Index

Symbols

--aliphatic-constraint ocli-molsearch-query-create-substructure command line option --auth-secret ocli-molsearch-db-create command line option --background ocli-molsearch-query-export command line option --cancel-after ocli-molsearch-query-create-substructure command line option --collection ocli-molsearch-db-create command line option --cpu ocli-molsearch-db-create command line option --cutoff ocli-molsearch-query-create-graphsim command line option --delete ocli-molsearch-db-share command line option ocli-packages-share command line option ocli-services-spec-share command line option ocli-services-task-share command line option --delete-image-file ocli-packages-import-from-orion-file command line option ocli-packages-upload-package-image command line option --description ocli-packages-init command line option ocli-services-task-create command line option ocli-services-task-update command line option --disk-space ocli-molsearch-db-create command line option --display-name ocli-molsearch-db-create command line option ocli-molsearch-db-update command line option --download ocli-cost-export command line option ocli-packages-export-base-image command line option --email ocli-packages-init command line option --exclude ocli-molsearch-query-download command line option --external ocli-services-task-create command line option --format ocli-molsearch-query-export command line option --fpname ocli-molsearch-query-create-graphsim command line option --from ocli-molsearch-db-logs command line option ocli-services-task-logs command line option --full-name ocli-packages-init command line option --gpu ocli-molsearch-db-create command line option --ids ocli-molsearch-query-download command line option ocli-molsearch-query-export command line option --image-tag ocli-packages-import-from-registry command line option --instance-type ocli-molsearch-db-create command line option --is-proxy ocli-molsearch-db-create command line option --isotope-constraint ocli-molsearch-query-create-substructure command line option --limit ocli-molsearch-db-list command line option ocli-molsearch-query-list command line option ocli-molsearch-query-list-results command line option ocli-packages-list command line option ocli-services-spec-list command line option ocli-services-task-list command line option --max-hits ocli-molsearch-query-create-exact command line option ocli-molsearch-query-create-fastrocs command line option ocli-molsearch-query-create-graphsim command line option ocli-molsearch-query-create-substructure command line option --measure ocli-molsearch-query-create-graphsim command line option --memory-mb ocli-molsearch-db-create command line option --module-name ocli-packages-init command line option --name ocli-molsearch-query-create-exact command line option ocli-molsearch-query-create-fastrocs command line option ocli-molsearch-query-create-graphsim command line option ocli-molsearch-query-create-substructure command line option ocli-molsearch-query-create-title command line option ocli-molsearch-query-export command line option ocli-molsearch-query-update command line option ocli-services-spec-list command line option ocli-services-task-create command line option ocli-services-task-list command line option ocli-services-task-update command line option --no-download ocli-cost-export command line option ocli-packages-export-base-image command line option --no-notify ocli-packages-export-base-image command line option --notify ocli-cost-export command line option ocli-packages-export-base-image command line option --offset ocli-molsearch-db-list command line option ocli-molsearch-query-list command line option ocli-molsearch-query-list-results command line option ocli-packages-list command line option ocli-services-spec-list command line option ocli-services-task-list command line option --orientation ocli-molsearch-query-create-fastrocs command line option --output-path ocli-cost-export command line option ocli-packages-create-environment-yaml command line option ocli-packages-export-base-image command line option ocli-packages-show-dockerfile command line option

--path ocli-molsearch-query-export command line option ocli-packages-upload-package-image command line option --pools ocli-molsearch-db-create command line option --programmatic ocli-molsearch-query-list command line option --project ocli-molsearch-query-create-exact command line option ocli-molsearch-query-create-fastrocs command line option ocli-molsearch-query-create-graphsim command line option ocli-molsearch-query-create-substructure command line option ocli-molsearch-query-create-title command line option ocli-molsearch-query-export command line option ocli-molsearch-query-list command line option ocli-packages-tag command line option --project-name ocli-packages-init command line option --project-slug ocli-packages-init command line option --pull-username ocli-packages-import-from-registry command line option --query-type ocli-molsearch-query-list command line option --random-starts ocli-molsearch-query-create-fastrocs command line option --redact-project-names ocli-cost-export command line option --registry-url ocli-packages-import-from-registry command line option --report-type ocli-cost-export command line option --saved ocli-molsearch-query-update command line option --search-type ocli-molsearch-db-create command line option ocli-molsearch-query-create-exact command line option --secret ocli-packages-import-from-registry command line option --section ocli-molsearch-db-create command line option ocli-molsearch-db-update command line option --server-address ocli-molsearch-db-create command line option --server-is-remote ocli-molsearch-db-create command line option --service ocli-packages-init command line option --shape-only ocli-molsearch-query-create-fastrocs command line option --share ocli-molsearch-db-share command line option ocli-packages-share command line option ocli-services-spec-share command line option ocli-services-task-share command line option --sim-type ocli-molsearch-query-create-fastrocs command line option --specification ocli-services-task-create command line option --state ocli-services-task-update command line option --stereo-constraint ocli-molsearch-query-create-substructure command line option --subsearch_query_type ocli-molsearch-query-create-substructure command line option --topology-constraint ocli-molsearch-query-create-substructure command line option --tversky-alpha ocli-molsearch-query-create-fastrocs command line option --until ocli-molsearch-db-logs command line option ocli-services-task-logs command line option --url ocli-services-task-create command line option --verbose ocli-packages-check-image command line option --verify-ssl-cert ocli-molsearch-db-create command line option --version ocli-packages-init command line option --wait ocli-molsearch-query-create-exact command line option ocli-molsearch-query-create-fastrocs command line option ocli-molsearch-query-create-graphsim command line option ocli-molsearch-query-create-substructure command line option --write ocli-molsearch-db-share command line option ocli-packages-share command line option ocli-services-spec-share command line option ocli-services-task-share command line option -d ocli-packages-import-from-orion-file command line option ocli-packages-upload-package-image command line option -o ocli-packages-create-environment-yaml command line option ocli-packages-export-base-image command line option ocli-packages-show-dockerfile command line option -p ocli-packages-upload-package-image command line option -r ocli-packages-import-from-registry command line option -s ocli-packages-import-from-registry command line option -t ocli-packages-import-from-registry command line option -u ocli-packages-import-from-registry command line option -v ocli-packages-check-image command line option

_

__iter__() (drconvert.ArchiveConverter method) (drconvert.CSVConverter method) (drconvert.MolFileConverter method) (drconvert.OEDUConverter method) (drconvert.RecordConvertToCSV method) (drconvert.RecordConvertToMols method) (drconvert.RecordConvertToOEDU method) (drconvert.SmilesFileConverter method)

A

add_attribute() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) add_directory() (artemis.packaging.OrionTestPackage method) add_field() (datarecord.OERecord method) add_file() (artemis.packaging.OrionTestPackage method) add_relation() (datarecord.OEFieldMeta method) AMI Analyze page API APIs apo protein apo proteins ArchiveConverter (class in drconvert)

artemis module artemis.packaging module artemis.test module artemis.wrappers module assertWorkFloeComplete() (artemis.test.FloeTestCase method) assign_paths() (orionclient.session.OrionSession method) asymmetric unit AUC AuthorizationRequired

B

B-factor Backoff (class in orionclient.utils) BadResponse Balance (class in orionclient.types) BASE_IMAGE ocli-packages-export-base-image command line option BaseParameter (class in floe.api.parameters)

begin() (floe.api.cubes.Cube method) binding receptor biological unit BooleanFieldParameter (class in orionplatform.parameters.fields) BooleanParameter (class in floe.api.parameters) bug-fix release

C

cancel() (artemis.wrappers.WorkFloeWrapper method) (orionclient.types.MolsearchQuery method) (orionclient.types.WorkFloeJob method) canonical isomeric SMILES canonical SMILES check_field() (datarecord.OERecord method) CheckCache() (datarecord.OERecord method) cheminformatics functions chiral atom chiral bond chunks() (orionplatform.parameters.files.FileStream method) CIP Classification (class in orionclient.types) clear() (datarecord.OEFieldMeta method) (datarecord.OERecord method) (datarecord.OERecordMeta method) clear_value() (datarecord.OERecord method) close() (orionclient.types.Shard method) (orionclient.types.ShardCollection method) CMD ocli-molsearch-db-help command line option ocli-molsearch-query-create-help command line option ocli-molsearch-query-help command line option ocli-packages-help command line option ocli-services-spec-help command line option ocli-services-task-help command line option CollectionInputParameter (class in orionplatform.parameters.collections) CollectionInputPort (class in orionplatform.ports) CollectionInputPortV2 (class in orionplatform.ports) CollectionOutputParameter (class in orionplatform.parameters.collections) CollectionOutputPort (class in orionplatform.ports) CollectionOutputPortV2 (class in orionplatform.ports) CollectionPortsMixin (class in orionplatform.mixins) collections collections() (orionplatform.parameters.collections.CollectionStream method) CollectionStream (class in orionplatform.parameters.collections) CollectionWrapper (class in artemis.wrappers) complete() (orionclient.types.File method) ComputeCube (class in floe.api.cubes) conformer conformers count (artemis.wrappers.OutputDatasetWrapper property) CPK create() (orionclient.types.Dataset class method) (orionclient.types.MolsearchDatabase class method) (orionclient.types.Shard class method) (orionclient.types.ShardCollection class method)

create_exact_query() (orionclient.types.MolsearchQuery class method) create_fastrocs_query() (orionclient.types.MolsearchQuery class method) create_graphsim_query() (orionclient.types.MolsearchQuery class method) create_link() (in module datarecord) (orionclient.session.OrionSession method) create_mdl_subsearch_query() (orionclient.types.MolsearchQuery class method) create_multipart_file() (orionclient.types.File class method) create_paths() (orionclient.session.OrionSession method) create_resource() (orionclient.session.OrionSession method) create_smarts_subsearch_query() (orionclient.types.MolsearchQuery class method) create_subsearch_query() (orionclient.types.MolsearchQuery class method) create_title_query() (orionclient.types.MolsearchQuery class method) CSV CSVConversionOptions (class in drconvert) CSVConverter (class in drconvert) cube emitting items execution order group group, parallel methods packaging parallel parameters port testing type Cube (class in floe.api.cubes) (class in orionclient.types) CubeGroup (class in floe.api.cubes) CubeParametersMixin (class in floe.api.cubes) Cubes cubes CubeTestRunner (class in floe.test) CUDA CurrentBalance (class in orionclient.types) CustomHandler (class in datarecord) CXSMILES CycleDetails (class in floe.api.cubes) cycles internals cyclic floes workflows

D

DATABASE ocli-molsearch-db-delete command line option ocli-molsearch-db-info command line option ocli-molsearch-db-load command line option ocli-molsearch-db-unload command line option ocli-molsearch-db-update command line option ocli-molsearch-query-create-exact command line option ocli-molsearch-query-create-fastrocs command line option ocli-molsearch-query-create-graphsim command line option ocli-molsearch-query-create-substructure command line option ocli-molsearch-query-create-title command line option datarecord module Dataset (class in orionclient.types) DatasetDimensionsTooLargeError DatasetInputParameter (class in orionplatform.parameters.datasets) DatasetOutputParameter (class in orionplatform.parameters.datasets) datasets DatasetStream (class in orionplatform.parameters.datasets) DatasetWrapper (class in artemis.wrappers) DecimalFieldParameter (class in orionplatform.parameters.fields) DecimalParameter (class in floe.api.parameters) delete user

delete() (orionclient.types.MolsearchDatabase method) (orionclient.types.MolsearchQuery method) delete_atom_record() (datarecord.OEMolRecord method) delete_bond_record() (datarecord.OEMolRecord method) delete_conf_record() (datarecord.OEMolRecord method) delete_field() (datarecord.OERecord method) delete_logs() (orionclient.types.WorkFloeJob method) delete_resource() (orionclient.session.OrionSession method) design unit dock docking download() (orionclient.types.Dataset method) (orionclient.types.File method) (orionclient.types.Shard method) download_query_to_file() (orionclient.types.MolsearchQuery method) download_to_file() (orionclient.types.Dataset method) (orionclient.types.File method) (orionclient.types.MolsearchQuery method) (orionclient.types.Shard method) drconvert module drconvert.pandas module drconvert.parquet module

E

emit() (floe.api.cubes.Cube method) emitting items cube end() (floe.api.cubes.Cube method)

excipient execution order, cube export() (orionclient.types.MolsearchQuery method)

F

FASTA feature release FieldParameter (class in orionplatform.parameters.fields) FieldSelector (class in orionplatform.parameters.fields) FieldSelectorParameter (class in orionplatform.parameters.fields) FILE ocli-molsearch-query-download command line option ocli-packages-download command line option File (class in orionclient.types) FileInputParameter (class in floe.api.parameters) (class in orionplatform.parameters.files) FileOutputParameter (class in floe.api.parameters) (class in orionplatform.parameters.files) files FileStream (class in orionplatform.parameters.files) FileWrapper (class in artemis.wrappers) filtering FILTERS ocli-molsearch-db-list command line option ocli-packages-list command line option ocli-services-spec-list command line option ocli-services-task-list command line option

finalize() (orionclient.types.Dataset method) fingerprint fit regression FloatFieldParameter (in module orionplatform.parameters.fields) floe floe.api.cubes module floe.api.parameters module floes cyclic FloeTestCase (class in artemis.test) flush() (datarecord.OERecord method) (orionclient.types.Dataset method) from_collection() (artemis.wrappers.CollectionWrapper class method) from_file() (artemis.wrappers.CollectionWrapper class method) (artemis.wrappers.DatasetWrapper class method) (artemis.wrappers.FileWrapper class method) from_json() (floe.api.parameters.BaseParameter class method) from_name() (orionclient.types.ServiceSpec class method) (orionclient.types.ServiceTask class method)

G

get() (artemis.wrappers.OutputCollectionWrapper method) get_atom_record() (datarecord.OEMolRecord method) get_atom_records() (datarecord.OEMolRecord method) get_attribute() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) get_attributes() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) get_bond_record() (datarecord.OEMolRecord method) get_bond_records() (datarecord.OEMolRecord method) get_bytes() (datarecord.OERecord method) get_child_record() (datarecord.OERecord method) get_child_records() (datarecord.OERecord method) get_conf_record() (datarecord.OEMolRecord method) get_conf_records() (datarecord.OEMolRecord method) get_converter() (in module drconvert) get_costs() (orionclient.types.WorkFloeJob method) get_count() (orionclient.types.ShardCollection method) get_current_balance() (orionclient.session.OrionSession method) get_current_project() (orionclient.session.OrionSession method) get_current_workfloe_job() (in module orionclient.helpers.floe) get_dataset() (artemis.wrappers.DatasetWrapper class method) get_default_output_folder() (orionclient.session.OrionSession method) get_environment_log() (orionclient.types.WorkFloePackage method) get_field() (datarecord.OERecord method) (orionclient.links.RecordLink method) (orionplatform.parameters.fields.FieldSelector method) get_field_meta() (datarecord.OERecord method) get_field_relations() (datarecord.OEFieldMeta method) get_file() (artemis.wrappers.FileWrapper class method) get_float_attribute() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) get_inspection_result() (orionclient.types.WorkFloePackage method) get_int_attribute() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) get_link() (orionclient.session.OrionSession method) get_matches() (orionclient.types.MolsearchQuery method) get_mol() (datarecord.OEMolRecord method)

get_mol_reference() (datarecord.OEMolRecord method) get_name() (datarecord.OEFieldMeta static method) (datarecord.OERecordMeta static method) get_options() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) get_orion_resource() (orionclient.links.OrionLink method) (orionclient.links.RecordLink method) (orionclient.links.ShardLink method) get_packages() (artemis.test.FloeTestCase method) get_parameter_group() (floe.api.cubes.Cube method) get_paths() (orionclient.session.OrionSession method) get_primary_mol_field() (datarecord.OEMolRecord method) get_profile_config() (in module orionclient.session) get_record() (orionclient.links.RecordLink method) get_record_meta() (datarecord.OERecord method) get_reference() (datarecord.OERecord method) get_related_fields() (datarecord.OEFieldMeta method) get_resource() (orionclient.session.OrionSession method) get_session() (in module orionclient.session) get_shard() (orionclient.links.ShardLink method) get_smiles() (orionclient.types.MolsearchQuery static method) get_source_id() (datarecord.OERecord method) get_str_attribute() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) get_user_profile() (orionclient.session.OrionSession method) get_value() (orionplatform.parameters.fields.FieldSelector method) get_version() (datarecord.OERecord static method) get_workfloe() (artemis.wrappers.WorkFloeWrapper class method) GetAtomRecords() (datarecord.OEMolRecord method) GetBondRecords() (datarecord.OEMolRecord method) GetImpl() (datarecord.OERecord method) GetValue() (datarecord.OEFieldMeta static method) (datarecord.OERecordMeta static method) GRASP group cube parallel cube

H

has_atom_record() (datarecord.OEMolRecord method) has_attribute() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) has_bond_record() (datarecord.OEMolRecord method) has_child_record() (datarecord.OERecord method) has_child_records() (datarecord.OERecord method) has_conf_record() (datarecord.OEMolRecord method)

has_field() (datarecord.OERecord method) has_mol() (datarecord.OEMolRecord method) has_option() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) has_value() (datarecord.OERecord method) HELM hypercubes

I

IDENTIFIER ocli-molsearch-db-list-shares command line option ocli-molsearch-db-logs command line option ocli-molsearch-db-share command line option ocli-molsearch-db-unshare command line option ocli-packages-delete command line option ocli-packages-deprecate command line option ocli-packages-download command line option ocli-packages-environment command line option ocli-packages-info command line option ocli-packages-inspection command line option ocli-packages-list-shares command line option ocli-packages-list-tags command line option ocli-packages-share command line option ocli-packages-tag command line option ocli-packages-undeprecate command line option ocli-packages-unshare command line option ocli-packages-untag command line option ocli-services-spec-info command line option ocli-services-spec-list-shares command line option ocli-services-spec-share command line option ocli-services-spec-unshare command line option ocli-services-task-delete command line option ocli-services-task-info command line option ocli-services-task-list-shares command line option ocli-services-task-logs command line option ocli-services-task-share command line option ocli-services-task-unshare command line option ocli-services-task-update command line option identifier (artemis.wrappers.CollectionWrapper property) (artemis.wrappers.DatasetWrapper property) (artemis.wrappers.FileWrapper property) (artemis.wrappers.OutputCollectionWrapper property) (artemis.wrappers.OutputDatasetWrapper property) (artemis.wrappers.OutputFileWrapper property) (artemis.wrappers.WorkFloeWrapper property)

IMAGE_FILE ocli-packages-import-from-orion-file command line option ocli-packages-upload-package-image command line option in-memory in_orion() (in module orionclient.session) InChI InChIKey input_ports() (floe.api.cubes.Cube method) INPUT_QUERY ocli-molsearch-query-create-substructure command line option InputMolFieldParameter (class in orionplatform.parameters.fields) InputSystemTagParameter (class in orionplatform.parameters.base) InstanceGroup (class in orionclient.types) IntegerFieldParameter (class in orionplatform.parameters.fields) IntegerParameter (class in floe.api.parameters) internals cycles InvalidAPIVersion InvalidCredentials Iridium is_authenticated() (orionclient.session.OrionSession method) is_empty() (datarecord.OERecord method) is_input() (floe.api.parameters.BaseParameter method) is_na() (datarecord.OERecord method) is_output() (floe.api.parameters.BaseParameter method) is_subset_of() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method)

J

job scheduling tag

JSON json() (floe.api.parameters.BaseParameter method) (floe.api.parameters.ParameterGroup method) JSONParameter (class in floe.api.parameters)

L

leave_project() (orionclient.session.OrionSession method) LedgerEntry (class in orionclient.types) LINGO LinkFieldParameter (class in orionplatform.parameters.fields) list_resources() (orionclient.session.OrionSession method) list_shards() (orionclient.types.ShardCollection method) list_shares() (orionclient.session.OrionSession method)

list_tags() (orionclient.session.OrionSession method) load() (orionclient.types.MolsearchDatabase method) logs (artemis.wrappers.WorkFloeWrapper property) logs() (orionclient.types.MolsearchDatabase method) (orionclient.types.ServiceTask method) (orionclient.types.WorkFloeJob method) ls_path() (orionclient.session.OrionSession method)

M

MACCS MANIFEST_PATH ocli-packages-create-environment-yaml command line option marching cubes MDL memory-mapped Merge() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) Meta (class in datarecord) Meta.Annotation (class in datarecord) Meta.Annotation.Author (in module datarecord) Meta.Annotation.Comments (in module datarecord) Meta.Annotation.Description (in module datarecord) Meta.Constraints (class in datarecord) Meta.Display (class in datarecord) Meta.Display.AsMean (in module datarecord) Meta.Display.AsRange (in module datarecord) Meta.Display.Chem (class in datarecord) Meta.Display.ColorBy (in module datarecord) Meta.Display.Hidden (in module datarecord) Meta.Display.HiddenByDefault (in module datarecord) Meta.Display.HiddenFrom3D (in module datarecord) Meta.Display.HiddenFromPlot (in module datarecord) Meta.Display.HiddenFromSpreadsheet (in module datarecord) Meta.Display.HiddenFromTileView (in module datarecord) Meta.Display.MarkerBy (in module datarecord) Meta.Display.Precision1 (in module datarecord) Meta.Display.Precision2 (in module datarecord) Meta.Display.Precision3 (in module datarecord) Meta.Display.Precision4 (in module datarecord) Meta.Display.PreferLog (in module datarecord) Meta.Display.SizeBy (in module datarecord) Meta.Display.Values (class in datarecord) Meta.Display.XAxis (in module datarecord) Meta.Display.YAxis (in module datarecord) Meta.Flags (class in datarecord) Meta.Flags.Calculated (in module datarecord) Meta.Flags.Categorical (in module datarecord) Meta.Flags.Deprecated (in module datarecord) Meta.Flags.DoNotSave (in module datarecord) Meta.Flags.Experimental (in module datarecord) Meta.Flags.GenericData (in module datarecord) Meta.Flags.ID (in module datarecord) Meta.Flags.Independent (in module datarecord) Meta.Flags.Invalid (in module datarecord) Meta.Flags.Optional (in module datarecord) Meta.Flags.Ordinal (in module datarecord) Meta.Flags.PDBData (in module datarecord) Meta.Flags.Predicted (in module datarecord) Meta.Flags.Range (in module datarecord) Meta.Flags.Readonly (in module datarecord) Meta.Flags.SDData (in module datarecord) Meta.Flags.UserCreated (in module datarecord) Meta.Hints (class in datarecord) Meta.Hints.Chem (class in datarecord) Meta.Hints.Chem.ChemicalName (in module datarecord) Meta.Hints.Chem.Conformer (in module datarecord) Meta.Hints.Chem.CXSMILES (in module datarecord) Meta.Hints.Chem.DNASequence (in module datarecord) Meta.Hints.Chem.FingerPrint (in module datarecord) Meta.Hints.Chem.GraphMol (in module datarecord) Meta.Hints.Chem.InChi (in module datarecord) Meta.Hints.Chem.InChiKey (in module datarecord) Meta.Hints.Chem.Ligand (in module datarecord) Meta.Hints.Chem.Markush (in module datarecord) Meta.Hints.Chem.MolReference (in module datarecord) Meta.Hints.Chem.OrionMolURL (in module datarecord) Meta.Hints.Chem.PrimaryMol (in module datarecord) Meta.Hints.Chem.PrimaryTarget (in module datarecord) Meta.Hints.Chem.Protein (in module datarecord) Meta.Hints.Chem.ProteinSequence (in module datarecord) Meta.Hints.Chem.Query (in module datarecord) Meta.Hints.Chem.Reaction (in module datarecord) Meta.Hints.Chem.Receptor (in module datarecord) Meta.Hints.Chem.RNASequence (in module datarecord) Meta.Hints.Chem.RotorOffsetCompression (in module datarecord) Meta.Hints.Chem.SelectivityTarget (in module datarecord) Meta.Hints.Chem.SMARTS (in module datarecord) Meta.Hints.Chem.SMILES (in module datarecord) Meta.Hints.Chem.Virtual (in module datarecord) Meta.Hints.Chem.VirtualID (in module datarecord) Meta.Hints.ClusterHead (in module datarecord) Meta.Hints.ClusterID (in module datarecord) Meta.Hints.ClusterX (in module datarecord) Meta.Hints.ClusterY (in module datarecord) Meta.Hints.Date (in module datarecord) Meta.Hints.Image (in module datarecord) Meta.Hints.Image_JPG (in module datarecord) Meta.Hints.Image_PNG (in module datarecord) Meta.Hints.Image_SVG (in module datarecord) Meta.Hints.ImageURL (in module datarecord) Meta.Hints.LargerValuesBetter (in module datarecord) Meta.Hints.ShardID (in module datarecord) Meta.Hints.SmallerValuesBetter (in module datarecord) Meta.Hints.URL (in module datarecord) Meta.Limits (class in datarecord) Meta.Limits.Lower (in module datarecord) Meta.Limits.Upper (in module datarecord) Meta.Relations (class in datarecord) Meta.Relations.AppliesTo (in module datarecord) Meta.Relations.Chem (class in datarecord) Meta.Relations.Chem.AtomDataFor (in module datarecord) Meta.Relations.Chem.BondDataFor (in module datarecord) Meta.Relations.Chem.ConfDataFor (in module datarecord) Meta.Relations.Chem.LigandFor (in module datarecord) Meta.Relations.Chem.MolDataFor (in module datarecord) Meta.Relations.Chem.QueryFor (in module datarecord) Meta.Relations.Chem.ReceptorFor (in module datarecord) Meta.Relations.ChildOf (in module datarecord) Meta.Relations.CommentFor (in module datarecord) Meta.Relations.DetailsFor (in module datarecord) Meta.Relations.ErrorsFor (in module datarecord) Meta.Relations.GroupID (in module datarecord) Meta.Relations.MeanFor (in module datarecord) Meta.Relations.MeasurementLowerLimitFor (in module datarecord) Meta.Relations.MeasurementUpperLimitFor (in module datarecord) Meta.Relations.QualifierFor (in module datarecord) Meta.Relations.ReplacedBy (in module datarecord) Meta.Relations.SplitFrom (in module datarecord) Meta.Relations.UnitsFor (in module datarecord) Meta.Source (class in datarecord) Meta.Source.ID (in module datarecord) Meta.Source.JobID (in module datarecord) Meta.Source.Query (in module datarecord) Meta.Source.ServiceID (in module datarecord) Meta.Source.Version (in module datarecord) Meta.Units (class in datarecord) Meta.Units.Amount (class in datarecord) Meta.Units.Amount.Item (in module datarecord) Meta.Units.Amount.Mol (in module datarecord) Meta.Units.Angle (class in datarecord) Meta.Units.Angle.deg (in module datarecord) Meta.Units.Angle.rad (in module datarecord) Meta.Units.Charge (class in datarecord) Meta.Units.Charge.Coulomb (in module datarecord) Meta.Units.Charge.PlanckCharge (in module datarecord) Meta.Units.Concentration (class in datarecord) Meta.Units.Concentration.M (in module datarecord) Meta.Units.Concentration.mg_per_kg (in module datarecord) Meta.Units.Concentration.mM (in module datarecord) Meta.Units.Concentration.ng_per_ml (in module datarecord) Meta.Units.Concentration.nM (in module datarecord)

Meta.Units.Concentration.ppb (in module datarecord) Meta.Units.Concentration.ppm (in module datarecord) Meta.Units.Concentration.uM (in module datarecord) Meta.Units.Current (class in datarecord) Meta.Units.Current.A (in module datarecord) Meta.Units.Current.mA (in module datarecord) Meta.Units.Current.uA (in module datarecord) Meta.Units.Density (class in datarecord) Meta.Units.Density.e_per_A3 (in module datarecord) Meta.Units.Density.n_per_A3 (in module datarecord) Meta.Units.DipoleMoment (class in datarecord) Meta.Units.DipoleMoment.D (in module datarecord) Meta.Units.DipoleMoment.statCm (in module datarecord) Meta.Units.ElectricalPotential (class in datarecord) Meta.Units.ElectricalPotential.V (in module datarecord) Meta.Units.Energy (class in datarecord) Meta.Units.Energy.Cal (in module datarecord) Meta.Units.Energy.eV (in module datarecord) Meta.Units.Energy.Hartree (in module datarecord) Meta.Units.Energy.J (in module datarecord) Meta.Units.Energy.kCal (in module datarecord) Meta.Units.Energy.kCal_per_mol (in module datarecord) Meta.Units.Energy.kJ (in module datarecord) Meta.Units.Energy.kJ_per_mol (in module datarecord) Meta.Units.Energy.kT (in module datarecord) Meta.Units.Energy.RT (in module datarecord) Meta.Units.Entropy (class in datarecord) Meta.Units.Entropy.kCal_per_mol_K (in module datarecord) Meta.Units.Entropy.kJ_per_mol_K (in module datarecord) Meta.Units.Force (class in datarecord) Meta.Units.Force.dyn (in module datarecord) Meta.Units.Force.eV_per_A (in module datarecord) Meta.Units.Force.H_per_Bohr (in module datarecord) Meta.Units.Force.kCal_per_mol_A (in module datarecord) Meta.Units.Force.kCal_per_mol_nm (in module datarecord) Meta.Units.Force.kCal_per_mol_rad (in module datarecord) Meta.Units.Force.kJ_per_mol_A (in module datarecord) Meta.Units.Force.kJ_per_mol_nm (in module datarecord) Meta.Units.Force.kJ_per_mol_rad (in module datarecord) Meta.Units.Force.N (in module datarecord) Meta.Units.Frequency (class in datarecord) Meta.Units.Frequency.GHz (in module datarecord) Meta.Units.Frequency.Hz (in module datarecord) Meta.Units.Frequency.kHz (in module datarecord) Meta.Units.Frequency.MHz (in module datarecord) Meta.Units.Frequency.Recip_cm (in module datarecord) Meta.Units.Frequency.THz (in module datarecord) Meta.Units.Length (class in datarecord) Meta.Units.Length.A (in module datarecord) Meta.Units.Length.Bohr (in module datarecord) Meta.Units.Length.m (in module datarecord) Meta.Units.Length.mm (in module datarecord) Meta.Units.Length.nm (in module datarecord) Meta.Units.Length.um (in module datarecord) Meta.Units.MagneticField (class in datarecord) Meta.Units.MagneticField.G (in module datarecord) Meta.Units.MagneticField.T (in module datarecord) Meta.Units.Mass (class in datarecord) Meta.Units.Mass.Da (in module datarecord) Meta.Units.Mass.g (in module datarecord) Meta.Units.Mass.kg (in module datarecord) Meta.Units.Mass.mg (in module datarecord) Meta.Units.Mass.ng (in module datarecord) Meta.Units.Mass.ug (in module datarecord) Meta.Units.Power (class in datarecord) Meta.Units.Power.W (in module datarecord) Meta.Units.Pressure (class in datarecord) Meta.Units.Pressure.atm (in module datarecord) Meta.Units.Pressure.bar (in module datarecord) Meta.Units.Pressure.kPa (in module datarecord) Meta.Units.Pressure.mmHg (in module datarecord) Meta.Units.Pressure.Pa (in module datarecord) Meta.Units.Pressure.torr (in module datarecord) Meta.Units.Temp (class in datarecord) Meta.Units.Temp.C (in module datarecord) Meta.Units.Temp.F (in module datarecord) Meta.Units.Temp.K (in module datarecord) Meta.Units.Time (class in datarecord) Meta.Units.Time.days (in module datarecord) Meta.Units.Time.fs (in module datarecord) Meta.Units.Time.hours (in module datarecord) Meta.Units.Time.min (in module datarecord) Meta.Units.Time.ms (in module datarecord) Meta.Units.Time.ns (in module datarecord) Meta.Units.Time.ps (in module datarecord) Meta.Units.Time.s (in module datarecord) Meta.Units.Time.us (in module datarecord) Meta.Units.Velocity (class in datarecord) Meta.Units.Velocity.A_per_ps (in module datarecord) Meta.Units.Velocity.m_per_s (in module datarecord) Meta.Units.Volume (class in datarecord) Meta.Units.Volume.A3 (in module datarecord) Meta.Units.Volume.l (in module datarecord) Meta.Units.Volume.ml (in module datarecord) Meta.Units.Volume.nl (in module datarecord) Meta.Units.Volume.ul (in module datarecord) metadata (artemis.wrappers.CollectionWrapper property) methods cube mkdir() (artemis.packaging.OrionTestPackage method) MMDS modify_parameter() (floe.api.cubes.Cube method) modify_parameter_group() (floe.api.cubes.Cube method) module artemis artemis.packaging artemis.test artemis.wrappers datarecord drconvert drconvert.pandas drconvert.parquet floe.api.cubes floe.api.parameters orion-platform orionclient.exceptions orionclient.helpers orionclient.links orionclient.session orionclient.types orionclient.utils orionplatform.exceptions orionplatform.mixins orionplatform.parameters.base orionplatform.parameters.collections orionplatform.parameters.datasets orionplatform.parameters.fields orionplatform.parameters.files orionplatform.parameters.secrets modules MOL MolConversionOptions (class in drconvert) molecular spreadsheet molecule sketcher MolFieldParameter (class in orionplatform.parameters.fields) MolFileConverter (class in drconvert) MolsearchDatabase (class in orionclient.types) MolsearchQuery (class in orionclient.types) Monte Carlo multistage workflows

N

neighbors() (floe.api.cubes.Cube method) nested workflows

nonterminal atom NotEnoughDiskError NotFoundResponse

O

ocli-cost-export command line option --download --no-download --notify --output-path --redact-project-names --report-type USERS ocli-molsearch-db-create command line option --auth-secret --collection --cpu --disk-space --display-name --gpu --instance-type --is-proxy --memory-mb --pools --search-type --section --server-address --server-is-remote --verify-ssl-cert ocli-molsearch-db-delete command line option DATABASE ocli-molsearch-db-help command line option CMD ocli-molsearch-db-info command line option DATABASE ocli-molsearch-db-list command line option --limit --offset FILTERS ocli-molsearch-db-list-shares command line option IDENTIFIER ocli-molsearch-db-load command line option DATABASE ocli-molsearch-db-logs command line option --from --until IDENTIFIER ocli-molsearch-db-share command line option --delete --share --write IDENTIFIER SHARE_IDS SHARE_TYPE ocli-molsearch-db-unload command line option DATABASE ocli-molsearch-db-unshare command line option IDENTIFIER SHARE_IDS SHARE_TYPE ocli-molsearch-db-update command line option --display-name --section DATABASE ocli-molsearch-query-cancel command line option QUERY ocli-molsearch-query-create-exact command line option --max-hits --name --project --search-type --wait DATABASE QUERY ocli-molsearch-query-create-fastrocs command line option --max-hits --name --orientation --project --random-starts --shape-only --sim-type --tversky-alpha --wait DATABASE QUERY_MOL_FILE_PATH ocli-molsearch-query-create-graphsim command line option --cutoff --fpname --max-hits --measure --name --project --wait DATABASE QUERY ocli-molsearch-query-create-help command line option CMD ocli-molsearch-query-create-substructure command line option --aliphatic-constraint --cancel-after --isotope-constraint --max-hits --name --project --stereo-constraint --subsearch_query_type --topology-constraint --wait DATABASE INPUT_QUERY ocli-molsearch-query-create-title command line option --name --project DATABASE TITLE ocli-molsearch-query-delete command line option QUERY ocli-molsearch-query-download command line option --exclude --ids FILE QUERY ocli-molsearch-query-export command line option --background --format --ids --name --path --project QUERY ocli-molsearch-query-help command line option CMD ocli-molsearch-query-info command line option QUERY ocli-molsearch-query-list command line option --limit --offset --programmatic --project --query-type ocli-molsearch-query-list-results command line option --limit --offset QUERY ocli-molsearch-query-smiles command line option TITLE ocli-molsearch-query-update command line option --name --saved QUERY ocli-packages-check-image command line option --verbose -v ocli-packages-create-environment-yaml command line option --output-path -o MANIFEST_PATH ocli-packages-delete command line option IDENTIFIER ocli-packages-deprecate command line option IDENTIFIER ocli-packages-download command line option FILE IDENTIFIER ocli-packages-environment command line option IDENTIFIER ocli-packages-export-base-image command line option --download --no-download --no-notify --notify --output-path -o BASE_IMAGE ocli-packages-help command line option CMD ocli-packages-import-from-orion-file command line option --delete-image-file -d IMAGE_FILE ocli-packages-import-from-registry command line option --image-tag --pull-username --registry-url --secret -r -s -t -u

ocli-packages-info command line option IDENTIFIER ocli-packages-init command line option --description --email --full-name --module-name --project-name --project-slug --service --version ocli-packages-inspection command line option IDENTIFIER ocli-packages-list command line option --limit --offset FILTERS ocli-packages-list-shares command line option IDENTIFIER ocli-packages-list-tags command line option IDENTIFIER ocli-packages-share command line option --delete --share --write IDENTIFIER SHARE_IDS SHARE_TYPE ocli-packages-show-dockerfile command line option --output-path -o ocli-packages-tag command line option --project IDENTIFIER TAGS ocli-packages-undeprecate command line option IDENTIFIER ocli-packages-unshare command line option IDENTIFIER SHARE_IDS SHARE_TYPE ocli-packages-untag command line option IDENTIFIER TAGS ocli-packages-upload command line option PACKAGE_PATH ocli-packages-upload-package-image command line option --delete-image-file --path -d -p IMAGE_FILE ocli-services-spec-help command line option CMD ocli-services-spec-info command line option IDENTIFIER ocli-services-spec-list command line option --limit --name --offset FILTERS ocli-services-spec-list-shares command line option IDENTIFIER ocli-services-spec-share command line option --delete --share --write IDENTIFIER SHARE_IDS SHARE_TYPE ocli-services-spec-unshare command line option IDENTIFIER SHARE_IDS SHARE_TYPE ocli-services-task-create command line option --description --external --name --specification --url ocli-services-task-delete command line option IDENTIFIER ocli-services-task-help command line option CMD ocli-services-task-info command line option IDENTIFIER ocli-services-task-list command line option --limit --name --offset FILTERS ocli-services-task-list-shares command line option IDENTIFIER ocli-services-task-logs command line option --from --until IDENTIFIER ocli-services-task-share command line option --delete --share --write IDENTIFIER SHARE_IDS SHARE_TYPE ocli-services-task-unshare command line option IDENTIFIER SHARE_IDS SHARE_TYPE ocli-services-task-update command line option --description --name --state IDENTIFIER OEB OEDUConverter (class in drconvert) OEField (class in datarecord) OEFieldMeta (class in datarecord) OEMatchField (class in datarecord) OEMolRecord (class in datarecord) OEPrimaryMolField (class in datarecord) OEReadRecord() (in module datarecord) OERecord (class in datarecord) OERecordMeta (class in datarecord) OEWriteRecord() (in module datarecord) open() (orionclient.types.ShardCollection method) order cube execution Orion back end Orion Platform orion-platform module orionclient.exceptions module orionclient.helpers module orionclient.links module orionclient.session module orionclient.types module orionclient.utils module OrionConnectionError OrionError OrionLink (class in orionclient.links) OrionLinkError orionplatform.exceptions module orionplatform.mixins module orionplatform.parameters.base module orionplatform.parameters.collections module orionplatform.parameters.datasets module orionplatform.parameters.fields module orionplatform.parameters.files module orionplatform.parameters.secrets module OrionServiceError OrionSession (class in orionclient.session) OrionTag (class in orionclient.types) OrionTestPackage (class in artemis.packaging) OrionTimeout OrionUser (class in orionclient.types) output_ports() (floe.api.cubes.Cube method) OutputCollectionWrapper (class in artemis.wrappers) OutputDatasetWrapper (class in artemis.wrappers) OutputFileWrapper (class in artemis.wrappers) OutputMolFieldParameter (class in orionplatform.parameters.fields) outputs() (artemis.wrappers.WorkFloeWrapper method)

P

package package() (artemis.packaging.OrionTestPackage method) PACKAGE_PATH ocli-packages-upload command line option packages packaging cube parallel cube cube group ParallelComputeCube (class in floe.api.cubes) ParallelCubeGroup (class in floe.api.cubes) ParallelMixin (class in floe.api.cubes) parameter_groups() (floe.api.cubes.Cube method) ParameterConnection (class in floe.api.cubes) ParameterException ParameterGroup (class in floe.api.parameters)

parameterize_workfloe() (in module orionclient.helpers.parameterize) parameters cube parameters() (floe.api.cubes.Cube method) parquet_to_dataframe() (in module drconvert.parquet) path (artemis.wrappers.OutputDatasetWrapper property) (artemis.wrappers.OutputFileWrapper property) PlatformException popcount port cube preliminary API PrimaryMolFieldParameter (class in orionplatform.parameters.fields) process() (floe.api.cubes.ComputeCube method) project Project (class in orionclient.types) PromotedParameterGroup (class in floe.api.parameters)

Q

QUERY ocli-molsearch-query-cancel command line option ocli-molsearch-query-create-exact command line option ocli-molsearch-query-create-graphsim command line option ocli-molsearch-query-delete command line option ocli-molsearch-query-download command line option ocli-molsearch-query-export command line option ocli-molsearch-query-info command line option ocli-molsearch-query-list-results command line option ocli-molsearch-query-update command line option

QUERY_MOL_FILE_PATH ocli-molsearch-query-create-fastrocs command line option

R

raster image RateLimitedResponse read_record_file_to_dataframe() (in module drconvert.pandas) reason (artemis.wrappers.WorkFloeWrapper property) receptor binding receptors record_file_to_parquet() (in module drconvert.parquet) record_to_dataframe() (in module drconvert.pandas) record_to_du() (drconvert.drconvert method) record_to_mol() (drconvert.drconvert method) RecordBytesInputPort (class in orionplatform.ports) RecordBytesOutputPort (class in orionplatform.ports) RecordConvertToCSV (class in drconvert) RecordConvertToMols (class in drconvert) RecordConvertToOEDU (class in drconvert) RecordInputPort (class in orionplatform.ports) RecordLink (class in orionclient.links) RecordOutputPort (class in orionplatform.ports)

RecordPortsMixin (class in orionplatform.mixins) records() (artemis.wrappers.OutputDatasetWrapper method) (orionclient.types.Dataset method) refresh_resource() (orionclient.session.OrionSession method) refresh_resource_until() (orionclient.session.OrionSession method) regression fit remove_attribute() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) remove_directory() (artemis.packaging.OrionTestPackage method) remove_file() (artemis.packaging.OrionTestPackage method) remove_option() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) remove_paths() (orionclient.session.OrionSession method) replace_parameter() (floe.api.parameters.ParameterGroup method) (floe.api.parameters.PromotedParameterGroup method) retrieve_token() (orionclient.session.OrionSession method) ROC curve rotatable bond

S

save() (artemis.packaging.OrionTestPackage method) scheduling job script scripts SDF Secret (class in orionclient.types) SecretInputParameter (class in orionplatform.parameters.secrets) SecretStream (class in orionplatform.parameters.secrets) send_inputs() (floe.test.CubeTestRunner method) serialization workflow ServiceSpec (class in orionclient.types) ServiceTask (class in orionclient.types) set_atom_record() (datarecord.OEMolRecord method) set_attribute() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) set_attributes() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) set_bond_record() (datarecord.OEMolRecord method) set_bytes() (datarecord.OERecord method) set_conf_record() (datarecord.OEMolRecord method) set_initializer_input() (floe.test.CubeTestRunner method) set_mol() (datarecord.OEMolRecord method) set_mol_reference() (datarecord.OEMolRecord method) set_option() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) set_options() (datarecord.OEFieldMeta method) (datarecord.OERecordMeta method) set_record_meta() (datarecord.OERecord method) set_reference() (datarecord.OERecord method) set_source_id() (datarecord.OERecord method) set_value() (orionclient.types.Secret method) setUpClass() (artemis.test.FloeTestCase class method) shard Shard (class in orionclient.types) shard collections ShardCollection (class in orionclient.types) ShardInputPort (class in orionplatform.ports) ShardLink (class in orionclient.links) ShardOutputPort (class in orionplatform.ports) ShardPortsMixin (class in orionplatform.mixins) shards() (orionplatform.parameters.collections.CollectionStream method)

SHARE_IDS ocli-molsearch-db-share command line option ocli-molsearch-db-unshare command line option ocli-packages-share command line option ocli-packages-unshare command line option ocli-services-spec-share command line option ocli-services-spec-unshare command line option ocli-services-task-share command line option ocli-services-task-unshare command line option share_resource() (orionclient.session.OrionSession method) SHARE_TYPE ocli-molsearch-db-share command line option ocli-molsearch-db-unshare command line option ocli-packages-share command line option ocli-packages-unshare command line option ocli-services-spec-share command line option ocli-services-spec-unshare command line option ocli-services-task-share command line option ocli-services-task-unshare command line option SinkCube (class in floe.api.cubes) size (artemis.wrappers.OutputFileWrapper property) sketcher sleep() (orionclient.utils.Backoff method) SMARTS SMILES SmilesFileConverter (class in drconvert) SMIRKS SourceCube (class in floe.api.cubes) spreadsheet molecular stable API start() (artemis.wrappers.WorkFloeWrapper method) (floe.test.CubeTestRunner method) (orionclient.types.WorkFloeJob class method) stat_path() (orionclient.session.OrionSession method) state (artemis.wrappers.WorkFloeWrapper property) status (artemis.wrappers.WorkFloeWrapper property) stereo atom stereo bond StringFieldParameter (class in orionplatform.parameters.fields) StringParameter (class in floe.api.parameters) structural key SVG

T

tag job tag_resource() (orionclient.session.OrionSession method) tagging TAGS ocli-packages-tag command line option ocli-packages-untag command line option Tanimoto TemporaryPath (class in orionclient.utils) testing cube thisown (datarecord.OEFieldMeta property) (datarecord.OEMolRecord property) (datarecord.OEPrimaryMolField property) (datarecord.OERecord property) (datarecord.OERecordMeta property)

TITLE ocli-molsearch-query-create-title command line option ocli-molsearch-query-smiles command line option Token (class in orionclient.types) trigger_debug_export() (orionclient.types.WorkFloeJob method) try_hard_to_create_shard() (in module orionclient.helpers.collections) try_hard_to_download_shard() (in module orionclient.helpers.collections) type cube Types (class in datarecord) Types.Record (in module datarecord) Types.RecordVec (in module datarecord)

U

unload() (orionclient.types.MolsearchDatabase method) unshare_resource() (orionclient.session.OrionSession method) untag_resource() (orionclient.session.OrionSession method) update() (orionclient.types.Shard method) (orionclient.types.ShardCollection method) update_resource() (orionclient.session.OrionSession method) upload() (orionclient.types.Dataset class method) (orionclient.types.File class method) (orionclient.types.Shard method) (orionclient.types.WorkFloePackage class method)

upload_file() (orionclient.types.Shard method) upload_part() (orionclient.types.File method) user delete UserProfile (class in orionclient.types) USERS ocli-cost-export command line option using_orion() (artemis.wrappers method)

V

validate() (floe.api.parameters.BaseParameter method) (floe.api.parameters.DecimalParameter method) (floe.api.parameters.IntegerParameter method) (floe.api.parameters.StringParameter method) (orionplatform.parameters.base.InputSystemTagParameter method)

validate_authentication() (orionclient.session.OrionSession method) ValidationError vector image

W

wait() (artemis.wrappers.WorkFloeWrapper method) wait_on() (floe.api.cubes.Cube method) WorkFloeJob (class in orionclient.types) WorkFloePackage (class in orionclient.types) WorkFloeSpec (class in orionclient.types) WorkFloeWrapper (class in artemis.wrappers) workflow serialization

workflows cyclic multistage nested write() (floe.api.cubes.SinkCube method) (orionclient.types.Dataset method)

Z

zwitterion

zwitterionic