Index

_

__init__() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) (drugforge.alchemy.interfaces.AlchemiscaleSettings method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper method) (drugforge.alchemy.schema.base.DefaultModel method) (drugforge.alchemy.schema.charge.OpenFFCharges method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (drugforge.data.operators.deduplicator.LigandDeDuplicator method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory method) (drugforge.data.readers.molfile.MolFileFactory method) (drugforge.data.schema.complex.Complex method) (drugforge.data.schema.complex.ComplexBase method) (drugforge.data.schema.experimental.ExperimentalCompoundData method) (drugforge.data.schema.identifiers.BespokeParameter method) (drugforge.data.schema.identifiers.BespokeParameters method) (drugforge.data.schema.identifiers.ChargeProvenance method) (drugforge.data.schema.identifiers.LigandIdentifiers method) (drugforge.data.schema.identifiers.LigandProvenance method) (drugforge.data.schema.identifiers.TargetIdentifiers method) (drugforge.data.schema.legacy.CrystalCompoundData method) (drugforge.data.schema.legacy.EnantiomerPair method) (drugforge.data.schema.legacy.EnantiomerPairList method) (drugforge.data.schema.ligand.ChemicalRelationship method) (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (drugforge.data.schema.pairs.CompoundStructurePair method) (drugforge.data.schema.pairs.PairBase method) (drugforge.data.schema.schema_base.DataModelAbstractBase method) (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.schema.schema_base.MoleculeFilter method) (drugforge.data.schema.sets.CompoundMultiStructure method) (drugforge.data.schema.sets.MultiStructureBase method) (drugforge.data.schema.target.Target method) (drugforge.data.services.aws.cloudfront.CloudFront method) (drugforge.data.services.aws.s3.S3 method) (drugforge.data.services.cdd.cdd_api.CDDAPI method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) (drugforge.data.services.postera.postera_factory.PosteraFactory method) (drugforge.data.services.services_config.CDDSettings method) (drugforge.data.services.services_config.CloudfrontSettings method) (drugforge.data.services.services_config.PosteraSettings method) (drugforge.data.services.services_config.S3Settings method) (drugforge.data.util.intenum.IntEnum method) (drugforge.data.util.logging.FileLogger method) (drugforge.data.util.logging.HiddenPrint method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.DockingDataset method) (drugforge.docking.analysis.DockingResults method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (drugforge.docking.schema.pose_generation.PosedLigands method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (drugforge.ml.data_augmentation.JitterFixed method) (drugforge.ml.dataset.DockedDataset method) (drugforge.ml.dataset.GraphDataset method) (drugforge.ml.dataset.GroupedDockedDataset method) (drugforge.ml.dataset.SplitDockedDataset method) (drugforge.ml.early_stopping.BestEarlyStopping method) (drugforge.ml.early_stopping.ConvergedEarlyStopping method) (drugforge.ml.early_stopping.GeneralizationLossEarlyStopping method) (drugforge.ml.early_stopping.PatientConvergedEarlyStopping method) (drugforge.ml.early_stopping.ProgressQuotientEarlyStopping method) (drugforge.ml.early_stopping.ThresholdEarlyStopping method) (drugforge.ml.loss.GaussianNLLLoss method) (drugforge.ml.loss.L1Loss method) (drugforge.ml.loss.MSELoss method) (drugforge.ml.loss.PoseCrossEntropyLoss method) (drugforge.ml.loss.RangeLoss method) (drugforge.ml.loss.SmoothL1Loss method) (drugforge.modeling.schema.PreppedComplex method) (drugforge.modeling.schema.PreppedTarget method) (drugforge.spectrum.blast.PDBEntry method) (drugforge.spectrum.blast.PDBRecord method) (drugforge.spectrum.seq_alignment.AAcid method) (drugforge.spectrum.seq_alignment.Alignment method) (drugforge.workflows.postera.manifold_artifacts.ArtifactType method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) (drugforge.workflows.postera.postera_uploader.PosteraUploader method)

A

AAcid (class in drugforge.spectrum.seq_alignment) active_site_chain() (in module drugforge.cli.cli_args) add_absolute_expt() (in module drugforge.alchemy.predict) add_command() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) add_identifiers_to_df() (in module drugforge.alchemy.predict) add_molecules() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) add_pic50_columns() (in module drugforge.alchemy.predict) add_relative_expt() (in module drugforge.alchemy.predict) add_seqres_to_openeye_protein() (in module drugforge.modeling.modeling) AlchemiscaleSettings (class in drugforge.alchemy.interfaces)

AlchemyDataSet (class in drugforge.alchemy.schema.prep_workflow) AlchemyPrepWorkflow (class in drugforge.alchemy.schema.prep_workflow) align_all_pdbs() (in module drugforge.data.services.rcsb.rcsb_download) Alignment (class in drugforge.spectrum.seq_alignment) allow_extra_args (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) allow_interspersed_args (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) append() (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) apply_bloom_abstraction() (in module drugforge.spectrum.fitness) ArtifactType (class in drugforge.workflows.postera.manifold_artifacts) as_integer_ratio() (drugforge.data.util.intenum.IntEnum method)

B

BespokeParameter (class in drugforge.data.schema.identifiers) BespokeParameters (class in drugforge.data.schema.identifiers) BestEarlyStopping (class in drugforge.ml.early_stopping) bit_count() (drugforge.data.util.intenum.IntEnum method) bit_length() (drugforge.data.util.intenum.IntEnum method)

blast_json() (in module drugforge.cli.cli_args) bloom_abstraction() (in module drugforge.spectrum.fitness) bsite_similarity() (in module drugforge.spectrum.blast) build_dimer_from_monomer() (in module drugforge.modeling.modeling) build_interaction_dict() (in module drugforge.dataviz.plip) bytes64_to_oedu() (in module drugforge.data.backend.openeye)

C

cache_dir() (in module drugforge.cli.cli_args) calc_mcs_residuals() (in module drugforge.alchemy.alchemize) calculate_rmsd_openeye() (in module drugforge.docking.analysis) calculate_tanimoto_oe() (in module drugforge.docking.analysis) callback (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) canonical_tautomer (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) capitalize() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) casefold() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) cast_uuids() (drugforge.data.schema.identifiers.LigandIdentifiers class method) cdd_to_schema() (in module drugforge.data.util.utils) cdd_to_schema_pair() (in module drugforge.data.util.utils) cdd_to_schema_v2() (in module drugforge.data.util.utils) CDDAPI (class in drugforge.data.services.cdd.cdd_api) CDDSettings (class in drugforge.data.services.services_config) center() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) ChargeProvenance (class in drugforge.data.schema.identifiers) check() (drugforge.ml.early_stopping.BestEarlyStopping method) (drugforge.ml.early_stopping.ConvergedEarlyStopping method) (drugforge.ml.early_stopping.GeneralizationLossEarlyStopping method) (drugforge.ml.early_stopping.PatientConvergedEarlyStopping method) (drugforge.ml.early_stopping.ProgressQuotientEarlyStopping method) (drugforge.ml.early_stopping.ThresholdEarlyStopping method) check_empty_dataframe() (in module drugforge.data.util.utils) check_filelist_has_elements() (in module drugforge.data.util.utils) check_name_length_and_truncate() (in module drugforge.data.util.utils) check_strings_for_equality_with_exclusion() (in module drugforge.data.schema.schema_base) ChemicalRelationship (class in drugforge.data.schema.ligand) choose_best_pdb_entry() (drugforge.spectrum.blast.PDBEntry class method) cinnabar_femap_get_largest_subnetwork() (in module drugforge.alchemy.cli.utils) cinnabar_femap_is_connected() (in module drugforge.alchemy.cli.utils) clean_result_network() (in module drugforge.alchemy.predict) clear() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) clear_SD_data() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (in module drugforge.data.backend.openeye) CloudFront (class in drugforge.data.services.aws.cloudfront) CloudfrontSettings (class in drugforge.data.services.services_config) collect_usage_pieces() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) colorbyrmsd() (in module drugforge.spectrum.calculate_rmsd) combine_files() (in module drugforge.data.util.utils) combine_protein_ligand() (in module drugforge.data.backend.openeye) command() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) command_class (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) commands (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) Complex (class in drugforge.data.schema.complex) ComplexBase (class in drugforge.data.schema.complex) CompoundMultiStructure (class in drugforge.data.schema.sets)

CompoundStructurePair (class in drugforge.data.schema.pairs) compute_clusters() (in module drugforge.alchemy.alchemize) compute_fint_score() (in module drugforge.dataviz.plip) conjugate() (drugforge.data.util.intenum.IntEnum method) construct_regex_function() (in module drugforge.data.util.utils) context_class (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) context_settings (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) ConvergedEarlyStopping (class in drugforge.ml.early_stopping) convert_chain_id() (in module drugforge.spectrum.calculate_rmsd) copy() (drugforge.alchemy.interfaces.AlchemiscaleSettings method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper method) (drugforge.alchemy.schema.base.DefaultModel method) (drugforge.alchemy.schema.charge.OpenFFCharges method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (drugforge.data.operators.deduplicator.LigandDeDuplicator method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory method) (drugforge.data.readers.molfile.MolFileFactory method) (drugforge.data.schema.complex.Complex method) (drugforge.data.schema.complex.ComplexBase method) (drugforge.data.schema.experimental.ExperimentalCompoundData method) (drugforge.data.schema.identifiers.BespokeParameter method) (drugforge.data.schema.identifiers.BespokeParameters method) (drugforge.data.schema.identifiers.ChargeProvenance method) (drugforge.data.schema.identifiers.LigandIdentifiers method) (drugforge.data.schema.identifiers.LigandProvenance method) (drugforge.data.schema.identifiers.TargetIdentifiers method) (drugforge.data.schema.legacy.CrystalCompoundData method) (drugforge.data.schema.legacy.EnantiomerPair method) (drugforge.data.schema.legacy.EnantiomerPairList method) (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (drugforge.data.schema.pairs.CompoundStructurePair method) (drugforge.data.schema.pairs.PairBase method) (drugforge.data.schema.schema_base.DataModelAbstractBase method) (drugforge.data.schema.schema_base.MoleculeFilter method) (drugforge.data.schema.sets.CompoundMultiStructure method) (drugforge.data.schema.sets.MultiStructureBase method) (drugforge.data.schema.target.Target method) (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) (drugforge.data.services.postera.postera_factory.PosteraFactory method) (drugforge.data.services.services_config.CDDSettings method) (drugforge.data.services.services_config.CloudfrontSettings method) (drugforge.data.services.services_config.PosteraSettings method) (drugforge.data.services.services_config.S3Settings method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (drugforge.docking.schema.pose_generation.PosedLigands method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (drugforge.modeling.schema.PreppedComplex method) (drugforge.modeling.schema.PreppedTarget method) (drugforge.spectrum.blast.PDBEntry method) (drugforge.spectrum.blast.PDBRecord method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) (drugforge.workflows.postera.postera_uploader.PosteraUploader method) core_smarts() (in module drugforge.cli.cli_args) count() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) create() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) create_absolute_report() (in module drugforge.alchemy.predict) create_alchemy_dataset() (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) create_relative_report() (in module drugforge.alchemy.predict) crystal_symmetry (drugforge.data.schema.target.Target property) CrystalCompoundData (class in drugforge.data.schema.legacy)

D

dask_args() (in module drugforge.cli.cli_args) dask_n_workers() (in module drugforge.cli.cli_args) dask_type() (in module drugforge.cli.cli_args) DataModelAbstractBase (class in drugforge.data.schema.schema_base) dataset_to_csv() (in module drugforge.ml.dataset) dataset_to_dataframe() (in module drugforge.ml.dataset) DataStorageType (class in drugforge.data.schema.schema_base) DefaultModel (class in drugforge.alchemy.schema.base) denominator (drugforge.data.util.intenum.IntEnum attribute) destroy() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) dG_to_pIC50() (in module drugforge.alchemy.predict) dg_to_postera_dataframe() (in module drugforge.alchemy.predict) do_MSA() (in module drugforge.spectrum.seq_alignment) DockedDataset (class in drugforge.ml.dataset) DockingDataset (class in drugforge.docking.analysis) DockingResultCols (class in drugforge.docking.docking_data_validation) DockingResults (class in drugforge.docking.analysis) download() (in module drugforge.data.services.fragalysis.fragalysis_download) download_cdd_data() (in module drugforge.alchemy.predict) download_file() (in module drugforge.data.util.utils) download_molecules() (in module drugforge.data.services.cdd.cdd_download) download_pdb_structure() (in module drugforge.data.services.rcsb.rcsb_download) download_PDBs() (in module drugforge.data.services.rcsb.rcsb_download) download_url() (in module drugforge.data.services.cdd.cdd_download) draw_mol() (in module drugforge.alchemy.predict) drop_non_output_columns() (in module drugforge.data.services.postera.manifold_data_validation) drugforge module drugforge.alchemy module drugforge.alchemy.alchemize module drugforge.alchemy.cli module drugforge.alchemy.cli.alchemy module drugforge.alchemy.cli.cli module drugforge.alchemy.cli.prep module drugforge.alchemy.cli.utils module drugforge.alchemy.interfaces module drugforge.alchemy.predict module drugforge.alchemy.schema module drugforge.alchemy.schema.atom_mapping module drugforge.alchemy.schema.base module drugforge.alchemy.schema.charge module drugforge.alchemy.schema.prep_workflow module drugforge.cli module drugforge.cli.cli_args module drugforge.data module drugforge.data.backend module drugforge.data.backend.openeye module drugforge.data.backend.rdkit module drugforge.data.metadata module drugforge.data.metadata.master_seqres module drugforge.data.metadata.master_seqres.fasta_to_seqres module drugforge.data.metadata.resources module drugforge.data.operators module drugforge.data.operators.deduplicator module drugforge.data.operators.state_expanders module drugforge.data.operators.state_expanders.expansion_tag module drugforge.data.operators.state_expanders.protomer_expander module drugforge.data.operators.state_expanders.state_expander module drugforge.data.operators.state_expanders.stereo_expander module drugforge.data.operators.state_expanders.tautomer_expander module drugforge.data.readers module drugforge.data.readers.meta_ligand_factory module drugforge.data.readers.molfile module drugforge.data.schema module drugforge.data.schema.complex module drugforge.data.schema.experimental module drugforge.data.schema.identifiers module drugforge.data.schema.legacy module drugforge.data.schema.ligand module drugforge.data.schema.pairs module drugforge.data.schema.schema_base module drugforge.data.schema.sets module drugforge.data.schema.target module drugforge.data.sequence module drugforge.data.services module

drugforge.data.services.aws module drugforge.data.services.aws.cloudfront module drugforge.data.services.aws.s3 module drugforge.data.services.cdd module drugforge.data.services.cdd.cdd_api module drugforge.data.services.cdd.cdd_download module drugforge.data.services.fragalysis module drugforge.data.services.fragalysis.fragalysis_download module drugforge.data.services.postera module drugforge.data.services.postera.manifold_data_validation module drugforge.data.services.postera.molecule_set module drugforge.data.services.postera.postera_api module drugforge.data.services.postera.postera_factory module drugforge.data.services.rcsb module drugforge.data.services.rcsb.rcsb_download module drugforge.data.services.services_config module drugforge.data.services.web_utils module drugforge.data.testing module drugforge.data.testing.test_resources module drugforge.data.util module drugforge.data.util.data_conversion module drugforge.data.util.execution_utils module drugforge.data.util.intenum module drugforge.data.util.logging module drugforge.data.util.stringenum module drugforge.data.util.utils module drugforge.dataviz module drugforge.dataviz.plip module drugforge.dataviz.resources module drugforge.dataviz.resources.fonts module drugforge.dataviz.show_contacts module drugforge.docking module drugforge.docking.analysis module drugforge.docking.docking_data_validation module drugforge.docking.schema module drugforge.docking.schema.pose_generation module drugforge.docking.selectors module drugforge.ml module drugforge.ml.data_augmentation module drugforge.ml.dataset module drugforge.ml.early_stopping module drugforge.ml.loss module drugforge.ml.pretrained_models module drugforge.ml.viz module drugforge.modeling module drugforge.modeling.modeling module drugforge.modeling.schema module drugforge.simulation module drugforge.spectrum module drugforge.spectrum.align_seq_match module drugforge.spectrum.blast module drugforge.spectrum.calculate_rmsd module drugforge.spectrum.fitness module drugforge.spectrum.seq_alignment module drugforge.workflows module drugforge.workflows.docking_workflows module drugforge.workflows.postera module drugforge.workflows.postera.manifold_artifacts module drugforge.workflows.postera.postera_uploader module drugforge.workflows.prep_workflows module du_to_complex() (in module drugforge.modeling.modeling)

E

email() (in module drugforge.cli.cli_args) EnantiomerPair (class in drugforge.data.schema.legacy) EnantiomerPairList (class in drugforge.data.schema.legacy) encode() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) endswith() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

EpikExpander (class in drugforge.data.operators.state_expanders.protomer_expander) estimate_n_workers() (in module drugforge.data.util.execution_utils) exists() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) expandtabs() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) ExperimentalCompoundData (class in drugforge.data.schema.experimental) extend() (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) extract_compounds_from_filenames() (in module drugforge.data.util.utils) extract_experimental_data() (in module drugforge.alchemy.predict) extract_zip() (in module drugforge.data.services.fragalysis.fragalysis_download)

F

failure_mode() (in module drugforge.cli.cli_args) fasta_align_data() (drugforge.spectrum.seq_alignment.Alignment static method) fasta_alignment() (in module drugforge.spectrum.align_seq_match) fetch_test_file() (in module drugforge.data.testing.test_resources) FileLogger (class in drugforge.data.util.logging) filter_molecules_dataframe() (in module drugforge.data.util.utils) find() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) find_bsite_resids() (in module drugforge.spectrum.calculate_rmsd) find_component_chains() (in module drugforge.modeling.modeling) fixed_inchi (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) fixed_inchikey (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) flattened (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) format() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) format_commands() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) format_epilog() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) format_help() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) format_help_text() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) format_map() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

format_options() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) format_usage() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) forward() (drugforge.ml.loss.GaussianNLLLoss method) (drugforge.ml.loss.L1Loss method) (drugforge.ml.loss.MSELoss method) (drugforge.ml.loss.PoseCrossEntropyLoss method) (drugforge.ml.loss.RangeLoss method) (drugforge.ml.loss.SmoothL1Loss method) fragalysis_dir() (in module drugforge.cli.cli_args) FragalysisTargets (class in drugforge.data.services.fragalysis.fragalysis_download) from_bytes() (drugforge.data.util.intenum.IntEnum class method) from_complex() (drugforge.modeling.schema.PreppedComplex class method) from_complexes() (drugforge.ml.dataset.DockedDataset class method) (drugforge.ml.dataset.GroupedDockedDataset class method) (drugforge.ml.dataset.SplitDockedDataset class method) from_exp_compounds() (drugforge.ml.dataset.GraphDataset class method) from_file() (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper class method) (drugforge.alchemy.schema.charge.OpenFFCharges class method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet class method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) from_files() (drugforge.ml.dataset.DockedDataset class method) (drugforge.ml.dataset.GroupedDockedDataset class method) (drugforge.ml.dataset.SplitDockedDataset class method) from_inchi() (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) from_iterable() (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags class method) (drugforge.data.services.postera.manifold_data_validation.OutputTags class method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase class method) (drugforge.data.services.postera.manifold_data_validation.TargetTags class method) (drugforge.data.services.postera.manifold_data_validation.VirusTags class method) from_ligands() (drugforge.ml.dataset.GraphDataset class method) from_mol2() (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) from_oemol() (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) from_openfe() (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) from_sdf() (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) from_sdf_str() (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) from_settings() (drugforge.data.services.aws.cloudfront.CloudFront class method) (drugforge.data.services.aws.s3.S3 class method) (drugforge.data.services.postera.molecule_set.MoleculeSetAPI class method) from_single_conformers() (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) from_smiles() (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) fromkeys() (drugforge.data.services.postera.molecule_set.Molecule class method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate class method)

G

GaussianNLLLoss (class in drugforge.ml.loss) gen_cache_w_default() (in module drugforge.cli.cli_args) gen_ref_pdb() (in module drugforge.cli.cli_args) GeneralizationLossEarlyStopping (class in drugforge.ml.early_stopping) generate_cloudfront_url() (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) generate_poses() (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) generate_signed_url() (drugforge.data.services.aws.cloudfront.CloudFront method) get() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method) get_args() (in module drugforge.data.metadata.master_seqres.fasta_to_seqres) get_async_export() (drugforge.data.services.cdd.cdd_api.CDDAPI method) get_best_structure_per_compound() (drugforge.docking.analysis.DockingResults method) get_binding_site_rmsd() (in module drugforge.spectrum.calculate_rmsd) get_blast_seqs() (in module drugforge.spectrum.blast) get_bsite() (in module drugforge.spectrum.blast) get_cdd_molecules() (in module drugforge.alchemy.cli.utils) get_chemical_relationship() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) get_colors_by_aa_group() (in module drugforge.spectrum.seq_alignment) get_colors_multi() (in module drugforge.spectrum.align_seq_match) get_colors_pairwise() (in module drugforge.spectrum.align_seq_match) get_colors_protein() (in module drugforge.spectrum.seq_alignment) get_command() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) get_cpus() (in module drugforge.alchemy.cli.utils) get_data_from_femap() (in module drugforge.alchemy.predict) get_dict_of_lists_from_dict_of_str() (in module drugforge.data.util.data_conversion) get_dict_of_lists_from_list_of_dicts() (in module drugforge.data.util.data_conversion) get_first_value_of_dict_of_lists() (in module drugforge.data.util.data_conversion) get_fitness_scores_bloom_by_target() (in module drugforge.spectrum.fitness) get_good_score() (in module drugforge.docking.analysis) get_grouped_df() (drugforge.docking.analysis.DockingResults method) get_help() (drugforge.alchemy.cli.utils.SpecialHelpOrder method)

get_help_option() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) get_help_option_names() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) get_ic50_data() (drugforge.data.services.cdd.cdd_api.CDDAPI method) get_id_from_name() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) get_idx_by_seq() (in module drugforge.spectrum.align_seq_match) get_interaction_color() (in module drugforge.dataviz.plip) get_interaction_fitness_color() (in module drugforge.dataviz.plip) get_interactions_plip() (in module drugforge.dataviz.plip) get_magnitude() (in module drugforge.alchemy.predict) get_molecules() (drugforge.data.services.cdd.cdd_api.CDDAPI method) (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) get_molecules_from_id_or_name() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) get_name_from_id() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) get_network_interfaces_with_dual_ip() (in module drugforge.data.util.execution_utils) get_oe_prep_opts() (in module drugforge.modeling.modeling) get_oe_structure_metadata_from_sequence() (in module drugforge.modeling.modeling) get_path_string() (in module drugforge.data.util.utils) get_platform() (in module drugforge.data.util.execution_utils) get_protocols() (drugforge.data.services.cdd.cdd_api.CDDAPI method) get_readout_rows() (drugforge.data.services.cdd.cdd_api.CDDAPI method) get_residue_mapping() (in module drugforge.spectrum.calculate_rmsd) get_SD_data() (in module drugforge.data.backend.openeye) (in module drugforge.data.backend.rdkit) get_sdf_fn_from_dataset() (in module drugforge.data.util.utils) get_short_help_str() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) get_single_conf_SD_data() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) get_structure_df() (drugforge.docking.analysis.DockingResults method) get_top_n_poses() (in module drugforge.alchemy.predict) get_usage() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) GraphDataset (class in drugforge.ml.dataset) group() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) group_class (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) GroupedDockedDataset (class in drugforge.ml.dataset) guess_network_interface() (in module drugforge.data.util.execution_utils)

H

has_defined_stereo (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) has_multiple_poses (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) has_perceived_stereo (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property)

has_same_charge() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) has_warhead() (in module drugforge.alchemy.cli.utils) hash (drugforge.data.schema.target.Target property) (drugforge.modeling.schema.PreppedTarget property) HiddenPrint (class in drugforge.data.util.logging) hyperthreading_is_enabled() (in module drugforge.data.util.execution_utils)

I

id_data_is_uuid_castable() (drugforge.workflows.postera.postera_uploader.PosteraUploader static method) ignore_unknown_options (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) imag (drugforge.data.util.intenum.IntEnum attribute) inchi (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) inchikey (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) index() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) initialize() (drugforge.data.services.aws.s3.S3 method) input_json() (in module drugforge.cli.cli_args) insert() (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) IntEnum (class in drugforge.data.util.intenum) InvalidLigandError InvalidTargetError invoke() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) is_backbone_residue() (in module drugforge.dataviz.plip) is_chemically_equal() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) is_protonation_state_isomer() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) is_stereoisomer() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) is_tautomer() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) is_valid_smiles() (in module drugforge.data.util.utils) isalnum() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) isalpha() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) isascii() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) isdecimal() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) isdigit() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

isidentifier() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) islower() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) isnumeric() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) isprintable() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) isspace() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) istitle() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) isupper() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) items() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method)

J

JitterFixed (class in drugforge.ml.data_augmentation) join() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

join_with_manifold_data() (drugforge.workflows.postera.postera_uploader.PosteraUploader static method)

K

KartografAtomMapper (class in drugforge.alchemy.schema.atom_mapping) keys() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method)

ki_to_dg() (in module drugforge.alchemy.predict)

L

L1Loss (class in drugforge.ml.loss) Ligand (class in drugforge.data.schema.ligand) LigandDeDuplicator (class in drugforge.data.operators.deduplicator) LigandIdentifiers (class in drugforge.data.schema.identifiers) LigandProvenance (class in drugforge.data.schema.identifiers) ligands() (in module drugforge.cli.cli_args) list_available() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) list_commands() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) list_commands_for_help() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) ljust() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) load_dataframes() (in module drugforge.docking.analysis) load_openeye_cif() (in module drugforge.data.backend.openeye) load_openeye_cif1() (in module drugforge.data.backend.openeye) load_openeye_design_unit() (in module drugforge.data.backend.openeye) load_openeye_mol2() (in module drugforge.data.backend.openeye) load_openeye_pdb() (in module drugforge.data.backend.openeye) load_openeye_sdf() (in module drugforge.data.backend.openeye) load_openeye_sdfs() (in module drugforge.data.backend.openeye) load_openeye_smi() (in module drugforge.data.backend.openeye)

load_sdf() (in module drugforge.data.backend.rdkit) load_yaml() (in module drugforge.data.services.postera.manifold_data_validation) loglevel() (in module drugforge.cli.cli_args) LomapAtomMapper (class in drugforge.alchemy.schema.atom_mapping) lower() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) lstrip() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

M

main() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) (in module drugforge.data.metadata.master_seqres.fasta_to_seqres) make_color_res_fitness() (in module drugforge.dataviz.plip) make_color_res_subpockets() (in module drugforge.dataviz.plip) make_context() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) make_design_unit() (in module drugforge.modeling.modeling) make_du_from_new_lig() (in module drugforge.modeling.modeling) make_manifold_tag_name_from_components() (in module drugforge.data.services.postera.manifold_data_validation) make_output_tags() (in module drugforge.data.services.postera.manifold_data_validation) make_parser() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) make_static_tags() (in module drugforge.data.services.postera.manifold_data_validation) make_tag_combinations_and_combine_with_static() (in module drugforge.data.services.postera.manifold_data_validation) make_target_tags() (in module drugforge.data.services.postera.manifold_data_validation) make_test_file_pooch_repo() (in module drugforge.data.testing.test_resources) make_virus_tags() (in module drugforge.data.services.postera.manifold_data_validation) maketrans() (drugforge.data.schema.schema_base.DataStorageType static method) (drugforge.data.schema.schema_base.MoleculeComponent static method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets static method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags static method) (drugforge.data.services.postera.manifold_data_validation.OutputTags static method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase static method) (drugforge.data.services.postera.manifold_data_validation.TargetTags static method) (drugforge.data.services.postera.manifold_data_validation.VirusTags static method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys static method) (drugforge.data.util.stringenum.StringEnum static method) (drugforge.docking.analysis.TanimotoType static method) (drugforge.docking.docking_data_validation.DockingResultCols static method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod static method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod static method) ManifoldAllowedTags (class in drugforge.data.services.postera.manifold_data_validation) ManifoldArtifactUploader (class in drugforge.workflows.postera.manifold_artifacts) map_output_col_to_manifold_tag() (in module drugforge.data.services.postera.manifold_data_validation) max_mismatches() (in module drugforge.cli.cli_args) md() (in module drugforge.cli.cli_args) md_args() (in module drugforge.cli.cli_args) md_openmm_platform() (in module drugforge.cli.cli_args) md_steps() (in module drugforge.cli.cli_args) MetaLigandFactory (class in drugforge.data.readers.meta_ligand_factory) ml_score() (in module drugforge.cli.cli_args) ml_scorers() (in module drugforge.cli.cli_args) model_config (drugforge.alchemy.interfaces.AlchemiscaleSettings attribute) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper attribute) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper attribute) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper attribute) (drugforge.alchemy.schema.base.DefaultModel attribute) (drugforge.alchemy.schema.charge.OpenFFCharges attribute) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet attribute) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow attribute) (drugforge.data.operators.deduplicator.LigandDeDuplicator attribute) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag attribute) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander attribute) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander attribute) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase attribute) (drugforge.data.operators.state_expanders.state_expander.StateExpansion attribute) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet attribute) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander attribute) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander attribute) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory attribute) (drugforge.data.readers.molfile.MolFileFactory attribute) (drugforge.data.schema.complex.Complex attribute) (drugforge.data.schema.complex.ComplexBase attribute) (drugforge.data.schema.experimental.ExperimentalCompoundData attribute) (drugforge.data.schema.identifiers.BespokeParameter attribute) (drugforge.data.schema.identifiers.BespokeParameters attribute) (drugforge.data.schema.identifiers.ChargeProvenance attribute) (drugforge.data.schema.identifiers.LigandIdentifiers attribute) (drugforge.data.schema.identifiers.LigandProvenance attribute) (drugforge.data.schema.identifiers.TargetIdentifiers attribute) (drugforge.data.schema.legacy.CrystalCompoundData attribute) (drugforge.data.schema.legacy.EnantiomerPair attribute) (drugforge.data.schema.legacy.EnantiomerPairList attribute) (drugforge.data.schema.ligand.Ligand attribute) (drugforge.data.schema.ligand.ReferenceLigand attribute) (drugforge.data.schema.pairs.CompoundStructurePair attribute) (drugforge.data.schema.pairs.PairBase attribute) (drugforge.data.schema.schema_base.DataModelAbstractBase attribute) (drugforge.data.schema.schema_base.MoleculeFilter attribute) (drugforge.data.schema.sets.CompoundMultiStructure attribute) (drugforge.data.schema.sets.MultiStructureBase attribute) (drugforge.data.schema.target.Target attribute) (drugforge.data.services.postera.postera_factory.PosteraFactory attribute) (drugforge.data.services.services_config.CDDSettings attribute) (drugforge.data.services.services_config.CloudfrontSettings attribute) (drugforge.data.services.services_config.PosteraSettings attribute) (drugforge.data.services.services_config.S3Settings attribute) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator attribute) (drugforge.docking.schema.pose_generation.PosedLigands attribute) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator attribute) (drugforge.modeling.schema.PreppedComplex attribute) (drugforge.modeling.schema.PreppedTarget attribute) (drugforge.spectrum.blast.PDBEntry attribute) (drugforge.spectrum.blast.PDBRecord attribute) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader attribute) (drugforge.workflows.postera.postera_uploader.PosteraUploader attribute) model_construct() (drugforge.alchemy.interfaces.AlchemiscaleSettings class method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper class method) (drugforge.alchemy.schema.base.DefaultModel class method) (drugforge.alchemy.schema.charge.OpenFFCharges class method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet class method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (drugforge.data.operators.deduplicator.LigandDeDuplicator class method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander class method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet class method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander class method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory class method) (drugforge.data.readers.molfile.MolFileFactory class method) (drugforge.data.schema.complex.Complex class method) (drugforge.data.schema.complex.ComplexBase class method) (drugforge.data.schema.experimental.ExperimentalCompoundData class method) (drugforge.data.schema.identifiers.BespokeParameter class method) (drugforge.data.schema.identifiers.BespokeParameters class method) (drugforge.data.schema.identifiers.ChargeProvenance class method) (drugforge.data.schema.identifiers.LigandIdentifiers class method) (drugforge.data.schema.identifiers.LigandProvenance class method) (drugforge.data.schema.identifiers.TargetIdentifiers class method) (drugforge.data.schema.legacy.CrystalCompoundData class method) (drugforge.data.schema.legacy.EnantiomerPair class method) (drugforge.data.schema.legacy.EnantiomerPairList class method) (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) (drugforge.data.schema.pairs.CompoundStructurePair class method) (drugforge.data.schema.pairs.PairBase class method) (drugforge.data.schema.schema_base.DataModelAbstractBase class method) (drugforge.data.schema.schema_base.MoleculeFilter class method) (drugforge.data.schema.sets.CompoundMultiStructure class method) (drugforge.data.schema.sets.MultiStructureBase class method) (drugforge.data.schema.target.Target class method) (drugforge.data.services.postera.postera_factory.PosteraFactory class method) (drugforge.data.services.services_config.CDDSettings class method) (drugforge.data.services.services_config.CloudfrontSettings class method) (drugforge.data.services.services_config.PosteraSettings class method) (drugforge.data.services.services_config.S3Settings class method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (drugforge.docking.schema.pose_generation.PosedLigands class method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (drugforge.modeling.schema.PreppedComplex class method) (drugforge.modeling.schema.PreppedTarget class method) (drugforge.spectrum.blast.PDBEntry class method) (drugforge.spectrum.blast.PDBRecord class method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader class method) (drugforge.workflows.postera.postera_uploader.PosteraUploader class method) model_copy() (drugforge.alchemy.interfaces.AlchemiscaleSettings method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper method) (drugforge.alchemy.schema.base.DefaultModel method) (drugforge.alchemy.schema.charge.OpenFFCharges method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (drugforge.data.operators.deduplicator.LigandDeDuplicator method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory method) (drugforge.data.readers.molfile.MolFileFactory method) (drugforge.data.schema.complex.Complex method) (drugforge.data.schema.complex.ComplexBase method) (drugforge.data.schema.experimental.ExperimentalCompoundData method) (drugforge.data.schema.identifiers.BespokeParameter method) (drugforge.data.schema.identifiers.BespokeParameters method) (drugforge.data.schema.identifiers.ChargeProvenance method) (drugforge.data.schema.identifiers.LigandIdentifiers method) (drugforge.data.schema.identifiers.LigandProvenance method) (drugforge.data.schema.identifiers.TargetIdentifiers method) (drugforge.data.schema.legacy.CrystalCompoundData method) (drugforge.data.schema.legacy.EnantiomerPair method) (drugforge.data.schema.legacy.EnantiomerPairList method) (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (drugforge.data.schema.pairs.CompoundStructurePair method) (drugforge.data.schema.pairs.PairBase method) (drugforge.data.schema.schema_base.DataModelAbstractBase method) (drugforge.data.schema.schema_base.MoleculeFilter method) (drugforge.data.schema.sets.CompoundMultiStructure method) (drugforge.data.schema.sets.MultiStructureBase method) (drugforge.data.schema.target.Target method) (drugforge.data.services.postera.postera_factory.PosteraFactory method) (drugforge.data.services.services_config.CDDSettings method) (drugforge.data.services.services_config.CloudfrontSettings method) (drugforge.data.services.services_config.PosteraSettings method) (drugforge.data.services.services_config.S3Settings method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (drugforge.docking.schema.pose_generation.PosedLigands method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (drugforge.modeling.schema.PreppedComplex method) (drugforge.modeling.schema.PreppedTarget method) (drugforge.spectrum.blast.PDBEntry method) (drugforge.spectrum.blast.PDBRecord method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) (drugforge.workflows.postera.postera_uploader.PosteraUploader method) model_dump() (drugforge.alchemy.interfaces.AlchemiscaleSettings method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper method) (drugforge.alchemy.schema.base.DefaultModel method) (drugforge.alchemy.schema.charge.OpenFFCharges method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (drugforge.data.operators.deduplicator.LigandDeDuplicator method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory method) (drugforge.data.readers.molfile.MolFileFactory method) (drugforge.data.schema.complex.Complex method) (drugforge.data.schema.complex.ComplexBase method) (drugforge.data.schema.experimental.ExperimentalCompoundData method) (drugforge.data.schema.identifiers.BespokeParameter method) (drugforge.data.schema.identifiers.BespokeParameters method) (drugforge.data.schema.identifiers.ChargeProvenance method) (drugforge.data.schema.identifiers.LigandIdentifiers method) (drugforge.data.schema.identifiers.LigandProvenance method) (drugforge.data.schema.identifiers.TargetIdentifiers method) (drugforge.data.schema.legacy.CrystalCompoundData method) (drugforge.data.schema.legacy.EnantiomerPair method) (drugforge.data.schema.legacy.EnantiomerPairList method) (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (drugforge.data.schema.pairs.CompoundStructurePair method) (drugforge.data.schema.pairs.PairBase method) (drugforge.data.schema.schema_base.DataModelAbstractBase method) (drugforge.data.schema.schema_base.MoleculeFilter method) (drugforge.data.schema.sets.CompoundMultiStructure method) (drugforge.data.schema.sets.MultiStructureBase method) (drugforge.data.schema.target.Target method) (drugforge.data.services.postera.postera_factory.PosteraFactory method) (drugforge.data.services.services_config.CDDSettings method) (drugforge.data.services.services_config.CloudfrontSettings method) (drugforge.data.services.services_config.PosteraSettings method) (drugforge.data.services.services_config.S3Settings method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (drugforge.docking.schema.pose_generation.PosedLigands method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (drugforge.modeling.schema.PreppedComplex method) (drugforge.modeling.schema.PreppedTarget method) (drugforge.spectrum.blast.PDBEntry method) (drugforge.spectrum.blast.PDBRecord method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) (drugforge.workflows.postera.postera_uploader.PosteraUploader method) model_dump_json() (drugforge.alchemy.interfaces.AlchemiscaleSettings method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper method) (drugforge.alchemy.schema.base.DefaultModel method) (drugforge.alchemy.schema.charge.OpenFFCharges method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (drugforge.data.operators.deduplicator.LigandDeDuplicator method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory method) (drugforge.data.readers.molfile.MolFileFactory method) (drugforge.data.schema.complex.Complex method) (drugforge.data.schema.complex.ComplexBase method) (drugforge.data.schema.experimental.ExperimentalCompoundData method) (drugforge.data.schema.identifiers.BespokeParameter method) (drugforge.data.schema.identifiers.BespokeParameters method) (drugforge.data.schema.identifiers.ChargeProvenance method) (drugforge.data.schema.identifiers.LigandIdentifiers method) (drugforge.data.schema.identifiers.LigandProvenance method) (drugforge.data.schema.identifiers.TargetIdentifiers method) (drugforge.data.schema.legacy.CrystalCompoundData method) (drugforge.data.schema.legacy.EnantiomerPair method) (drugforge.data.schema.legacy.EnantiomerPairList method) (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (drugforge.data.schema.pairs.CompoundStructurePair method) (drugforge.data.schema.pairs.PairBase method) (drugforge.data.schema.schema_base.DataModelAbstractBase method) (drugforge.data.schema.schema_base.MoleculeFilter method) (drugforge.data.schema.sets.CompoundMultiStructure method) (drugforge.data.schema.sets.MultiStructureBase method) (drugforge.data.schema.target.Target method) (drugforge.data.services.postera.postera_factory.PosteraFactory method) (drugforge.data.services.services_config.CDDSettings method) (drugforge.data.services.services_config.CloudfrontSettings method) (drugforge.data.services.services_config.PosteraSettings method) (drugforge.data.services.services_config.S3Settings method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (drugforge.docking.schema.pose_generation.PosedLigands method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (drugforge.modeling.schema.PreppedComplex method) (drugforge.modeling.schema.PreppedTarget method) (drugforge.spectrum.blast.PDBEntry method) (drugforge.spectrum.blast.PDBRecord method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) (drugforge.workflows.postera.postera_uploader.PosteraUploader method) model_extra (drugforge.alchemy.interfaces.AlchemiscaleSettings property) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper property) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper property) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper property) (drugforge.alchemy.schema.base.DefaultModel property) (drugforge.alchemy.schema.charge.OpenFFCharges property) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet property) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow property) (drugforge.data.operators.deduplicator.LigandDeDuplicator property) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag property) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander property) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander property) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase property) (drugforge.data.operators.state_expanders.state_expander.StateExpansion property) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet property) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander property) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander property) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory property) (drugforge.data.readers.molfile.MolFileFactory property) (drugforge.data.schema.complex.Complex property) (drugforge.data.schema.complex.ComplexBase property) (drugforge.data.schema.experimental.ExperimentalCompoundData property) (drugforge.data.schema.identifiers.BespokeParameter property) (drugforge.data.schema.identifiers.BespokeParameters property) (drugforge.data.schema.identifiers.ChargeProvenance property) (drugforge.data.schema.identifiers.LigandIdentifiers property) (drugforge.data.schema.identifiers.LigandProvenance property) (drugforge.data.schema.identifiers.TargetIdentifiers property) (drugforge.data.schema.legacy.CrystalCompoundData property) (drugforge.data.schema.legacy.EnantiomerPair property) (drugforge.data.schema.legacy.EnantiomerPairList property) (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) (drugforge.data.schema.pairs.CompoundStructurePair property) (drugforge.data.schema.pairs.PairBase property) (drugforge.data.schema.schema_base.DataModelAbstractBase property) (drugforge.data.schema.schema_base.MoleculeFilter property) (drugforge.data.schema.sets.CompoundMultiStructure property) (drugforge.data.schema.sets.MultiStructureBase property) (drugforge.data.schema.target.Target property) (drugforge.data.services.postera.postera_factory.PosteraFactory property) (drugforge.data.services.services_config.CDDSettings property) (drugforge.data.services.services_config.CloudfrontSettings property) (drugforge.data.services.services_config.PosteraSettings property) (drugforge.data.services.services_config.S3Settings property) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator property) (drugforge.docking.schema.pose_generation.PosedLigands property) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator property) (drugforge.modeling.schema.PreppedComplex property) (drugforge.modeling.schema.PreppedTarget property) (drugforge.spectrum.blast.PDBEntry property) (drugforge.spectrum.blast.PDBRecord property) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader property) (drugforge.workflows.postera.postera_uploader.PosteraUploader property) model_fields_set (drugforge.alchemy.interfaces.AlchemiscaleSettings property) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper property) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper property) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper property) (drugforge.alchemy.schema.base.DefaultModel property) (drugforge.alchemy.schema.charge.OpenFFCharges property) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet property) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow property) (drugforge.data.operators.deduplicator.LigandDeDuplicator property) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag property) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander property) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander property) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase property) (drugforge.data.operators.state_expanders.state_expander.StateExpansion property) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet property) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander property) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander property) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory property) (drugforge.data.readers.molfile.MolFileFactory property) (drugforge.data.schema.complex.Complex property) (drugforge.data.schema.complex.ComplexBase property) (drugforge.data.schema.experimental.ExperimentalCompoundData property) (drugforge.data.schema.identifiers.BespokeParameter property) (drugforge.data.schema.identifiers.BespokeParameters property) (drugforge.data.schema.identifiers.ChargeProvenance property) (drugforge.data.schema.identifiers.LigandIdentifiers property) (drugforge.data.schema.identifiers.LigandProvenance property) (drugforge.data.schema.identifiers.TargetIdentifiers property) (drugforge.data.schema.legacy.CrystalCompoundData property) (drugforge.data.schema.legacy.EnantiomerPair property) (drugforge.data.schema.legacy.EnantiomerPairList property) (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) (drugforge.data.schema.pairs.CompoundStructurePair property) (drugforge.data.schema.pairs.PairBase property) (drugforge.data.schema.schema_base.DataModelAbstractBase property) (drugforge.data.schema.schema_base.MoleculeFilter property) (drugforge.data.schema.sets.CompoundMultiStructure property) (drugforge.data.schema.sets.MultiStructureBase property) (drugforge.data.schema.target.Target property) (drugforge.data.services.postera.postera_factory.PosteraFactory property) (drugforge.data.services.services_config.CDDSettings property) (drugforge.data.services.services_config.CloudfrontSettings property) (drugforge.data.services.services_config.PosteraSettings property) (drugforge.data.services.services_config.S3Settings property) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator property) (drugforge.docking.schema.pose_generation.PosedLigands property) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator property) (drugforge.modeling.schema.PreppedComplex property) (drugforge.modeling.schema.PreppedTarget property) (drugforge.spectrum.blast.PDBEntry property) (drugforge.spectrum.blast.PDBRecord property) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader property) (drugforge.workflows.postera.postera_uploader.PosteraUploader property) model_json_schema() (drugforge.alchemy.interfaces.AlchemiscaleSettings class method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper class method) (drugforge.alchemy.schema.base.DefaultModel class method) (drugforge.alchemy.schema.charge.OpenFFCharges class method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet class method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (drugforge.data.operators.deduplicator.LigandDeDuplicator class method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander class method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet class method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander class method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory class method) (drugforge.data.readers.molfile.MolFileFactory class method) (drugforge.data.schema.complex.Complex class method) (drugforge.data.schema.complex.ComplexBase class method) (drugforge.data.schema.experimental.ExperimentalCompoundData class method) (drugforge.data.schema.identifiers.BespokeParameter class method) (drugforge.data.schema.identifiers.BespokeParameters class method) (drugforge.data.schema.identifiers.ChargeProvenance class method) (drugforge.data.schema.identifiers.LigandIdentifiers class method) (drugforge.data.schema.identifiers.LigandProvenance class method) (drugforge.data.schema.identifiers.TargetIdentifiers class method) (drugforge.data.schema.legacy.CrystalCompoundData class method) (drugforge.data.schema.legacy.EnantiomerPair class method) (drugforge.data.schema.legacy.EnantiomerPairList class method) (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) (drugforge.data.schema.pairs.CompoundStructurePair class method) (drugforge.data.schema.pairs.PairBase class method) (drugforge.data.schema.schema_base.DataModelAbstractBase class method) (drugforge.data.schema.schema_base.MoleculeFilter class method) (drugforge.data.schema.sets.CompoundMultiStructure class method) (drugforge.data.schema.sets.MultiStructureBase class method) (drugforge.data.schema.target.Target class method) (drugforge.data.services.postera.postera_factory.PosteraFactory class method) (drugforge.data.services.services_config.CDDSettings class method) (drugforge.data.services.services_config.CloudfrontSettings class method) (drugforge.data.services.services_config.PosteraSettings class method) (drugforge.data.services.services_config.S3Settings class method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (drugforge.docking.schema.pose_generation.PosedLigands class method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (drugforge.modeling.schema.PreppedComplex class method) (drugforge.modeling.schema.PreppedTarget class method) (drugforge.spectrum.blast.PDBEntry class method) (drugforge.spectrum.blast.PDBRecord class method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader class method) (drugforge.workflows.postera.postera_uploader.PosteraUploader class method)

model_parametrized_name() (drugforge.alchemy.interfaces.AlchemiscaleSettings class method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper class method) (drugforge.alchemy.schema.base.DefaultModel class method) (drugforge.alchemy.schema.charge.OpenFFCharges class method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet class method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (drugforge.data.operators.deduplicator.LigandDeDuplicator class method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander class method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet class method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander class method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory class method) (drugforge.data.readers.molfile.MolFileFactory class method) (drugforge.data.schema.complex.Complex class method) (drugforge.data.schema.complex.ComplexBase class method) (drugforge.data.schema.experimental.ExperimentalCompoundData class method) (drugforge.data.schema.identifiers.BespokeParameter class method) (drugforge.data.schema.identifiers.BespokeParameters class method) (drugforge.data.schema.identifiers.ChargeProvenance class method) (drugforge.data.schema.identifiers.LigandIdentifiers class method) (drugforge.data.schema.identifiers.LigandProvenance class method) (drugforge.data.schema.identifiers.TargetIdentifiers class method) (drugforge.data.schema.legacy.CrystalCompoundData class method) (drugforge.data.schema.legacy.EnantiomerPair class method) (drugforge.data.schema.legacy.EnantiomerPairList class method) (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) (drugforge.data.schema.pairs.CompoundStructurePair class method) (drugforge.data.schema.pairs.PairBase class method) (drugforge.data.schema.schema_base.DataModelAbstractBase class method) (drugforge.data.schema.schema_base.MoleculeFilter class method) (drugforge.data.schema.sets.CompoundMultiStructure class method) (drugforge.data.schema.sets.MultiStructureBase class method) (drugforge.data.schema.target.Target class method) (drugforge.data.services.postera.postera_factory.PosteraFactory class method) (drugforge.data.services.services_config.CDDSettings class method) (drugforge.data.services.services_config.CloudfrontSettings class method) (drugforge.data.services.services_config.PosteraSettings class method) (drugforge.data.services.services_config.S3Settings class method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (drugforge.docking.schema.pose_generation.PosedLigands class method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (drugforge.modeling.schema.PreppedComplex class method) (drugforge.modeling.schema.PreppedTarget class method) (drugforge.spectrum.blast.PDBEntry class method) (drugforge.spectrum.blast.PDBRecord class method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader class method) (drugforge.workflows.postera.postera_uploader.PosteraUploader class method) model_post_init() (drugforge.alchemy.interfaces.AlchemiscaleSettings method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper method) (drugforge.alchemy.schema.base.DefaultModel method) (drugforge.alchemy.schema.charge.OpenFFCharges method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) (drugforge.data.operators.deduplicator.LigandDeDuplicator method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory method) (drugforge.data.readers.molfile.MolFileFactory method) (drugforge.data.schema.complex.Complex method) (drugforge.data.schema.complex.ComplexBase method) (drugforge.data.schema.experimental.ExperimentalCompoundData method) (drugforge.data.schema.identifiers.BespokeParameter method) (drugforge.data.schema.identifiers.BespokeParameters method) (drugforge.data.schema.identifiers.ChargeProvenance method) (drugforge.data.schema.identifiers.LigandIdentifiers method) (drugforge.data.schema.identifiers.LigandProvenance method) (drugforge.data.schema.identifiers.TargetIdentifiers method) (drugforge.data.schema.legacy.CrystalCompoundData method) (drugforge.data.schema.legacy.EnantiomerPair method) (drugforge.data.schema.legacy.EnantiomerPairList method) (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (drugforge.data.schema.pairs.CompoundStructurePair method) (drugforge.data.schema.pairs.PairBase method) (drugforge.data.schema.schema_base.DataModelAbstractBase method) (drugforge.data.schema.schema_base.MoleculeFilter method) (drugforge.data.schema.sets.CompoundMultiStructure method) (drugforge.data.schema.sets.MultiStructureBase method) (drugforge.data.schema.target.Target method) (drugforge.data.services.postera.postera_factory.PosteraFactory method) (drugforge.data.services.services_config.CDDSettings method) (drugforge.data.services.services_config.CloudfrontSettings method) (drugforge.data.services.services_config.PosteraSettings method) (drugforge.data.services.services_config.S3Settings method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (drugforge.docking.schema.pose_generation.PosedLigands method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) (drugforge.modeling.schema.PreppedComplex method) (drugforge.modeling.schema.PreppedTarget method) (drugforge.spectrum.blast.PDBEntry method) (drugforge.spectrum.blast.PDBRecord method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) (drugforge.workflows.postera.postera_uploader.PosteraUploader method) model_rebuild() (drugforge.alchemy.interfaces.AlchemiscaleSettings class method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper class method) (drugforge.alchemy.schema.base.DefaultModel class method) (drugforge.alchemy.schema.charge.OpenFFCharges class method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet class method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (drugforge.data.operators.deduplicator.LigandDeDuplicator class method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander class method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet class method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander class method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory class method) (drugforge.data.readers.molfile.MolFileFactory class method) (drugforge.data.schema.complex.Complex class method) (drugforge.data.schema.complex.ComplexBase class method) (drugforge.data.schema.experimental.ExperimentalCompoundData class method) (drugforge.data.schema.identifiers.BespokeParameter class method) (drugforge.data.schema.identifiers.BespokeParameters class method) (drugforge.data.schema.identifiers.ChargeProvenance class method) (drugforge.data.schema.identifiers.LigandIdentifiers class method) (drugforge.data.schema.identifiers.LigandProvenance class method) (drugforge.data.schema.identifiers.TargetIdentifiers class method) (drugforge.data.schema.legacy.CrystalCompoundData class method) (drugforge.data.schema.legacy.EnantiomerPair class method) (drugforge.data.schema.legacy.EnantiomerPairList class method) (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) (drugforge.data.schema.pairs.CompoundStructurePair class method) (drugforge.data.schema.pairs.PairBase class method) (drugforge.data.schema.schema_base.DataModelAbstractBase class method) (drugforge.data.schema.schema_base.MoleculeFilter class method) (drugforge.data.schema.sets.CompoundMultiStructure class method) (drugforge.data.schema.sets.MultiStructureBase class method) (drugforge.data.schema.target.Target class method) (drugforge.data.services.postera.postera_factory.PosteraFactory class method) (drugforge.data.services.services_config.CDDSettings class method) (drugforge.data.services.services_config.CloudfrontSettings class method) (drugforge.data.services.services_config.PosteraSettings class method) (drugforge.data.services.services_config.S3Settings class method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (drugforge.docking.schema.pose_generation.PosedLigands class method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (drugforge.modeling.schema.PreppedComplex class method) (drugforge.modeling.schema.PreppedTarget class method) (drugforge.spectrum.blast.PDBEntry class method) (drugforge.spectrum.blast.PDBRecord class method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader class method) (drugforge.workflows.postera.postera_uploader.PosteraUploader class method) model_validate() (drugforge.alchemy.interfaces.AlchemiscaleSettings class method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper class method) (drugforge.alchemy.schema.base.DefaultModel class method) (drugforge.alchemy.schema.charge.OpenFFCharges class method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet class method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (drugforge.data.operators.deduplicator.LigandDeDuplicator class method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander class method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet class method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander class method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory class method) (drugforge.data.readers.molfile.MolFileFactory class method) (drugforge.data.schema.complex.Complex class method) (drugforge.data.schema.complex.ComplexBase class method) (drugforge.data.schema.experimental.ExperimentalCompoundData class method) (drugforge.data.schema.identifiers.BespokeParameter class method) (drugforge.data.schema.identifiers.BespokeParameters class method) (drugforge.data.schema.identifiers.ChargeProvenance class method) (drugforge.data.schema.identifiers.LigandIdentifiers class method) (drugforge.data.schema.identifiers.LigandProvenance class method) (drugforge.data.schema.identifiers.TargetIdentifiers class method) (drugforge.data.schema.legacy.CrystalCompoundData class method) (drugforge.data.schema.legacy.EnantiomerPair class method) (drugforge.data.schema.legacy.EnantiomerPairList class method) (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) (drugforge.data.schema.pairs.CompoundStructurePair class method) (drugforge.data.schema.pairs.PairBase class method) (drugforge.data.schema.schema_base.DataModelAbstractBase class method) (drugforge.data.schema.schema_base.MoleculeFilter class method) (drugforge.data.schema.sets.CompoundMultiStructure class method) (drugforge.data.schema.sets.MultiStructureBase class method) (drugforge.data.schema.target.Target class method) (drugforge.data.services.postera.postera_factory.PosteraFactory class method) (drugforge.data.services.services_config.CDDSettings class method) (drugforge.data.services.services_config.CloudfrontSettings class method) (drugforge.data.services.services_config.PosteraSettings class method) (drugforge.data.services.services_config.S3Settings class method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (drugforge.docking.schema.pose_generation.PosedLigands class method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (drugforge.modeling.schema.PreppedComplex class method) (drugforge.modeling.schema.PreppedTarget class method) (drugforge.spectrum.blast.PDBEntry class method) (drugforge.spectrum.blast.PDBRecord class method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader class method) (drugforge.workflows.postera.postera_uploader.PosteraUploader class method) model_validate_json() (drugforge.alchemy.interfaces.AlchemiscaleSettings class method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper class method) (drugforge.alchemy.schema.base.DefaultModel class method) (drugforge.alchemy.schema.charge.OpenFFCharges class method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet class method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (drugforge.data.operators.deduplicator.LigandDeDuplicator class method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander class method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet class method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander class method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory class method) (drugforge.data.readers.molfile.MolFileFactory class method) (drugforge.data.schema.complex.Complex class method) (drugforge.data.schema.complex.ComplexBase class method) (drugforge.data.schema.experimental.ExperimentalCompoundData class method) (drugforge.data.schema.identifiers.BespokeParameter class method) (drugforge.data.schema.identifiers.BespokeParameters class method) (drugforge.data.schema.identifiers.ChargeProvenance class method) (drugforge.data.schema.identifiers.LigandIdentifiers class method) (drugforge.data.schema.identifiers.LigandProvenance class method) (drugforge.data.schema.identifiers.TargetIdentifiers class method) (drugforge.data.schema.legacy.CrystalCompoundData class method) (drugforge.data.schema.legacy.EnantiomerPair class method) (drugforge.data.schema.legacy.EnantiomerPairList class method) (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) (drugforge.data.schema.pairs.CompoundStructurePair class method) (drugforge.data.schema.pairs.PairBase class method) (drugforge.data.schema.schema_base.DataModelAbstractBase class method) (drugforge.data.schema.schema_base.MoleculeFilter class method) (drugforge.data.schema.sets.CompoundMultiStructure class method) (drugforge.data.schema.sets.MultiStructureBase class method) (drugforge.data.schema.target.Target class method) (drugforge.data.services.postera.postera_factory.PosteraFactory class method) (drugforge.data.services.services_config.CDDSettings class method) (drugforge.data.services.services_config.CloudfrontSettings class method) (drugforge.data.services.services_config.PosteraSettings class method) (drugforge.data.services.services_config.S3Settings class method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (drugforge.docking.schema.pose_generation.PosedLigands class method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (drugforge.modeling.schema.PreppedComplex class method) (drugforge.modeling.schema.PreppedTarget class method) (drugforge.spectrum.blast.PDBEntry class method) (drugforge.spectrum.blast.PDBRecord class method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader class method) (drugforge.workflows.postera.postera_uploader.PosteraUploader class method) model_validate_strings() (drugforge.alchemy.interfaces.AlchemiscaleSettings class method) (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper class method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper class method) (drugforge.alchemy.schema.base.DefaultModel class method) (drugforge.alchemy.schema.charge.OpenFFCharges class method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet class method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow class method) (drugforge.data.operators.deduplicator.LigandDeDuplicator class method) (drugforge.data.operators.state_expanders.expansion_tag.StateExpansionTag class method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander class method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander class method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansion class method) (drugforge.data.operators.state_expanders.state_expander.StateExpansionSet class method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander class method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander class method) (drugforge.data.readers.meta_ligand_factory.MetaLigandFactory class method) (drugforge.data.readers.molfile.MolFileFactory class method) (drugforge.data.schema.complex.Complex class method) (drugforge.data.schema.complex.ComplexBase class method) (drugforge.data.schema.experimental.ExperimentalCompoundData class method) (drugforge.data.schema.identifiers.BespokeParameter class method) (drugforge.data.schema.identifiers.BespokeParameters class method) (drugforge.data.schema.identifiers.ChargeProvenance class method) (drugforge.data.schema.identifiers.LigandIdentifiers class method) (drugforge.data.schema.identifiers.LigandProvenance class method) (drugforge.data.schema.identifiers.TargetIdentifiers class method) (drugforge.data.schema.legacy.CrystalCompoundData class method) (drugforge.data.schema.legacy.EnantiomerPair class method) (drugforge.data.schema.legacy.EnantiomerPairList class method) (drugforge.data.schema.ligand.Ligand class method) (drugforge.data.schema.ligand.ReferenceLigand class method) (drugforge.data.schema.pairs.CompoundStructurePair class method) (drugforge.data.schema.pairs.PairBase class method) (drugforge.data.schema.schema_base.DataModelAbstractBase class method) (drugforge.data.schema.schema_base.MoleculeFilter class method) (drugforge.data.schema.sets.CompoundMultiStructure class method) (drugforge.data.schema.sets.MultiStructureBase class method) (drugforge.data.schema.target.Target class method) (drugforge.data.services.postera.postera_factory.PosteraFactory class method) (drugforge.data.services.services_config.CDDSettings class method) (drugforge.data.services.services_config.CloudfrontSettings class method) (drugforge.data.services.services_config.PosteraSettings class method) (drugforge.data.services.services_config.S3Settings class method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator class method) (drugforge.docking.schema.pose_generation.PosedLigands class method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator class method) (drugforge.modeling.schema.PreppedComplex class method) (drugforge.modeling.schema.PreppedTarget class method) (drugforge.spectrum.blast.PDBEntry class method) (drugforge.spectrum.blast.PDBRecord class method) (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader class method) (drugforge.workflows.postera.postera_uploader.PosteraUploader class method) module drugforge drugforge.alchemy drugforge.alchemy.alchemize drugforge.alchemy.cli drugforge.alchemy.cli.alchemy drugforge.alchemy.cli.cli drugforge.alchemy.cli.prep drugforge.alchemy.cli.utils drugforge.alchemy.interfaces drugforge.alchemy.predict drugforge.alchemy.schema drugforge.alchemy.schema.atom_mapping drugforge.alchemy.schema.base drugforge.alchemy.schema.charge drugforge.alchemy.schema.prep_workflow drugforge.cli drugforge.cli.cli_args drugforge.data drugforge.data.backend drugforge.data.backend.openeye drugforge.data.backend.rdkit drugforge.data.metadata drugforge.data.metadata.master_seqres drugforge.data.metadata.master_seqres.fasta_to_seqres drugforge.data.metadata.resources drugforge.data.operators drugforge.data.operators.deduplicator drugforge.data.operators.state_expanders drugforge.data.operators.state_expanders.expansion_tag drugforge.data.operators.state_expanders.protomer_expander drugforge.data.operators.state_expanders.state_expander drugforge.data.operators.state_expanders.stereo_expander drugforge.data.operators.state_expanders.tautomer_expander drugforge.data.readers drugforge.data.readers.meta_ligand_factory drugforge.data.readers.molfile drugforge.data.schema drugforge.data.schema.complex drugforge.data.schema.experimental drugforge.data.schema.identifiers drugforge.data.schema.legacy drugforge.data.schema.ligand drugforge.data.schema.pairs drugforge.data.schema.schema_base drugforge.data.schema.sets drugforge.data.schema.target drugforge.data.sequence drugforge.data.services drugforge.data.services.aws drugforge.data.services.aws.cloudfront drugforge.data.services.aws.s3 drugforge.data.services.cdd drugforge.data.services.cdd.cdd_api drugforge.data.services.cdd.cdd_download drugforge.data.services.fragalysis drugforge.data.services.fragalysis.fragalysis_download drugforge.data.services.postera drugforge.data.services.postera.manifold_data_validation drugforge.data.services.postera.molecule_set drugforge.data.services.postera.postera_api drugforge.data.services.postera.postera_factory drugforge.data.services.rcsb drugforge.data.services.rcsb.rcsb_download drugforge.data.services.services_config drugforge.data.services.web_utils drugforge.data.testing drugforge.data.testing.test_resources drugforge.data.util drugforge.data.util.data_conversion drugforge.data.util.execution_utils drugforge.data.util.intenum drugforge.data.util.logging drugforge.data.util.stringenum drugforge.data.util.utils drugforge.dataviz drugforge.dataviz.plip drugforge.dataviz.resources drugforge.dataviz.resources.fonts drugforge.dataviz.show_contacts drugforge.docking drugforge.docking.analysis drugforge.docking.docking_data_validation drugforge.docking.schema drugforge.docking.schema.pose_generation drugforge.docking.selectors drugforge.ml drugforge.ml.data_augmentation drugforge.ml.dataset drugforge.ml.early_stopping drugforge.ml.loss drugforge.ml.pretrained_models drugforge.ml.viz drugforge.modeling drugforge.modeling.modeling drugforge.modeling.schema drugforge.simulation drugforge.spectrum drugforge.spectrum.align_seq_match drugforge.spectrum.blast drugforge.spectrum.calculate_rmsd drugforge.spectrum.fitness drugforge.spectrum.seq_alignment drugforge.workflows drugforge.workflows.docking_workflows drugforge.workflows.postera drugforge.workflows.postera.manifold_artifacts drugforge.workflows.postera.postera_uploader drugforge.workflows.prep_workflows Molecule (class in drugforge.data.services.postera.molecule_set) MoleculeComponent (class in drugforge.data.schema.schema_base) MoleculeFilter (class in drugforge.data.schema.schema_base) MoleculeList (class in drugforge.data.services.postera.molecule_set) MoleculeSetAPI (class in drugforge.data.services.postera.molecule_set) MoleculeSetKeys (class in drugforge.data.services.postera.molecule_set) MoleculeUpdate (class in drugforge.data.services.postera.molecule_set) MoleculeUpdateList (class in drugforge.data.services.postera.molecule_set) MolFileFactory (class in drugforge.data.readers.molfile) MSELoss (class in drugforge.ml.loss) multimer() (in module drugforge.cli.cli_args) MultiStructureBase (class in drugforge.data.schema.sets) mutate_residues() (in module drugforge.modeling.modeling)

N

n_chains() (in module drugforge.cli.cli_args) name (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) negative_log() (in module drugforge.alchemy.predict) neutralized (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property)

non_iso_smiles (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) normalize_fitness() (in module drugforge.spectrum.fitness) num_poses (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) numerator (drugforge.data.util.intenum.IntEnum attribute)

O

oe_smiles_roundtrip() (in module drugforge.data.backend.openeye) oedu_to_bytes64() (in module drugforge.data.backend.openeye) oemol_to_inchi() (in module drugforge.data.backend.openeye) oemol_to_inchikey() (in module drugforge.data.backend.openeye) oemol_to_pdb_string() (in module drugforge.data.backend.openeye) oemol_to_sdf_string() (in module drugforge.data.backend.openeye) oemol_to_smiles() (in module drugforge.data.backend.openeye)

openeye_copy_pdb_data() (in module drugforge.data.backend.openeye) openeye_perceive_residues() (in module drugforge.data.backend.openeye) OpenEyeConstrainedPoseGenerator (class in drugforge.docking.schema.pose_generation) OpenFFCharges (class in drugforge.alchemy.schema.charge) output_dir() (in module drugforge.cli.cli_args) OutputTags (class in drugforge.data.services.postera.manifold_data_validation) overwrite() (in module drugforge.cli.cli_args)

P

PairBase (class in drugforge.data.schema.pairs) pairwise_alignment() (in module drugforge.spectrum.align_seq_match) params (drugforge.alchemy.cli.utils.SpecialHelpOrder attribute) parse_blast() (in module drugforge.spectrum.blast) parse_fitness_json() (in module drugforge.spectrum.fitness) parse_fluorescence_data_cdd() (in module drugforge.data.util.utils) parse_fragalysis() (in module drugforge.data.services.fragalysis.fragalysis_download) parse_pdb_blast_results() (drugforge.spectrum.blast.PDBEntry static method) parse_xtal() (in module drugforge.data.services.fragalysis.fragalysis_download) partial_sanitize() (in module drugforge.alchemy.alchemize) partition() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) PatientConvergedEarlyStopping (class in drugforge.ml.early_stopping) pdb_file() (in module drugforge.cli.cli_args) pdb_string_to_oemol() (in module drugforge.data.backend.openeye) pdb_to_seq() (in module drugforge.spectrum.blast) PDBEntry (class in drugforge.spectrum.blast) PDBRecord (class in drugforge.spectrum.blast) PersesAtomMapper (class in drugforge.alchemy.schema.atom_mapping) pic50_to_dg() (in module drugforge.alchemy.predict) plot_model_preds_scatter() (in module drugforge.ml.viz) plot_split_losses() (in module drugforge.ml.viz) plotmol_absolute() (in module drugforge.alchemy.predict) plotmol_relative() (in module drugforge.alchemy.predict) pop() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) popitem() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method)

pose_experimental_molecules() (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method) PoseCrossEntropyLoss (class in drugforge.ml.loss) PosedLigands (class in drugforge.docking.schema.pose_generation) PoseEnergyMethod (class in drugforge.docking.schema.pose_generation) poser() (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) PoseSelectionMethod (class in drugforge.docking.schema.pose_generation) postera() (in module drugforge.cli.cli_args) postera_args() (in module drugforge.cli.cli_args) postera_molset_name() (in module drugforge.cli.cli_args) postera_upload() (in module drugforge.cli.cli_args) PosteraFactory (class in drugforge.data.services.postera.postera_factory) PosteraSettings (class in drugforge.data.services.services_config) PosteraUploader (class in drugforge.workflows.postera.postera_uploader) PreppedComplex (class in drugforge.modeling.schema) PreppedTarget (class in drugforge.modeling.schema) print_header() (in module drugforge.alchemy.cli.utils) print_message() (in module drugforge.alchemy.cli.utils) print_SD_data() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (in module drugforge.data.backend.openeye) ProgressQuotientEarlyStopping (class in drugforge.ml.early_stopping) ProtomerExpander (class in drugforge.data.operators.state_expanders.protomer_expander) provenance() (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper method) (drugforge.alchemy.schema.charge.OpenFFCharges method) (drugforge.data.operators.state_expanders.protomer_expander.EpikExpander method) (drugforge.data.operators.state_expanders.protomer_expander.ProtomerExpander method) (drugforge.data.operators.state_expanders.state_expander.StateExpanderBase method) (drugforge.data.operators.state_expanders.stereo_expander.StereoExpander method) (drugforge.data.operators.state_expanders.tautomer_expander.TautomerExpander method) (drugforge.docking.schema.pose_generation.OpenEyeConstrainedPoseGenerator method) (drugforge.docking.schema.pose_generation.RDKitConstrainedPoseGenerator method) pull() (drugforge.data.services.postera.postera_factory.PosteraFactory method) pull_all() (drugforge.data.services.postera.postera_factory.PosteraFactory method) pull_from_postera() (in module drugforge.alchemy.cli.utils) push() (drugforge.workflows.postera.postera_uploader.PosteraUploader method) push_dir() (drugforge.data.services.aws.s3.S3 method) push_file() (drugforge.data.services.aws.s3.S3 method) pymol_alignment() (in module drugforge.data.services.rcsb.rcsb_download) pymol_save() (in module drugforge.cli.cli_args)

R

RangeLoss (class in drugforge.ml.loss) rdkit_mol_to_sdf_str() (in module drugforge.data.backend.rdkit) rdkit_smiles_roundtrip() (in module drugforge.data.backend.rdkit) RDKitConstrainedPoseGenerator (class in drugforge.docking.schema.pose_generation) read_file_directly() (in module drugforge.data.schema.schema_base) real (drugforge.data.util.intenum.IntEnum attribute) ref_chain() (in module drugforge.cli.cli_args) ReferenceLigand (class in drugforge.data.schema.ligand) remove() (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) remove_duplicates() (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) (drugforge.workflows.postera.postera_uploader.PosteraUploader method) removeprefix() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) removesuffix() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) rename_output_columns_for_manifold() (in module drugforge.data.services.postera.manifold_data_validation) replace() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) report_alchemize_clusters() (in module drugforge.alchemy.cli.utils) rescue_outsiders() (in module drugforge.alchemy.alchemize) reset() (drugforge.data.services.aws.s3.S3 method) result_callback() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) retrieve_pdb() (drugforge.spectrum.blast.PDBEntry method) reverse() (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) rfind() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

rindex() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) rjust() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) rmsd_alignment() (in module drugforge.spectrum.calculate_rmsd) rpartition() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) rsplit() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) rstrip() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

S

S3 (class in drugforge.data.services.aws.s3) S3Error S3Settings (class in drugforge.data.services.services_config) save_alignment_pymol() (in module drugforge.spectrum.calculate_rmsd) save_openeye_design_unit() (in module drugforge.data.backend.openeye) save_openeye_pdb() (in module drugforge.data.backend.openeye) save_openeye_sdf() (in module drugforge.data.backend.openeye) save_openeye_sdfs() (in module drugforge.data.backend.openeye) save_posed_ligands() (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet method) save_pymol_seq_align() (in module drugforge.spectrum.align_seq_match) save_receptor_grid() (in module drugforge.data.backend.openeye) save_to_cache() (in module drugforge.cli.cli_args) schema_dict_get_val_overload() (in module drugforge.data.schema.schema_base) sdf_str_to_rdkit_mol() (in module drugforge.data.backend.rdkit) sdf_string_to_oemol() (in module drugforge.data.backend.openeye) search_host() (in module drugforge.spectrum.blast) select_best_colabfold() (in module drugforge.spectrum.calculate_rmsd) seq_file() (in module drugforge.cli.cli_args) seq_type() (in module drugforge.cli.cli_args) seqres_by_target() (in module drugforge.data.sequence) seqres_to_res_list() (in module drugforge.data.util.utils) set_expansion() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) set_SD_data() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) (in module drugforge.data.backend.openeye) (in module drugforge.data.backend.rdkit) setdefault() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method) settings_customise_sources() (drugforge.alchemy.interfaces.AlchemiscaleSettings class method) (drugforge.data.services.services_config.CDDSettings class method) (drugforge.data.services.services_config.CloudfrontSettings class method) (drugforge.data.services.services_config.PosteraSettings class method) (drugforge.data.services.services_config.S3Settings class method) shell_complete() (drugforge.alchemy.cli.utils.SpecialHelpOrder method) shift_and_add_prediction_error() (in module drugforge.alchemy.predict) show_contacts() (in module drugforge.dataviz.show_contacts) size (drugforge.data.schema.complex.Complex property) (drugforge.data.schema.complex.ComplexBase property) (drugforge.data.schema.identifiers.LigandIdentifiers property) (drugforge.data.schema.identifiers.LigandProvenance property) (drugforge.data.schema.identifiers.TargetIdentifiers property) (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) (drugforge.data.schema.schema_base.DataModelAbstractBase property) (drugforge.data.schema.target.Target property) (drugforge.modeling.schema.PreppedComplex property) (drugforge.modeling.schema.PreppedTarget property) smiles (drugforge.data.schema.ligand.Ligand property) (drugforge.data.schema.ligand.ReferenceLigand property) smiles_to_oemol() (in module drugforge.data.backend.openeye) SmoothL1Loss (class in drugforge.ml.loss) sort() (drugforge.data.services.postera.molecule_set.MoleculeList method) (drugforge.data.services.postera.molecule_set.MoleculeUpdateList method) sort_confs_by_sd_tag_value() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) SpecialHelpOrder (class in drugforge.alchemy.cli.utils) split() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) split_openeye_design_unit() (in module drugforge.data.backend.openeye)

split_openeye_mol() (in module drugforge.data.backend.openeye) SplitDockedDataset (class in drugforge.ml.dataset) splitlines() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) spruce_protein() (in module drugforge.modeling.modeling) startswith() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) StateExpanderBase (class in drugforge.data.operators.state_expanders.state_expander) StateExpansion (class in drugforge.data.operators.state_expanders.state_expander) StateExpansionSet (class in drugforge.data.operators.state_expanders.state_expander) StateExpansionTag (class in drugforge.data.operators.state_expanders.expansion_tag) StaticTags (in module drugforge.data.services.postera.manifold_data_validation) step_loss() (drugforge.ml.loss.L1Loss method) (drugforge.ml.loss.MSELoss method) (drugforge.ml.loss.SmoothL1Loss method) StereoExpander (class in drugforge.data.operators.state_expanders.stereo_expander) StringEnum (class in drugforge.data.util.stringenum) strip() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) strip_smiles_salts() (in module drugforge.data.util.utils) structure_dir() (in module drugforge.cli.cli_args) superpose_molecule() (in module drugforge.modeling.modeling) swapcase() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

T

TagEnumBase (class in drugforge.data.services.postera.manifold_data_validation) TanimotoType (class in drugforge.docking.analysis) Target (class in drugforge.data.schema.target) target() (in module drugforge.cli.cli_args) target_has_fitness_data() (in module drugforge.spectrum.fitness) TargetIdentifiers (class in drugforge.data.schema.identifiers) TargetTags (class in drugforge.data.services.postera.manifold_data_validation) TautomerExpander (class in drugforge.data.operators.state_expanders.tautomer_expander) ThresholdEarlyStopping (class in drugforge.ml.early_stopping) title() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) to_bytes() (drugforge.data.util.intenum.IntEnum method) to_combined_oemol() (drugforge.data.schema.complex.Complex method) to_file() (drugforge.alchemy.schema.atom_mapping.KartografAtomMapper method) (drugforge.alchemy.schema.atom_mapping.LomapAtomMapper method) (drugforge.alchemy.schema.atom_mapping.PersesAtomMapper method) (drugforge.alchemy.schema.charge.OpenFFCharges method) (drugforge.alchemy.schema.prep_workflow.AlchemyDataSet method) (drugforge.alchemy.schema.prep_workflow.AlchemyPrepWorkflow method)

to_oemol() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) to_openfe() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) to_pdb_file() (drugforge.modeling.schema.PreppedTarget method) to_rdkit() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) to_SD_tags() (drugforge.data.schema.experimental.ExperimentalCompoundData method) to_sdf() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) to_sdf_str() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) to_single_conformers() (drugforge.data.schema.ligand.Ligand method) (drugforge.data.schema.ligand.ReferenceLigand method) to_uri() (drugforge.data.services.aws.s3.S3 method) token_name() (drugforge.data.services.cdd.cdd_api.CDDAPI class method) (drugforge.data.services.postera.molecule_set.MoleculeSetAPI class method) translate() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method) trim_small_chains() (in module drugforge.data.backend.openeye)

U

unique_name (drugforge.data.schema.complex.Complex property) (drugforge.data.schema.complex.ComplexBase property) (drugforge.modeling.schema.PreppedComplex property) update() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method) update_molecules() (drugforge.data.services.postera.molecule_set.MoleculeSetAPI method) upload_artifacts() (drugforge.workflows.postera.manifold_artifacts.ManifoldArtifactUploader method) upload_to_postera() (in module drugforge.alchemy.cli.utils) upper() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)

use_dask() (in module drugforge.cli.cli_args) use_only_cache() (in module drugforge.cli.cli_args) utf8len() (in module drugforge.data.schema.schema_base)

V

values() (drugforge.data.services.postera.molecule_set.Molecule method) (drugforge.data.services.postera.molecule_set.MoleculeUpdate method)

view_alignment() (drugforge.spectrum.seq_alignment.Alignment method) VirusTags (class in drugforge.data.services.postera.manifold_data_validation)

W

write_all_rmsds_to_reference() (in module drugforge.docking.analysis) write_clusters() (in module drugforge.alchemy.alchemize)

write_file_directly() (in module drugforge.data.schema.schema_base) write_ligands_to_multi_sdf() (in module drugforge.data.schema.ligand)

Z

zfill() (drugforge.data.schema.schema_base.DataStorageType method) (drugforge.data.schema.schema_base.MoleculeComponent method) (drugforge.data.services.fragalysis.fragalysis_download.FragalysisTargets method) (drugforge.data.services.postera.manifold_data_validation.ManifoldAllowedTags method) (drugforge.data.services.postera.manifold_data_validation.OutputTags method) (drugforge.data.services.postera.manifold_data_validation.TagEnumBase method) (drugforge.data.services.postera.manifold_data_validation.TargetTags method) (drugforge.data.services.postera.manifold_data_validation.VirusTags method) (drugforge.data.services.postera.molecule_set.MoleculeSetKeys method) (drugforge.data.util.stringenum.StringEnum method) (drugforge.docking.analysis.TanimotoType method) (drugforge.docking.docking_data_validation.DockingResultCols method) (drugforge.docking.schema.pose_generation.PoseEnergyMethod method) (drugforge.docking.schema.pose_generation.PoseSelectionMethod method)