) (asapdiscovery.docking.scorer.GATScorer static method) (asapdiscovery.docking.scorer.MLModelScorer static method) (asapdiscovery.docking.scorer.SchnetScorer static method) from_ligands() (asapdiscovery.ml.dataset.GraphDataset class method) from_local_model_spec() (asapdiscovery.ml.inference.E3nnInference class method) (asapdiscovery.ml.inference.GATInference class method) (asapdiscovery.ml.inference.InferenceBase class method) (asapdiscovery.ml.inference.SchnetInference class method) (asapdiscovery.ml.inference.StructuralInference class method) from_ml_model_spec() (asapdiscovery.ml.inference.E3nnInference class method) (asapdiscovery.ml.inference.GATInference class method) (asapdiscovery.ml.inference.InferenceBase class method) (asapdiscovery.ml.inference.SchnetInference class method) (asapdiscovery.ml.inference.StructuralInference class method) from_model_name() (asapdiscovery.ml.inference.E3nnInference class method) (asapdiscovery.ml.inference.GATInference class method) (asapdiscovery.ml.inference.InferenceBase class method) (asapdiscovery.ml.inference.SchnetInference class method) (asapdiscovery.ml.inference.StructuralInference class method) from_oemol() (asapdiscovery.data.schema.ligand.Ligand class method) (asapdiscovery.data.schema.ligand.ReferenceLigand class method) from_sdf() (asapdiscovery.data.schema.ligand.Ligand class method) (asapdiscovery.data.schema.ligand.ReferenceLigand class method) from_settings() (asapdiscovery.data.services.aws.cloudfront.CloudFront class method) (asapdiscovery.data.services.aws.s3.S3 class method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI class method) from_smiles() (asapdiscovery.data.schema.ligand.Ligand class method) (asapdiscovery.data.schema.ligand.ReferenceLigand class method) from_str_files() (asapdiscovery.ml.config.DatasetConfig class method) from_yaml() (asapdiscovery.ml.models.MLModelRegistry class method) fromkeys() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method)

G

gat_args() (in module asapdiscovery.ml.cli_args) GATInference (class in asapdiscovery.ml.inference) GATScorer (class in asapdiscovery.docking.scorer) GaussianNLLLoss (class in asapdiscovery.ml.loss) gen_cache_w_default() (in module asapdiscovery.cli.cli_args) gen_ref_pdb() (in module asapdiscovery.genetics.cli_args) generate_cloudfront_url() (asapdiscovery.data.services.postera.manifold_artifacts.ManifoldArtifactUploader method) generate_network() (asapdiscovery.alchemy.schema.network.NetworkPlanner method) generate_poses() (asapdiscovery.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (asapdiscovery.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) generate_signed_url() (asapdiscovery.data.services.aws.cloudfront.CloudFront method) get() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) get_actioned_weights() (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) get_args() (in module asapdiscovery.data.metadata.master_seqres.fasta_to_seqres) get_async_export() (asapdiscovery.data.services.cdd.cdd_api.CDDAPI method) get_best_structure_per_compound() (asapdiscovery.docking.analysis.DockingResults method) get_blast_seqs() (in module asapdiscovery.genetics.blast) get_buffer() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) get_cdd_molecules() (in module asapdiscovery.alchemy.cli.utils) get_chemical_relationship() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) get_color_dict() (asapdiscovery.dataviz.html_viz.HTMLVisualizer method) get_colors_protein() (in module asapdiscovery.genetics.seq_alignment) get_command() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) get_data_from_femap() (in module asapdiscovery.alchemy.predict) get_dict_of_lists_from_dict_of_str() (in module asapdiscovery.data.util.data_conversion) get_dict_of_lists_from_list_of_dicts() (in module asapdiscovery.data.util.data_conversion) get_extra_state() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) get_first_value_of_dict_of_lists() (in module asapdiscovery.data.util.data_conversion) get_fitness_scores_bloom_by_target() (in module asapdiscovery.genetics.fitness) get_good_score() (in module asapdiscovery.docking.analysis) get_grouped_df() (asapdiscovery.docking.analysis.DockingResults method) get_help() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) get_help_option() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) get_help_option_names() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) get_ic50_data() (asapdiscovery.data.services.cdd.cdd_api.CDDAPI method) get_id_from_name() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) get_implemented_model_types() (asapdiscovery.ml.models.MLModelRegistry method) get_inference_cls_from_model_type() (in module asapdiscovery.ml.inference) get_interaction_color() (in module asapdiscovery.data.backend.plip) get_interaction_fitness_color() (in module asapdiscovery.data.backend.plip) get_interactions_plip() (in module asapdiscovery.data.backend.plip)

get_latest_model_for_target_and_type() (asapdiscovery.ml.models.MLModelRegistry method) get_magnitude() (in module asapdiscovery.alchemy.predict) get_ml_scorer_cls_from_model_type() (in module asapdiscovery.docking.scorer) get_model() (asapdiscovery.ml.models.MLModelRegistry method) get_models_for_target() (asapdiscovery.ml.models.MLModelRegistry method) get_models_for_target_and_type() (asapdiscovery.ml.models.MLModelRegistry method) get_molecules() (asapdiscovery.data.services.cdd.cdd_api.CDDAPI method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) get_molecules_from_id_or_name() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) get_name_from_id() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) get_network_interfaces_with_dual_ip() (in module asapdiscovery.data.util.execution_utils) get_oe_prep_opts() (in module asapdiscovery.modeling.modeling) get_oe_structure_metadata_from_sequence() (in module asapdiscovery.modeling.modeling) get_output() (asapdiscovery.docking.docking.DockingResult method) (asapdiscovery.docking.openeye.POSITDockingResults method) get_parameter() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) get_planning_function() (asapdiscovery.alchemy.schema.network.MaximalPlanner method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner method) (asapdiscovery.alchemy.schema.network.RadialPlanner method) get_platform() (in module asapdiscovery.data.util.execution_utils) get_protocols() (asapdiscovery.data.services.cdd.cdd_api.CDDAPI method) get_readout_rows() (asapdiscovery.data.services.cdd.cdd_api.CDDAPI method) get_SD_data() (in module asapdiscovery.data.backend.openeye) (in module asapdiscovery.data.backend.rdkit) get_sdf_fn_from_dataset() (in module asapdiscovery.data.util.utils) get_short_help_str() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) get_similarity() (in module asapdiscovery.alchemy.utils) get_single_conf_SD_data() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) get_structure_df() (asapdiscovery.docking.analysis.DockingResults method) get_submodule() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) get_tag_for_color_method() (asapdiscovery.dataviz.html_viz.HTMLVisualizer method) get_targets_with_models() (asapdiscovery.ml.models.MLModelRegistry method) get_usage() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) get_values() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector class method) GIFVisualizer (class in asapdiscovery.dataviz.gif_viz) graph_ds_args() (in module asapdiscovery.ml.cli_args) GraphDataset (class in asapdiscovery.ml.dataset) group() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) group_class (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) grouped() (in module asapdiscovery.ml.cli_args) GroupedDockedDataset (class in asapdiscovery.ml.dataset) guess_network_interface() (in module asapdiscovery.data.util.execution_utils)

H

half() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) has_defined_stereo (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) has_multiple_poses (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) has_perceived_stereo (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) has_same_charge() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method)

has_warhead() (in module asapdiscovery.alchemy.cli.utils) hash (asapdiscovery.data.schema.target.PreppedTarget property) (asapdiscovery.data.schema.target.Target property) hidden_channels() (in module asapdiscovery.ml.cli_args) hidden_feats() (in module asapdiscovery.ml.cli_args) HiddenPrint (class in asapdiscovery.data.util.logging) html_pose_viz() (asapdiscovery.dataviz.html_viz.HTMLVisualizer method) HTMLVisualizer (class in asapdiscovery.dataviz.html_viz) hydrogenMass (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) hyperthreading_is_enabled() (in module asapdiscovery.data.util.execution_utils)

I

id_data_is_uuid_castable() (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader static method) ignore_unknown_options (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) in_feats() (in module asapdiscovery.ml.cli_args) inchi (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) inchikey (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) index() (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams method) (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) InferenceBase (class in asapdiscovery.ml.inference) initialize() (asapdiscovery.data.services.aws.s3.S3 method) (asapdiscovery.ml.sweep.Sweeper method) (asapdiscovery.ml.trainer.Trainer method) input_json() (in module asapdiscovery.cli.cli_args) insert() (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) InvalidLigandError InvalidTargetError invoke() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) ipu() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) irreps_edge_attr() (in module asapdiscovery.ml.cli_args) irreps_hidden() (in module asapdiscovery.ml.cli_args) is_backbone_residue() (in module asapdiscovery.data.backend.plip) is_chemically_equal() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) is_protonation_state_isomer() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) is_stereoisomer() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) is_tautomer() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) is_valid_receptor_system() (in module asapdiscovery.alchemy.utils) is_valid_smiles() (in module asapdiscovery.data.util.utils) isalnum() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) isalpha() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) isascii() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) isdecimal() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) isdigit() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method)

isidentifier() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) islower() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) isnumeric() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) isprintable() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) isspace() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) istitle() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) isupper() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) items() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method)

J

JitterFixed (class in asapdiscovery.ml.data_augmentation) join() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) join_with_manifold_data() (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader static method) json() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleFailure method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleSettings method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork method) (asapdiscovery.alchemy.schema.fec.SolventSettings method) (asapdiscovery.alchemy.schema.fec.TransformationResult method) (asapdiscovery.alchemy.schema.network.MaximalPlanner method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner method) (asapdiscovery.alchemy.schema.network.NetworkPlanner method) (asapdiscovery.alchemy.schema.network.PlannedNetwork method) (asapdiscovery.alchemy.schema.network.RadialPlanner method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (asapdiscovery.data.operators.deduplicator.LigandDeDuplicator method) (asapdiscovery.data.operators.selectors.mcs_selector.MCSSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveOneOutSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveSimilarOutSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.PairwiseSelector method) (asapdiscovery.data.operators.selectors.pairwise_selector.SelfDockingSelector method) (asapdiscovery.data.operators.selectors.selector.SelectorBase method) (asapdiscovery.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (asapdiscovery.data.operators.state_expanders.protomer_expander.EpikExpander method) (asapdiscovery.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpanderBase method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansion method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansionSet method) (asapdiscovery.data.operators.state_expanders.stereo_expander.StereoExpander method) (asapdiscovery.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (asapdiscovery.data.readers.meta_ligand_factory.MetaLigandFactory method) (asapdiscovery.data.readers.meta_structure_factory.MetaStructureFactory method) (asapdiscovery.data.readers.molfile.MolFileFactory method) (asapdiscovery.data.readers.structure_dir.StructureDirFactory method) (asapdiscovery.data.schema.complex.Complex method) (asapdiscovery.data.schema.complex.ComplexBase method) (asapdiscovery.data.schema.complex.PreppedComplex method) (asapdiscovery.data.schema.experimental.ExperimentalCompoundData method) (asapdiscovery.data.schema.identifiers.LigandIdentifiers method) (asapdiscovery.data.schema.identifiers.LigandProvenance method) (asapdiscovery.data.schema.identifiers.TargetIdentifiers method) (asapdiscovery.data.schema.legacy.CrystalCompoundData method) (asapdiscovery.data.schema.legacy.EnantiomerPair method) (asapdiscovery.data.schema.legacy.EnantiomerPairList method) (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) (asapdiscovery.data.schema.pairs.CompoundStructurePair method) (asapdiscovery.data.schema.pairs.PairBase method) (asapdiscovery.data.schema.schema_base.DataModelAbstractBase method) (asapdiscovery.data.schema.sets.CompoundMultiStructure method) (asapdiscovery.data.schema.sets.MultiStructureBase method) (asapdiscovery.data.schema.target.PreppedTarget method) (asapdiscovery.data.schema.target.Target method) (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory method) (asapdiscovery.data.services.postera.manifold_artifacts.ManifoldArtifactUploader method) (asapdiscovery.data.services.postera.postera_factory.PosteraFactory method) (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader method) (asapdiscovery.data.services.services_config.CDDSettings method) (asapdiscovery.data.services.services_config.CloudfrontSettings method) (asapdiscovery.data.services.services_config.PosteraSettings method) (asapdiscovery.data.services.services_config.S3Settings method) (asapdiscovery.dataviz.gif_viz.GIFVisualizer method) (asapdiscovery.dataviz.html_viz.HTMLVisualizer method) (asapdiscovery.dataviz.visualizer.VisualizerBase method) (asapdiscovery.docking.docking.DockingBase method) (asapdiscovery.docking.docking.DockingInputBase method) (asapdiscovery.docking.docking.DockingInputMultiStructure method) (asapdiscovery.docking.docking.DockingInputPair method) (asapdiscovery.docking.docking.DockingResult method) (asapdiscovery.docking.openeye.POSITDocker method) (asapdiscovery.docking.openeye.POSITDockingResults method) (asapdiscovery.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (asapdiscovery.docking.schema.pose_generation.PosedLigands method) (asapdiscovery.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (asapdiscovery.docking.scorer.ChemGauss4Scorer method) (asapdiscovery.docking.scorer.E3MLModelScorer method) (asapdiscovery.docking.scorer.E3NNScorer method) (asapdiscovery.docking.scorer.FINTScorer method) (asapdiscovery.docking.scorer.GATScorer method) (asapdiscovery.docking.scorer.MetaScorer method) (asapdiscovery.docking.scorer.MLModelScorer method) (asapdiscovery.docking.scorer.SchnetScorer method) (asapdiscovery.docking.scorer.Score method) (asapdiscovery.docking.scorer.ScorerBase method) (asapdiscovery.genetics.blast.PDBEntry method) (asapdiscovery.genetics.blast.PDBRecord method) (asapdiscovery.ml.config.ConfigBase method) (asapdiscovery.ml.config.DataAugConfig method) (asapdiscovery.ml.config.DatasetConfig method) (asapdiscovery.ml.config.DatasetSplitterConfig method) (asapdiscovery.ml.config.EarlyStoppingConfig method) (asapdiscovery.ml.config.LossFunctionConfig method) (asapdiscovery.ml.config.OptimizerConfig method) (asapdiscovery.ml.inference.E3nnInference method) (asapdiscovery.ml.inference.GATInference method) (asapdiscovery.ml.inference.InferenceBase method) (asapdiscovery.ml.inference.SchnetInference method) (asapdiscovery.ml.inference.StructuralInference method) (asapdiscovery.ml.models.LocalMLModelSpec method) (asapdiscovery.ml.models.MLModelBase method) (asapdiscovery.ml.models.MLModelRegistry method) (asapdiscovery.ml.models.MLModelSpec method) (asapdiscovery.ml.sweep.Sweeper method) (asapdiscovery.ml.trainer.Trainer method) (asapdiscovery.modeling.protein_prep.ProteinPrepper method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase method) (asapdiscovery.modeling.schema.MoleculeFilter method) (asapdiscovery.simulation.simulate.SimulationResult method) (asapdiscovery.simulation.simulate.SimulatorBase method) (asapdiscovery.simulation.simulate.VanillaMDSimulator method) (asapdiscovery.simulation.szybki.SzybkiFreeformResult method) (asapdiscovery.workflows.docking_workflows.cross_docking.CrossDockingWorkflowInputs method) (asapdiscovery.workflows.docking_workflows.large_scale_docking.LargeScaleDockingInputs method) (asapdiscovery.workflows.docking_workflows.small_scale_docking.SmallScaleDockingInputs method) (asapdiscovery.workflows.docking_workflows.workflows.DockingWorkflowInputsBase method) (asapdiscovery.workflows.docking_workflows.workflows.PosteraDockingWorkflowInputs method) (asapdiscovery.workflows.prep_workflows.protein_prep.ProteinPrepInputs method)

json_loads() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper.Config method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper.Config method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper.Config method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory.Config method) (asapdiscovery.alchemy.schema.fec.SolventSettings.Config method) (asapdiscovery.alchemy.schema.network.MaximalPlanner.Config method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner.Config method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner.Config method) (asapdiscovery.alchemy.schema.network.NetworkPlanner.Config method) (asapdiscovery.alchemy.schema.network.RadialPlanner.Config method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet.Config method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow.Config method)

K

KartografAtomMapper (class in asapdiscovery.alchemy.schema.atom_mapping) KartografAtomMapper.Config (class in asapdiscovery.alchemy.schema.atom_mapping)

keys() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) ki_to_dg() (in module asapdiscovery.alchemy.predict)

L

large_scale_docking_workflow() (in module asapdiscovery.workflows.docking_workflows.large_scale_docking) LargeScaleDockingInputs (class in asapdiscovery.workflows.docking_workflows.large_scale_docking) LeaveOneOutSelector (class in asapdiscovery.data.operators.selectors.pairwise_selector) LeaveSimilarOutSelector (class in asapdiscovery.data.operators.selectors.pairwise_selector) lig() (in module asapdiscovery.ml.cli_args) Ligand (class in asapdiscovery.data.schema.ligand) LigandDeDuplicator (class in asapdiscovery.data.operators.deduplicator) LigandIdentifiers (class in asapdiscovery.data.schema.identifiers) LigandProvenance (class in asapdiscovery.data.schema.identifiers) ligands() (in module asapdiscovery.cli.cli_args) list_available() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) list_commands() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) list_commands_for_help() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) ljust() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) lmax() (in module asapdiscovery.ml.cli_args) load() (asapdiscovery.data.readers.structure_dir.StructureDirFactory method) (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory method) load_cache() (asapdiscovery.modeling.protein_prep.ProteinPrepper static method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase static method) load_cache_files() (asapdiscovery.ml.sweep.Sweeper class method) (asapdiscovery.ml.trainer.Trainer class method) load_cache_files_lists() (asapdiscovery.ml.sweep.Sweeper class method) (asapdiscovery.ml.trainer.Trainer class method) load_config() (asapdiscovery.ml.sweep.Sweeper class method) load_dataframes() (in module asapdiscovery.docking.analysis) load_openeye_cif() (in module asapdiscovery.data.backend.openeye) load_openeye_cif1() (in module asapdiscovery.data.backend.openeye) load_openeye_design_unit() (in module asapdiscovery.data.backend.openeye) load_openeye_pdb() (in module asapdiscovery.data.backend.openeye) load_openeye_sdf() (in module asapdiscovery.data.backend.openeye) load_openeye_sdfs() (in module asapdiscovery.data.backend.openeye) load_openeye_smi() (in module asapdiscovery.data.backend.openeye) load_sdf() (in module asapdiscovery.data.backend.rdkit) load_state_dict() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) load_yaml() (in module asapdiscovery.data.services.postera.manifold_data_validation) LocalMLModelSpec (class in asapdiscovery.ml.models) loglevel() (in module asapdiscovery.cli.cli_args)

LomapAtomMapper (class in asapdiscovery.alchemy.schema.atom_mapping) LomapAtomMapper.Config (class in asapdiscovery.alchemy.schema.atom_mapping) loss_args() (in module asapdiscovery.ml.cli_args) loss_config_cache() (in module asapdiscovery.ml.cli_args) loss_config_cache_overwrite() (in module asapdiscovery.ml.cli_args) loss_dict() (in module asapdiscovery.ml.cli_args) loss_type() (in module asapdiscovery.ml.cli_args) LossFunctionConfig (class in asapdiscovery.ml.config) LossFunctionType (class in asapdiscovery.ml.config) lower() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) lr() (in module asapdiscovery.ml.cli_args) lstrip() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method)

M

main() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) (in module asapdiscovery.data.metadata.master_seqres.fasta_to_seqres) make_color_res_fitness() (in module asapdiscovery.data.backend.plip) make_color_res_subpockets() (in module asapdiscovery.data.backend.plip) make_context() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) make_dask_client_meta() (in module asapdiscovery.data.util.dask_utils) make_design_unit() (in module asapdiscovery.modeling.modeling) make_df_from_docking_results() (asapdiscovery.docking.docking.DockingResult static method) (asapdiscovery.docking.openeye.POSITDockingResults static method) make_logoplot_input() (asapdiscovery.dataviz.html_viz.HTMLVisualizer method) make_manifold_tag_name_from_components() (in module asapdiscovery.data.services.postera.manifold_data_validation) make_output_tags() (in module asapdiscovery.data.services.postera.manifold_data_validation) make_parser() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) make_static_tags() (in module asapdiscovery.data.services.postera.manifold_data_validation) make_tag_combinations_and_combine_with_static() (in module asapdiscovery.data.services.postera.manifold_data_validation) make_target_tags() (in module asapdiscovery.data.services.postera.manifold_data_validation) make_test_file_pooch_repo() (in module asapdiscovery.data.testing.test_resources) make_virus_tags() (in module asapdiscovery.data.services.postera.manifold_data_validation) maketrans() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector static method) (asapdiscovery.data.schema.schema_base.DataStorageType static method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags static method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags static method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase static method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags static method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags static method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys static method) (asapdiscovery.data.util.dask_utils.BackendType static method) (asapdiscovery.data.util.dask_utils.DaskType static method) (asapdiscovery.data.util.dask_utils.FailureMode static method) (asapdiscovery.data.util.stringenum.StringEnum static method) (asapdiscovery.dataviz.html_viz.ColorMethod static method) (asapdiscovery.docking.analysis.TanimotoType static method) (asapdiscovery.docking.docking_data_validation.DockingResultCols static method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod static method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod static method) (asapdiscovery.docking.scorer.ScoreType static method) (asapdiscovery.docking.scorer.ScoreUnits static method) (asapdiscovery.ml.config.DataAugType static method) (asapdiscovery.ml.config.DatasetSplitterType static method) (asapdiscovery.ml.config.DatasetType static method) (asapdiscovery.ml.config.EarlyStoppingType static method) (asapdiscovery.ml.config.LossFunctionType static method) (asapdiscovery.ml.config.OptimizerType static method) (asapdiscovery.modeling.protein_prep.CacheType static method) (asapdiscovery.modeling.schema.MoleculeComponent static method) (asapdiscovery.simulation.simulate.OpenMMPlatform static method) ManifoldAllowedTags (class in asapdiscovery.data.services.postera.manifold_data_validation) ManifoldArtifactUploader (class in asapdiscovery.data.services.postera.manifold_artifacts) map_output_col_to_manifold_tag() (in module asapdiscovery.data.services.postera.manifold_data_validation) max_comb_neg() (in module asapdiscovery.ml.cli_args) max_comb_scale() (in module asapdiscovery.ml.cli_args) max_num_neighbors() (in module asapdiscovery.ml.cli_args) max_z() (in module asapdiscovery.ml.cli_args) MaximalPlanner (class in asapdiscovery.alchemy.schema.network) MaximalPlanner.Config (class in asapdiscovery.alchemy.schema.network) MCSSelector (class in asapdiscovery.data.operators.selectors.mcs_selector) md() (in module asapdiscovery.cli.cli_args) md_args() (in module asapdiscovery.cli.cli_args) md_openmm_platform() (in module asapdiscovery.cli.cli_args) md_steps() (in module asapdiscovery.cli.cli_args) mean() (in module asapdiscovery.ml.cli_args) MetaLigandFactory (class in asapdiscovery.data.readers.meta_ligand_factory) MetaScorer (class in asapdiscovery.docking.scorer) MetaStructureFactory (class in asapdiscovery.data.readers.meta_structure_factory) MinimalRedundantPlanner (class in asapdiscovery.alchemy.schema.network) MinimalRedundantPlanner.Config (class in asapdiscovery.alchemy.schema.network) MinimalSpanningPlanner (class in asapdiscovery.alchemy.schema.network) MinimalSpanningPlanner.Config (class in asapdiscovery.alchemy.schema.network) ml_scorer() (in module asapdiscovery.cli.cli_args) ml_scorers_must_be_valid() (asapdiscovery.workflows.docking_workflows.large_scale_docking.LargeScaleDockingInputs class method) (asapdiscovery.workflows.docking_workflows.small_scale_docking.SmallScaleDockingInputs class method) MLModelBase (class in asapdiscovery.ml.models) MLModelRegistry (class in asapdiscovery.ml.models) MLModelScorer (class in asapdiscovery.docking.scorer) MLModelSpec (class in asapdiscovery.ml.models) model (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) model_config_cache() (in module asapdiscovery.ml.cli_args) model_config_cache_overwrite() (in module asapdiscovery.ml.cli_args) model_rand_seed() (in module asapdiscovery.ml.cli_args) module asapdiscovery asapdiscovery.alchemy asapdiscovery.alchemy.cli asapdiscovery.alchemy.cli.alchemy asapdiscovery.alchemy.cli.cli asapdiscovery.alchemy.cli.prep asapdiscovery.alchemy.cli.utils asapdiscovery.alchemy.predict asapdiscovery.alchemy.schema asapdiscovery.alchemy.schema.atom_mapping asapdiscovery.alchemy.schema.base asapdiscovery.alchemy.schema.fec asapdiscovery.alchemy.schema.forcefield asapdiscovery.alchemy.schema.network asapdiscovery.alchemy.schema.prep_workflow asapdiscovery.alchemy.utils asapdiscovery.cli asapdiscovery.cli.cli asapdiscovery.cli.cli_args asapdiscovery.data asapdiscovery.data.backend asapdiscovery.data.backend.openeye asapdiscovery.data.backend.plip asapdiscovery.data.backend.rdkit asapdiscovery.data.metadata asapdiscovery.data.metadata.master_seqres asapdiscovery.data.metadata.master_seqres.fasta_to_seqres asapdiscovery.data.metadata.resources asapdiscovery.data.operators asapdiscovery.data.operators.deduplicator asapdiscovery.data.operators.selectors asapdiscovery.data.operators.selectors.mcs_selector asapdiscovery.data.operators.selectors.pairwise_selector asapdiscovery.data.operators.selectors.selector asapdiscovery.data.operators.selectors.selector_list asapdiscovery.data.operators.state_expanders asapdiscovery.data.operators.state_expanders.expansion_tag asapdiscovery.data.operators.state_expanders.protomer_expander asapdiscovery.data.operators.state_expanders.state_expander asapdiscovery.data.operators.state_expanders.stereo_expander asapdiscovery.data.operators.state_expanders.tautomer_expander asapdiscovery.data.readers asapdiscovery.data.readers.meta_ligand_factory asapdiscovery.data.readers.meta_structure_factory asapdiscovery.data.readers.molfile asapdiscovery.data.readers.structure_dir asapdiscovery.data.schema asapdiscovery.data.schema.complex asapdiscovery.data.schema.experimental asapdiscovery.data.schema.identifiers asapdiscovery.data.schema.legacy asapdiscovery.data.schema.ligand asapdiscovery.data.schema.pairs asapdiscovery.data.schema.schema_base asapdiscovery.data.schema.sets asapdiscovery.data.schema.target asapdiscovery.data.sequence asapdiscovery.data.services asapdiscovery.data.services.aws asapdiscovery.data.services.aws.cloudfront asapdiscovery.data.services.aws.s3 asapdiscovery.data.services.cdd asapdiscovery.data.services.cdd.cdd_api asapdiscovery.data.services.cdd.cdd_download asapdiscovery.data.services.fragalysis asapdiscovery.data.services.fragalysis.fragalysis_download asapdiscovery.data.services.fragalysis.fragalysis_reader asapdiscovery.data.services.postera asapdiscovery.data.services.postera.manifold_artifacts asapdiscovery.data.services.postera.manifold_data_validation asapdiscovery.data.services.postera.molecule_set asapdiscovery.data.services.postera.postera_api asapdiscovery.data.services.postera.postera_factory asapdiscovery.data.services.postera.postera_uploader asapdiscovery.data.services.rcsb asapdiscovery.data.services.rcsb.rcsb_download asapdiscovery.data.services.services_config asapdiscovery.data.services.web_utils asapdiscovery.data.testing asapdiscovery.data.testing.test_resources asapdiscovery.data.util asapdiscovery.data.util.dask_utils asapdiscovery.data.util.data_conversion asapdiscovery.data.util.execution_utils asapdiscovery.data.util.logging asapdiscovery.data.util.stringenum asapdiscovery.data.util.utils asapdiscovery.dataviz asapdiscovery.dataviz.gif_viz asapdiscovery.dataviz.html_viz asapdiscovery.dataviz.resources asapdiscovery.dataviz.resources.fonts asapdiscovery.dataviz.show_contacts asapdiscovery.dataviz.visualizer asapdiscovery.docking asapdiscovery.docking.analysis asapdiscovery.docking.docking asapdiscovery.docking.docking_data_validation asapdiscovery.docking.openeye asapdiscovery.docking.schema asapdiscovery.docking.schema.pose_generation asapdiscovery.docking.scorer asapdiscovery.genetics asapdiscovery.genetics.blast asapdiscovery.genetics.calculate_rmsd asapdiscovery.genetics.cli asapdiscovery.genetics.cli_args asapdiscovery.genetics.example asapdiscovery.genetics.fitness asapdiscovery.genetics.seq_alignment asapdiscovery.ml asapdiscovery.ml.cli asapdiscovery.ml.cli_args asapdiscovery.ml.cli_sweep asapdiscovery.ml.config asapdiscovery.ml.data_augmentation asapdiscovery.ml.dataset asapdiscovery.ml.es asapdiscovery.ml.inference asapdiscovery.ml.loss asapdiscovery.ml.models asapdiscovery.ml.pretrained_models asapdiscovery.ml.sweep asapdiscovery.ml.trainer asapdiscovery.modeling asapdiscovery.modeling.modeling asapdiscovery.modeling.protein_prep asapdiscovery.modeling.schema asapdiscovery.simulation asapdiscovery.simulation.simulate asapdiscovery.simulation.szybki asapdiscovery.workflows asapdiscovery.workflows.docking_workflows asapdiscovery.workflows.docking_workflows.cli asapdiscovery.workflows.docking_workflows.cross_docking asapdiscovery.workflows.docking_workflows.large_scale_docking asapdiscovery.workflows.docking_workflows.small_scale_docking asapdiscovery.workflows.docking_workflows.workflows asapdiscovery.workflows.prep_workflows asapdiscovery.workflows.prep_workflows.cli asapdiscovery.workflows.prep_workflows.protein_prep

modules() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) Molecule (class in asapdiscovery.data.services.postera.molecule_set) MoleculeComponent (class in asapdiscovery.modeling.schema) MoleculeFilter (class in asapdiscovery.modeling.schema) MoleculeList (class in asapdiscovery.data.services.postera.molecule_set) MoleculeSetAPI (class in asapdiscovery.data.services.postera.molecule_set) MoleculeSetKeys (class in asapdiscovery.data.services.postera.molecule_set) MoleculeUpdate (class in asapdiscovery.data.services.postera.molecule_set) MoleculeUpdateList (class in asapdiscovery.data.services.postera.molecule_set) MolFileFactory (class in asapdiscovery.data.readers.molfile) momentum() (in module asapdiscovery.ml.cli_args) MSELoss (class in asapdiscovery.ml.loss) mtenn_args() (in module asapdiscovery.ml.cli_args) multimer() (in module asapdiscovery.genetics.cli_args) MultiStructureBase (class in asapdiscovery.data.schema.sets) mutate_residues() (in module asapdiscovery.modeling.modeling)

N

n_chains() (in module asapdiscovery.genetics.cli_args) n_epochs() (in module asapdiscovery.ml.cli_args) name (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) name() (asapdiscovery.alchemy.schema.fec.TransformationResult method) (in module asapdiscovery.ml.cli_args) named_buffers() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) named_children() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) named_modules() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) named_parameters() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) negative_log() (in module asapdiscovery.alchemy.predict) neighbor_dist() (in module asapdiscovery.ml.cli_args) network_status() (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) NetworkPlanner (class in asapdiscovery.alchemy.schema.network) NetworkPlanner.Config (class in asapdiscovery.alchemy.schema.network) neutralized (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property)

non_iso_smiles (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) nonbondedCutoff (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) nonbondedMethod (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) normalize_fitness() (in module asapdiscovery.genetics.fitness) num_atom_types() (in module asapdiscovery.ml.cli_args) num_basis() (in module asapdiscovery.ml.cli_args) num_filters() (in module asapdiscovery.ml.cli_args) num_gaussians() (in module asapdiscovery.ml.cli_args) num_heads() (in module asapdiscovery.ml.cli_args) num_interactions() (in module asapdiscovery.ml.cli_args) num_layers_e3nn() (in module asapdiscovery.ml.cli_args) num_layers_gat() (in module asapdiscovery.ml.cli_args) num_layers_visnet() (in module asapdiscovery.ml.cli_args) num_neighbors() (in module asapdiscovery.ml.cli_args) num_nodes() (in module asapdiscovery.ml.cli_args) num_poses (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) num_radial_layers() (in module asapdiscovery.ml.cli_args) num_radial_neurons() (in module asapdiscovery.ml.cli_args) num_rbf() (in module asapdiscovery.ml.cli_args)

O

oe_smiles_roundtrip() (in module asapdiscovery.data.backend.openeye) oedu_to_bytes64() (in module asapdiscovery.data.backend.openeye) oemol_to_inchi() (in module asapdiscovery.data.backend.openeye) oemol_to_inchikey() (in module asapdiscovery.data.backend.openeye) oemol_to_pdb_string() (in module asapdiscovery.data.backend.openeye) oemol_to_sdf_string() (in module asapdiscovery.data.backend.openeye) oemol_to_smiles() (in module asapdiscovery.data.backend.openeye) omega_dense_check() (asapdiscovery.docking.openeye.POSITDocker class method) openeye_copy_pdb_data() (in module asapdiscovery.data.backend.openeye) openeye_perceive_residues() (in module asapdiscovery.data.backend.openeye) OpenEyeConstrainedPoseGenerator (class in asapdiscovery.docking.schema.pose_generation)

OpenMMPlatform (class in asapdiscovery.simulation.simulate) optim_args() (in module asapdiscovery.ml.cli_args) optimizer_config_cache() (in module asapdiscovery.ml.cli_args) optimizer_config_cache_overwrite() (in module asapdiscovery.ml.cli_args) optimizer_type() (in module asapdiscovery.ml.cli_args) OptimizerConfig (class in asapdiscovery.ml.config) OptimizerType (class in asapdiscovery.ml.config) output_dir() (in module asapdiscovery.cli.cli_args) (in module asapdiscovery.ml.cli_args) OutputTags (class in asapdiscovery.data.services.postera.manifold_data_validation) overwrite() (in module asapdiscovery.cli.cli_args) overwrite_args() (in module asapdiscovery.ml.cli_args)

P

padding (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) PairBase (class in asapdiscovery.data.schema.pairs) PairwiseSelector (class in asapdiscovery.data.operators.selectors.pairwise_selector) parameters() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) params (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder attribute) parse_args() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) parse_blast() (in module asapdiscovery.genetics.blast) parse_extra_config() (asapdiscovery.ml.sweep.Sweeper class method) (asapdiscovery.ml.trainer.Trainer class method) parse_fitness_json() (in module asapdiscovery.genetics.fitness) parse_fluorescence_data_cdd() (in module asapdiscovery.data.util.utils) parse_fragalysis() (in module asapdiscovery.data.services.fragalysis.fragalysis_download) parse_pdb_blast_results() (asapdiscovery.genetics.blast.PDBEntry static method) parse_xtal() (in module asapdiscovery.data.services.fragalysis.fragalysis_download) partition() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) PatientConvergedEarlyStopping (class in asapdiscovery.ml.es) pdb_file() (in module asapdiscovery.cli.cli_args) pdb_string_to_oemol() (in module asapdiscovery.data.backend.openeye) pdb_to_seq() (in module asapdiscovery.genetics.blast) PDBEntry (class in asapdiscovery.genetics.blast) PDBRecord (class in asapdiscovery.genetics.blast) PersesAtomMapper (class in asapdiscovery.alchemy.schema.atom_mapping) PersesAtomMapper.Config (class in asapdiscovery.alchemy.schema.atom_mapping) pic50_to_dg() (in module asapdiscovery.alchemy.predict) PlannedNetwork (class in asapdiscovery.alchemy.schema.network) PlannedNetwork.Config (class in asapdiscovery.alchemy.schema.network) plotmol_absolute() (in module asapdiscovery.alchemy.predict) plotmol_relative() (in module asapdiscovery.alchemy.predict) pop() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) popitem() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method)

pose_experimental_molecules() (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) PosedLigands (class in asapdiscovery.docking.schema.pose_generation) PoseEnergyMethod (class in asapdiscovery.docking.schema.pose_generation) PoseSelectionMethod (class in asapdiscovery.docking.schema.pose_generation) POSIT_METHOD (class in asapdiscovery.docking.openeye) POSIT_RELAX_MODE (class in asapdiscovery.docking.openeye) POSITDocker (class in asapdiscovery.docking.openeye) POSITDockingResults (class in asapdiscovery.docking.openeye) postera() (in module asapdiscovery.cli.cli_args) postera_args() (in module asapdiscovery.cli.cli_args) postera_molset_name() (in module asapdiscovery.cli.cli_args) postera_upload() (in module asapdiscovery.cli.cli_args) PosteraDockingWorkflowInputs (class in asapdiscovery.workflows.docking_workflows.workflows) PosteraFactory (class in asapdiscovery.data.services.postera.postera_factory) PosteraSettings (class in asapdiscovery.data.services.services_config) PosteraUploader (class in asapdiscovery.data.services.postera.postera_uploader) pred_km() (in module asapdiscovery.ml.cli_args) pred_readout() (in module asapdiscovery.ml.cli_args) pred_substrate() (in module asapdiscovery.ml.cli_args) predict() (asapdiscovery.ml.inference.E3nnInference method) (asapdiscovery.ml.inference.GATInference method) (asapdiscovery.ml.inference.InferenceBase method) (asapdiscovery.ml.inference.SchnetInference method) (asapdiscovery.ml.inference.StructuralInference method) predict_from_oemol() (asapdiscovery.ml.inference.E3nnInference method) (asapdiscovery.ml.inference.SchnetInference method) (asapdiscovery.ml.inference.StructuralInference method) predict_from_smiles() (asapdiscovery.ml.inference.GATInference method) predict_from_structure_file() (asapdiscovery.ml.inference.E3nnInference method) (asapdiscovery.ml.inference.SchnetInference method) (asapdiscovery.ml.inference.StructuralInference method) prep() (asapdiscovery.modeling.protein_prep.ProteinPrepper method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase method) PreppedComplex (class in asapdiscovery.data.schema.complex) PreppedTarget (class in asapdiscovery.data.schema.target) print_header() (in module asapdiscovery.alchemy.cli.utils) print_SD_data() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) (in module asapdiscovery.data.backend.openeye) process_fragalysis_pdb() (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory static method) proj() (in module asapdiscovery.ml.cli_args) protein_prep_workflow() (in module asapdiscovery.workflows.prep_workflows.protein_prep) ProteinPrepInputs (class in asapdiscovery.workflows.prep_workflows.protein_prep) ProteinPrepper (class in asapdiscovery.modeling.protein_prep) ProteinPrepperBase (class in asapdiscovery.modeling.protein_prep) ProtomerExpander (class in asapdiscovery.data.operators.state_expanders.protomer_expander) provenance() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper method) (asapdiscovery.data.operators.state_expanders.protomer_expander.EpikExpander method) (asapdiscovery.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpanderBase method) (asapdiscovery.data.operators.state_expanders.stereo_expander.StereoExpander method) (asapdiscovery.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (asapdiscovery.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (asapdiscovery.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) pull() (asapdiscovery.data.services.postera.postera_factory.PosteraFactory method) (asapdiscovery.ml.models.MLModelSpec method) pull_all() (asapdiscovery.data.services.postera.postera_factory.PosteraFactory method) pull_from_postera() (in module asapdiscovery.alchemy.cli.utils) push() (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader method) push_file() (asapdiscovery.data.services.aws.s3.S3 method) pymol_alignment() (in module asapdiscovery.data.services.rcsb.rcsb_download)

R

RadialPlanner (class in asapdiscovery.alchemy.schema.network) RadialPlanner.Config (class in asapdiscovery.alchemy.schema.network) rdkit_smiles_roundtrip() (in module asapdiscovery.data.backend.rdkit) RDKitConstrainedPoseGenerator (class in asapdiscovery.docking.schema.pose_generation) read_file_directly() (in module asapdiscovery.data.schema.schema_base) readout() (in module asapdiscovery.ml.cli_args) reduce_op() (in module asapdiscovery.ml.cli_args) ReferenceLigand (class in asapdiscovery.data.schema.ligand) register_backward_hook() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_buffer() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_forward_hook() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_forward_pre_hook() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_full_backward_hook() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_full_backward_pre_hook() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_load_state_dict_post_hook() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_ml_scorer() (in module asapdiscovery.docking.scorer) register_module() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_parameter() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) register_state_dict_pre_hook() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) remove() (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) remove_duplicates() (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader method) removeprefix() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) removesuffix() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) rename_output_columns_for_manifold() (in module asapdiscovery.data.services.postera.manifold_data_validation) replace() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) request_rcsb_pdbid() (asapdiscovery.genetics.blast.PDBEntry static method) requires_grad_() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) reset() (asapdiscovery.data.services.aws.s3.S3 method) residuals() (in module asapdiscovery.ml.cli_args) restart_tasks() (asapdiscovery.alchemy.utils.AlchemiscaleHelper method) result_callback() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) result_cls (asapdiscovery.docking.openeye.POSITDocker attribute) retrieve_pdb() (asapdiscovery.genetics.blast.PDBEntry method) reverse() (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) rfind() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method)

rho() (in module asapdiscovery.ml.cli_args) rigidWater (asapdiscovery.alchemy.schema.forcefield.ForceFieldParams attribute) rindex() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) rjust() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) rmsd_alignment() (in module asapdiscovery.genetics.calculate_rmsd) rpartition() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) rsplit() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) rstrip() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) run_all_szybki() (asapdiscovery.simulation.szybki.SzybkiFreeformConformerAnalyzer method) run_oe_posit_docking() (asapdiscovery.docking.openeye.POSITDocker static method) run_szybki_on_ligand() (asapdiscovery.simulation.szybki.SzybkiFreeformConformerAnalyzer method)

S

S3 (class in asapdiscovery.data.services.aws.s3) S3Error S3Settings (class in asapdiscovery.data.services.services_config) save_alignment_pymol() (in module asapdiscovery.genetics.calculate_rmsd) save_openeye_design_unit() (in module asapdiscovery.data.backend.openeye) save_openeye_pdb() (in module asapdiscovery.data.backend.openeye) save_openeye_sdf() (in module asapdiscovery.data.backend.openeye) save_openeye_sdfs() (in module asapdiscovery.data.backend.openeye) save_posed_ligands() (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet method) save_receptor_grid() (in module asapdiscovery.data.backend.openeye) save_to_cache() (in module asapdiscovery.cli.cli_args) schema_dict_get_val_overload() (in module asapdiscovery.data.schema.schema_base) schnet_args() (in module asapdiscovery.ml.cli_args) SchnetInference (class in asapdiscovery.ml.inference) SchnetScorer (class in asapdiscovery.docking.scorer) Score (class in asapdiscovery.docking.scorer) score() (asapdiscovery.docking.scorer.ChemGauss4Scorer method) (asapdiscovery.docking.scorer.E3MLModelScorer method) (asapdiscovery.docking.scorer.E3NNScorer method) (asapdiscovery.docking.scorer.FINTScorer method) (asapdiscovery.docking.scorer.GATScorer method) (asapdiscovery.docking.scorer.MetaScorer method) (asapdiscovery.docking.scorer.MLModelScorer method) (asapdiscovery.docking.scorer.SchnetScorer method) (asapdiscovery.docking.scorer.ScorerBase method) ScorerBase (class in asapdiscovery.docking.scorer) scores_to_df() (asapdiscovery.docking.scorer.ChemGauss4Scorer static method) (asapdiscovery.docking.scorer.E3MLModelScorer static method) (asapdiscovery.docking.scorer.E3NNScorer static method) (asapdiscovery.docking.scorer.FINTScorer static method) (asapdiscovery.docking.scorer.GATScorer static method) (asapdiscovery.docking.scorer.MLModelScorer static method) (asapdiscovery.docking.scorer.SchnetScorer static method) (asapdiscovery.docking.scorer.ScorerBase static method) ScoreType (class in asapdiscovery.docking.scorer) ScoreUnits (class in asapdiscovery.docking.scorer) sdf_str_to_rdkit_mol() (in module asapdiscovery.data.backend.rdkit) sdf_string_to_oemol() (in module asapdiscovery.data.backend.openeye) search_host() (in module asapdiscovery.genetics.blast) select_best_colabfold() (in module asapdiscovery.genetics.calculate_rmsd) select_reference_for_compounds() (in module asapdiscovery.alchemy.utils) selector_cls (asapdiscovery.data.operators.selectors.selector_list.StructureSelector property) SelectorBase (class in asapdiscovery.data.operators.selectors.selector) SelfDockingSelector (class in asapdiscovery.data.operators.selectors.pairwise_selector) semiquant_fill() (in module asapdiscovery.ml.cli_args) seq_file() (in module asapdiscovery.genetics.cli_args) seq_type() (in module asapdiscovery.genetics.cli_args) seqres_by_target() (in module asapdiscovery.data.sequence) seqres_to_res_list() (in module asapdiscovery.data.util.utils) set_dask_config() (in module asapdiscovery.data.util.dask_utils) set_expansion() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) set_extra_state() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) set_SD_data() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) (in module asapdiscovery.data.backend.openeye) (in module asapdiscovery.data.backend.rdkit) setdefault() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) share_memory() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) shell_complete() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) shift_and_add_prediction_error() (in module asapdiscovery.alchemy.predict) show_contacts() (in module asapdiscovery.dataviz.show_contacts) SimulationResult (class in asapdiscovery.simulation.simulate) SimulatorBase (class in asapdiscovery.simulation.simulate) size (asapdiscovery.data.schema.complex.Complex property) (asapdiscovery.data.schema.complex.ComplexBase property) (asapdiscovery.data.schema.complex.PreppedComplex property) (asapdiscovery.data.schema.identifiers.LigandIdentifiers property) (asapdiscovery.data.schema.identifiers.LigandProvenance property) (asapdiscovery.data.schema.identifiers.TargetIdentifiers property) (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) (asapdiscovery.data.schema.schema_base.DataModelAbstractBase property) (asapdiscovery.data.schema.target.PreppedTarget property) (asapdiscovery.data.schema.target.Target property) small_scale_docking_workflow() (in module asapdiscovery.workflows.docking_workflows.small_scale_docking) SmallScaleDockingInputs (class in asapdiscovery.workflows.docking_workflows.small_scale_docking) smiles (asapdiscovery.data.schema.ligand.Ligand property) (asapdiscovery.data.schema.ligand.ReferenceLigand property) smiles_to_oemol() (in module asapdiscovery.data.backend.openeye) SolventSettings (class in asapdiscovery.alchemy.schema.fec) SolventSettings.Config (class in asapdiscovery.alchemy.schema.fec) sort() (asapdiscovery.data.services.postera.molecule_set.MoleculeList method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdateList method) sort_by_mcs() (in module asapdiscovery.data.operators.selectors.mcs_selector) sort_confs_by_sd_tag_value() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) SpecialHelpOrder (class in asapdiscovery.alchemy.cli.utils) split() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterConfig method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) split_openeye_design_unit() (in module asapdiscovery.modeling.modeling) split_openeye_mol() (in module asapdiscovery.modeling.modeling) splitlines() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method)

spruce_protein() (in module asapdiscovery.modeling.modeling) start_continue_sweep() (asapdiscovery.ml.sweep.Sweeper method) start_epoch() (in module asapdiscovery.ml.cli_args) startswith() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) state_dict() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) StateExpanderBase (class in asapdiscovery.data.operators.state_expanders.state_expander) StateExpansion (class in asapdiscovery.data.operators.state_expanders.state_expander) StateExpansionSet (class in asapdiscovery.data.operators.state_expanders.state_expander) StateExpansionTag (class in asapdiscovery.data.operators.state_expanders.expansion_tag) StaticTags (in module asapdiscovery.data.services.postera.manifold_data_validation) std() (in module asapdiscovery.ml.cli_args) step_loss() (asapdiscovery.ml.loss.MSELoss method) StereoExpander (class in asapdiscovery.data.operators.state_expanders.stereo_expander) str_files() (in module asapdiscovery.ml.cli_args) str_fn_cpd_regex() (in module asapdiscovery.ml.cli_args) str_fn_xtal_regex() (in module asapdiscovery.ml.cli_args) strategy() (in module asapdiscovery.ml.cli_args) StringEnum (class in asapdiscovery.data.util.stringenum) strip() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) strip_smiles_salts() (in module asapdiscovery.data.util.utils) struct_ds_args() (in module asapdiscovery.ml.cli_args) StructuralInference (class in asapdiscovery.ml.inference) structure_dir() (in module asapdiscovery.cli.cli_args) StructureDirFactory (class in asapdiscovery.data.readers.structure_dir) StructureSelector (class in asapdiscovery.data.operators.selectors.selector_list) superpose_molecule() (in module asapdiscovery.modeling.modeling) swapcase() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) sweep_args() (in module asapdiscovery.ml.cli_args) sweep_config() (in module asapdiscovery.ml.cli_args) sweep_config_cache() (in module asapdiscovery.ml.cli_args) sweep_config_cache_overwrite() (in module asapdiscovery.ml.cli_args) sweep_start_only() (in module asapdiscovery.ml.cli_args) Sweeper (class in asapdiscovery.ml.sweep) SzybkiFreeformConformerAnalyzer (class in asapdiscovery.simulation.szybki) SzybkiFreeformResult (class in asapdiscovery.simulation.szybki) SzybkiResultCols (class in asapdiscovery.simulation.szybki)

T

TagEnumBase (class in asapdiscovery.data.services.postera.manifold_data_validation) TanimotoType (class in asapdiscovery.docking.analysis) Target (class in asapdiscovery.data.schema.target) target() (in module asapdiscovery.cli.cli_args) target_has_fitness_data() (in module asapdiscovery.genetics.fitness) target_prop() (in module asapdiscovery.ml.cli_args) TargetIdentifiers (class in asapdiscovery.data.schema.identifiers) TargetTags (class in asapdiscovery.data.services.postera.manifold_data_validation) TautomerExpander (class in asapdiscovery.data.operators.state_expanders.tautomer_expander) test_frac() (in module asapdiscovery.ml.cli_args) title() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) to() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) to_alchemical_network() (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork method) to_cinnabar_measurements() (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults method) to_combined_oemol() (asapdiscovery.data.schema.complex.Complex method) to_df() (asapdiscovery.docking.openeye.POSITDockingResults method) to_empty() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) to_fe_map() (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults method) to_file() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleFailure method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork method) (asapdiscovery.alchemy.schema.fec.SolventSettings method) (asapdiscovery.alchemy.schema.fec.TransformationResult method) (asapdiscovery.alchemy.schema.network.MaximalPlanner method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner method) (asapdiscovery.alchemy.schema.network.NetworkPlanner method) (asapdiscovery.alchemy.schema.network.PlannedNetwork method) (asapdiscovery.alchemy.schema.network.RadialPlanner method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) to_info_dict() (asapdiscovery.alchemy.cli.utils.SpecialHelpOrder method) to_ligand_network() (asapdiscovery.alchemy.schema.network.PlannedNetwork method) to_oemol() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method)

to_openfe() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) to_openfe_ligands() (asapdiscovery.alchemy.schema.network.PlannedNetwork method) to_openfe_protocol() (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork method) to_pdb_file() (asapdiscovery.data.schema.target.PreppedTarget method) to_posed_oemol() (asapdiscovery.docking.docking.DockingResult method) (asapdiscovery.docking.openeye.POSITDockingResults method) to_protein() (asapdiscovery.docking.docking.DockingResult method) (asapdiscovery.docking.openeye.POSITDockingResults method) to_rdkit() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) to_SD_tags() (asapdiscovery.data.schema.experimental.ExperimentalCompoundData method) to_sdf() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) to_sdf_str() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) to_single_conformers() (asapdiscovery.data.schema.ligand.Ligand method) (asapdiscovery.data.schema.ligand.ReferenceLigand method) token_name() (asapdiscovery.data.services.cdd.cdd_api.CDDAPI class method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI class method) train() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) (asapdiscovery.ml.sweep.Sweeper method) (asapdiscovery.ml.trainer.Trainer method) train_frac() (in module asapdiscovery.ml.cli_args) trainable_rbf() (in module asapdiscovery.ml.cli_args) trainable_vecnorm() (in module asapdiscovery.ml.cli_args) Trainer (class in asapdiscovery.ml.trainer) trainer_args() (in module asapdiscovery.ml.cli_args) trainer_config_cache() (in module asapdiscovery.ml.cli_args) trainer_config_cache_overwrite() (in module asapdiscovery.ml.cli_args) TransformationResult (class in asapdiscovery.alchemy.schema.fec) TransformationResult.Config (class in asapdiscovery.alchemy.schema.fec) translate() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) trim_small_chains() (in module asapdiscovery.modeling.modeling) truncate_num_steps() (in module asapdiscovery.simulation.simulate) type() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method)

U

unique_name (asapdiscovery.data.schema.complex.Complex property) (asapdiscovery.data.schema.complex.ComplexBase property) (asapdiscovery.data.schema.complex.PreppedComplex property) update() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) update_forward_refs() (asapdiscovery.alchemy.schema.atom_mapping.KartografAtomMapper class method) (asapdiscovery.alchemy.schema.atom_mapping.LomapAtomMapper class method) (asapdiscovery.alchemy.schema.atom_mapping.PersesAtomMapper class method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleFailure class method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleResults class method) (asapdiscovery.alchemy.schema.fec.AlchemiscaleSettings class method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationFactory class method) (asapdiscovery.alchemy.schema.fec.FreeEnergyCalculationNetwork class method) (asapdiscovery.alchemy.schema.fec.SolventSettings class method) (asapdiscovery.alchemy.schema.fec.TransformationResult class method) (asapdiscovery.alchemy.schema.network.MaximalPlanner class method) (asapdiscovery.alchemy.schema.network.MinimalRedundantPlanner class method) (asapdiscovery.alchemy.schema.network.MinimalSpanningPlanner class method) (asapdiscovery.alchemy.schema.network.NetworkPlanner class method) (asapdiscovery.alchemy.schema.network.PlannedNetwork class method) (asapdiscovery.alchemy.schema.network.RadialPlanner class method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyDataSet class method) (asapdiscovery.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (asapdiscovery.data.operators.deduplicator.LigandDeDuplicator class method) (asapdiscovery.data.operators.selectors.mcs_selector.MCSSelector class method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveOneOutSelector class method) (asapdiscovery.data.operators.selectors.pairwise_selector.LeaveSimilarOutSelector class method) (asapdiscovery.data.operators.selectors.pairwise_selector.PairwiseSelector class method) (asapdiscovery.data.operators.selectors.pairwise_selector.SelfDockingSelector class method) (asapdiscovery.data.operators.selectors.selector.SelectorBase class method) (asapdiscovery.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (asapdiscovery.data.operators.state_expanders.protomer_expander.EpikExpander class method) (asapdiscovery.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpanderBase class method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansion class method) (asapdiscovery.data.operators.state_expanders.state_expander.StateExpansionSet class method) (asapdiscovery.data.operators.state_expanders.stereo_expander.StereoExpander class method) (asapdiscovery.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (asapdiscovery.data.readers.meta_ligand_factory.MetaLigandFactory class method) (asapdiscovery.data.readers.meta_structure_factory.MetaStructureFactory class method) (asapdiscovery.data.readers.molfile.MolFileFactory class method) (asapdiscovery.data.readers.structure_dir.StructureDirFactory class method) (asapdiscovery.data.schema.complex.Complex class method) (asapdiscovery.data.schema.complex.ComplexBase class method) (asapdiscovery.data.schema.complex.PreppedComplex class method) (asapdiscovery.data.schema.experimental.ExperimentalCompoundData class method) (asapdiscovery.data.schema.identifiers.LigandIdentifiers class method) (asapdiscovery.data.schema.identifiers.LigandProvenance class method) (asapdiscovery.data.schema.identifiers.TargetIdentifiers class method) (asapdiscovery.data.schema.legacy.CrystalCompoundData class method) (asapdiscovery.data.schema.legacy.EnantiomerPair class method) (asapdiscovery.data.schema.legacy.EnantiomerPairList class method) (asapdiscovery.data.schema.ligand.Ligand class method) (asapdiscovery.data.schema.ligand.ReferenceLigand class method) (asapdiscovery.data.schema.pairs.CompoundStructurePair class method) (asapdiscovery.data.schema.pairs.PairBase class method) (asapdiscovery.data.schema.schema_base.DataModelAbstractBase class method) (asapdiscovery.data.schema.sets.CompoundMultiStructure class method) (asapdiscovery.data.schema.sets.MultiStructureBase class method) (asapdiscovery.data.schema.target.PreppedTarget class method) (asapdiscovery.data.schema.target.Target class method) (asapdiscovery.data.services.fragalysis.fragalysis_reader.FragalysisFactory class method) (asapdiscovery.data.services.postera.manifold_artifacts.ManifoldArtifactUploader class method) (asapdiscovery.data.services.postera.postera_factory.PosteraFactory class method) (asapdiscovery.data.services.postera.postera_uploader.PosteraUploader class method) (asapdiscovery.data.services.services_config.CDDSettings class method) (asapdiscovery.data.services.services_config.CloudfrontSettings class method) (asapdiscovery.data.services.services_config.PosteraSettings class method) (asapdiscovery.data.services.services_config.S3Settings class method) (asapdiscovery.dataviz.gif_viz.GIFVisualizer class method) (asapdiscovery.dataviz.html_viz.HTMLVisualizer class method) (asapdiscovery.dataviz.visualizer.VisualizerBase class method) (asapdiscovery.docking.docking.DockingBase class method) (asapdiscovery.docking.docking.DockingInputBase class method) (asapdiscovery.docking.docking.DockingInputMultiStructure class method) (asapdiscovery.docking.docking.DockingInputPair class method) (asapdiscovery.docking.docking.DockingResult class method) (asapdiscovery.docking.openeye.POSITDocker class method) (asapdiscovery.docking.openeye.POSITDockingResults class method) (asapdiscovery.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (asapdiscovery.docking.schema.pose_generation.PosedLigands class method) (asapdiscovery.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (asapdiscovery.docking.scorer.ChemGauss4Scorer class method) (asapdiscovery.docking.scorer.E3MLModelScorer class method) (asapdiscovery.docking.scorer.E3NNScorer class method) (asapdiscovery.docking.scorer.FINTScorer class method) (asapdiscovery.docking.scorer.GATScorer class method) (asapdiscovery.docking.scorer.MetaScorer class method) (asapdiscovery.docking.scorer.MLModelScorer class method) (asapdiscovery.docking.scorer.SchnetScorer class method) (asapdiscovery.docking.scorer.Score class method) (asapdiscovery.docking.scorer.ScorerBase class method) (asapdiscovery.genetics.blast.PDBEntry class method) (asapdiscovery.genetics.blast.PDBRecord class method) (asapdiscovery.ml.config.ConfigBase class method) (asapdiscovery.ml.config.DataAugConfig class method) (asapdiscovery.ml.config.DatasetConfig class method) (asapdiscovery.ml.config.DatasetSplitterConfig class method) (asapdiscovery.ml.config.EarlyStoppingConfig class method) (asapdiscovery.ml.config.LossFunctionConfig class method) (asapdiscovery.ml.config.OptimizerConfig class method) (asapdiscovery.ml.inference.E3nnInference class method) (asapdiscovery.ml.inference.GATInference class method) (asapdiscovery.ml.inference.InferenceBase class method) (asapdiscovery.ml.inference.SchnetInference class method) (asapdiscovery.ml.inference.StructuralInference class method) (asapdiscovery.ml.models.LocalMLModelSpec class method) (asapdiscovery.ml.models.MLModelBase class method) (asapdiscovery.ml.models.MLModelRegistry class method) (asapdiscovery.ml.models.MLModelSpec class method) (asapdiscovery.ml.sweep.Sweeper class method) (asapdiscovery.ml.trainer.Trainer class method) (asapdiscovery.modeling.protein_prep.ProteinPrepper class method) (asapdiscovery.modeling.protein_prep.ProteinPrepperBase class method) (asapdiscovery.modeling.schema.MoleculeFilter class method) (asapdiscovery.simulation.simulate.SimulationResult class method) (asapdiscovery.simulation.simulate.SimulatorBase class method) (asapdiscovery.simulation.simulate.VanillaMDSimulator class method) (asapdiscovery.simulation.szybki.SzybkiFreeformResult class method) (asapdiscovery.workflows.docking_workflows.cross_docking.CrossDockingWorkflowInputs class method) (asapdiscovery.workflows.docking_workflows.large_scale_docking.LargeScaleDockingInputs class method) (asapdiscovery.workflows.docking_workflows.small_scale_docking.SmallScaleDockingInputs class method) (asapdiscovery.workflows.docking_workflows.workflows.DockingWorkflowInputsBase class method) (asapdiscovery.workflows.docking_workflows.workflows.PosteraDockingWorkflowInputs class method) (asapdiscovery.workflows.prep_workflows.protein_prep.ProteinPrepInputs class method)

update_molecules() (asapdiscovery.data.services.postera.molecule_set.MoleculeSetAPI method) upload_artifacts() (asapdiscovery.data.services.postera.manifold_artifacts.ManifoldArtifactUploader method) upload_to_postera() (in module asapdiscovery.alchemy.cli.utils) upper() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method) use_dask() (in module asapdiscovery.cli.cli_args) use_only_cache() (in module asapdiscovery.cli.cli_args) use_wandb() (in module asapdiscovery.ml.cli_args) utf8len() (in module asapdiscovery.data.schema.schema_base)

V

val_frac() (in module asapdiscovery.ml.cli_args) values() (asapdiscovery.data.services.postera.molecule_set.Molecule method) (asapdiscovery.data.services.postera.molecule_set.MoleculeUpdate method) VanillaMDSimulator (class in asapdiscovery.simulation.simulate) vecnorm_type() (in module asapdiscovery.ml.cli_args)

vertex() (in module asapdiscovery.ml.cli_args) view_alignment() (asapdiscovery.genetics.seq_alignment.Alignment method) VirusTags (class in asapdiscovery.data.services.postera.manifold_data_validation) visnet_args() (in module asapdiscovery.ml.cli_args) VisualizerBase (class in asapdiscovery.dataviz.visualizer)

W

wandb_args() (in module asapdiscovery.ml.cli_args) wandb_init() (asapdiscovery.ml.sweep.Sweeper method) (asapdiscovery.ml.trainer.Trainer method) weight_decay() (in module asapdiscovery.ml.cli_args) weights_path() (in module asapdiscovery.ml.cli_args) write_all_rmsds_to_reference() (in module asapdiscovery.docking.analysis) write_docking_files() (asapdiscovery.docking.docking.DockingBase static method) (asapdiscovery.docking.docking.DockingResult method) (asapdiscovery.docking.openeye.POSITDocker static method) (asapdiscovery.docking.openeye.POSITDockingResults method)

write_file_directly() (in module asapdiscovery.data.schema.schema_base) write_html() (asapdiscovery.dataviz.html_viz.HTMLVisualizer static method) write_ligands_to_multi_sdf() (in module asapdiscovery.data.schema.ligand) write_results_to_multi_sdf() (in module asapdiscovery.docking.docking)

X

xpu() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method)

Z

zero_grad() (asapdiscovery.ml.loss.GaussianNLLLoss method) (asapdiscovery.ml.loss.MSELoss method) zfill() (asapdiscovery.data.operators.selectors.selector_list.StructureSelector method) (asapdiscovery.data.schema.schema_base.DataStorageType method) (asapdiscovery.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (asapdiscovery.data.services.postera.manifold_data_validation.OutputTags method) (asapdiscovery.data.services.postera.manifold_data_validation.TagEnumBase method) (asapdiscovery.data.services.postera.manifold_data_validation.TargetTags method) (asapdiscovery.data.services.postera.manifold_data_validation.VirusTags method) (asapdiscovery.data.services.postera.molecule_set.MoleculeSetKeys method) (asapdiscovery.data.util.dask_utils.BackendType method) (asapdiscovery.data.util.dask_utils.DaskType method) (asapdiscovery.data.util.dask_utils.FailureMode method) (asapdiscovery.data.util.stringenum.StringEnum method) (asapdiscovery.dataviz.html_viz.ColorMethod method) (asapdiscovery.docking.analysis.TanimotoType method) (asapdiscovery.docking.docking_data_validation.DockingResultCols method) (asapdiscovery.docking.schema.pose_generation.PoseEnergyMethod method) (asapdiscovery.docking.schema.pose_generation.PoseSelectionMethod method) (asapdiscovery.docking.scorer.ScoreType method) (asapdiscovery.docking.scorer.ScoreUnits method) (asapdiscovery.ml.config.DataAugType method) (asapdiscovery.ml.config.DatasetSplitterType method) (asapdiscovery.ml.config.DatasetType method) (asapdiscovery.ml.config.EarlyStoppingType method) (asapdiscovery.ml.config.LossFunctionType method) (asapdiscovery.ml.config.OptimizerType method) (asapdiscovery.modeling.protein_prep.CacheType method) (asapdiscovery.modeling.schema.MoleculeComponent method) (asapdiscovery.simulation.simulate.OpenMMPlatform method)