FastROCS Plus

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/FastROCS

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/DB Search/FastROCS

  • Task-based/Virtual Screening - Ligand-Based

Description

Overlays a FastROCS collection onto up to 200 shape or molecule queries and outputs a single FastROCS hit list using the best result (i.e., highest similarity to any query) to rank molecules. This floe also optionally re-scores the top FastROCS molecules with ROCS, Docking and a consensus of both, creating a separate hit list for each.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input Query Dataset(s) (input_query_datasets): One or more datasets containing molecules and/or shape queries. Queries can come from multiple datasets or a single dataset with one or more queries. The ‘2D Sketcher’ can also be used to create a query, in which case a reasonable set of conformers of the sketched molecule will be generated and used as queries (see ‘Query Conformer Generation Mode’ option parameter). The total number of queries is limited to 200. Compute costs will scale roughly linearly with the number of queries PLUS 10,i.e., cost is roughly proportional to <number of queries + 10>.

  • Required

  • Type: data_source

FastROCS Input Collection (fastrocs_input_collection): FastROCS collection to screen against. OpenEye supplied several pre-generated vendor molecule collections in Organization Data. The ‘Prepare Giga Collections’ or ‘Giga Docking Collection to Hi-res FastROCS Collection’ floes can also be used to create suitable collections for this floe.

  • Required

  • Type: collection_source

Design Unit(s) (Optional) (design_units_optional): If a design unit is supplied here the top scoring molecules from FastROCS will be docked to the design unit and the results outputted in a separate hit list. Up to 10 design units can be supplied from one or more datasets. If multiple design units are supplied the specific a single docking hit list is still created using the score from the best design unit for each docked molecule (see the ‘Dock Re-scoring Mode’ parameter description).’

  • Type: data_source

Shape Query(s) for ROCS Re-scoring (Optional) (shape_querys_for_rocs_re_scoring_optional): Optional dataset(s) with one or more shape queries to be used for the ROCS re-scoring IN PLACE of the queries passed to ‘Input Query Dataset(s)’. This dataset only accepts shape queries, not molecule queries. This parameter allows the ROCS re-scoring step to use shape queries that are not supported by FastROCS (e.g. shape queries with grids). If a dataset(s) is supplied to this parameter ROCS re-scoring will automatically be turned on and the setting of the ‘Options: Re-scoring -> ROCS Re-scoring Mode’ parameter will be ignored.

  • Type: data_source

Outputs

FastROCS Hit List Dataset (fastrocs_hit_list_dataset): Output dataset that will contain the top hits directly from FastROCS.

  • Required

  • Type: dataset_out

  • Default: FastROCS Hit List

FastROCS Novelty Hit List Dataset (fastrocs_novelty_hit_list_dataset): Molecules in this output dataset will be sorted by FastROCS score. The molecule in this hit list contain molecules that tend to have high 3D similarity and low 2D similarity to the query(s).

  • Required

  • Type: dataset_out

  • Default: FastROCS Novelty Hit List

ROCS Hit List Dataset (rocs_hit_list_dataset): Output hit list dataset from ROCS re-scoring of the top FastROCS hits. This dataset will not be created if the ‘ROCS Re-scoring Mode’ parameter is set to ‘Off’.

  • Required

  • Type: dataset_out

  • Default: ROCS Hit List

ROCS Novelty Hit List Dataset (rocs_novelty_hit_list_dataset): Molecules in this output dataset will be sorted by ROCS score. The molecule in this hit list contain molecules that tend to have high 3D similarity and low 2D similarity to the query(s).

  • Required

  • Type: dataset_out

  • Default: ROCS Novelty Hit List

Dock Hit List Dataset (dock_hit_list_dataset): Output hit list dataset from docking the top FastROCS hits. This dataset will only be created if at least one design unit is supplied to the ‘Design Unit(s) (Optional)’ parameter.

  • Required

  • Type: dataset_out

  • Default: Dock Hit List

Consensus ROCS Hit List Dataset (consensus_rocs_hit_list_dataset): Consensus output hit list ranked by ROCS Combo Tanimoto. This hit list will only be created if both ROCS and Dock re-scoring are enabled (see the ‘Design Unit(s) (Optional)’ and ‘ROCS Re-scoring Mode’ parameters).

  • Required

  • Type: dataset_out

  • Default: Consensus ROCS Hit List

Consensus Dock Hit List Dataset (consensus_dock_hit_list_dataset): Consensus output hit list ranked by docking score. This hit list will only be created if both ROCS and Dock re-scoring are enabled (see the ‘Design Unit(s) (Optional)’ and ‘ROCS Re-scoring Mode’ parameters).

  • Required

  • Type: dataset_out

  • Default: Consensus Dock Hit List

Output Query Dataset (output_query_dataset): This output dataset will contain a copy of the input queries (see the ‘Input Query Dataset(s)’ parameter). In addition to the query, this dataset will include an integer id field that also appears in the ROCS/FastROCS hit list records so the query associated with the molecule can be identified (This is primarily useful when multiple queries are used). Note that if the ‘Shape Query(s) for ROCS Re-scoring (Optional)’ is specified this dataset will not contain the queries used for FastROCS but not ROCS re-scoring (see the ‘Outputs-> Output ROCS Re-score Shape Query Dataset’ parameter in that case).

  • Required

  • Type: dataset_out

  • Default: FastROCS Queries

Output ROCS Re-score Shape Query Dataset (output_rocs_re_score_shape_query_dataset): This output dataset will contain a copy of the input shape query(s) set to ‘Shape Query(s) for ROCS Re-scoring (Optional)’. If the ‘Shape Query(s) for ROCS Re-scoring (Optional)’ is not specified this dataset will not be createdbecause the query(s) for ROCS re-scoring will be the same as those for FastROCS (see the ‘Outputs -> Output Query Dataset’ parameter).In addition to the query, this dataset will include and integer id field that also appears in the ROCS hit list records so the query associated with the molecule can be identified. (This is primarily useful when multiple shape queries are used.)

  • Required

  • Type: dataset_out

  • Default: ROCS Re-score Shape Queries

Design Unit Dataset (design_unit_dataset): Output dataset with a copy of the input design unit(s) (see the ‘Design Unit(s) (Optional)’ parameter). In addition to the design unit this dataset will include an integer id field. This id will also appear in the dock hit list records so the design unit associated with the molecule can be identified. (This is primarily useful when multiple design units are used.)This dataset will only be created if design units are sent to this floe.

  • Required

  • Type: dataset_out

  • Default: Design Units

Raw Results Collection (Optional) (raw_results_collection_optional): The name of an output collection that will contain a number of molecules approximately equal to the setting of ‘Options: Advanced -> Number of Molecules to Re-score’. If either ROCS or Docking re-scoring is turned on (ROCS is on by default) this collection will contain the entire set of top scoring FastROCS molecules that were re-scoring. If both ROCS and Docking re-scoring are turned off the collection will contain the top scoring FastROCS molecules. The format of the individual shards of the collection are .oedb which, if downloaded locally, can be read with the toolkits OEReadMolRecords function. If this parameter is not specified this output collection will not be created.

  • Type: collection_sink

Temporary Collection (temporary_collection): This collection is created by the floe for internal use during the run and is automatically deleted by the floe when it finishes.

  • Required

  • Type: collection_sink

  • Default: FastROCS Temporary Collection

Options

Hit List Size (hit_list_size): Size of all output hit lists. (Max value 100,000, Min Value 1000).

  • Required

  • Type: integer

  • Default: 10000

FastROCS Similarity Type (fastrocs_similarity_type): Type of FastROCS Similarity to use to rank molecules sent to the FastROCS, ROCS and consensus ROCS hit lists. This method will also be used by ROCS re-scoring if it is enabled (ROCS re-scoring is enabled by default) and shape queries explicitly for the ROCS re-scoring have not been set using the ‘Shape Query(s) for ROCS Re-scoring’ parameter.

  • Type: string

  • Default: Tanimoto Combo

  • Choices: [‘Tanimoto Combo’, ‘Ref Tversky’, ‘Fit Tversky’, ‘Shape Tanimoto’, ‘Shape Ref Tversky’, ‘Shape Fit Tversky’]

Options: Query

Query Conformer Generation Mode (query_conformer_generation_mode): Method used to generate conformer(s) of the molecules queries (shape queries are always accepted as is).

‘input’: Uses conformer of the molecule query as is (molecule queries without coordinates will fail in this mode).

‘omega’: Generate query molecule conformations with omega.

‘dock’: Use the best pose of the query molecule docked to the design unit(s) This mode requires that design units be supplied to the ‘Design Unit(s) (Optional)’ parameter.

‘auto’ : Molecule queries with 3d coordinates will be used as is. Molecules queries without 3d coordinates will used ‘dock’ mode if design unit(s) are supplied to the floe and ‘omega’ mode otherwise.

  • Type: string

  • Default: auto

  • Choices: [‘input’, ‘omega’, ‘dock’, ‘auto’]

Multi Conformer Mol Query Mode (multi_conformer_mol_query_mode): Controls how query molecules with multiple conformers are handled.

‘fail’: records with molecule with multiple conformers will fail.

‘active’: The active conformer of the molecule (this is typically the first conformer and often lowest energy) will be used.

‘first10’ : The first 10 conformers of the molecule will be used.

‘limit’: All conformers of the molecule up to this cubes limit for total queries.

‘all’ : all conformers of the molecule will be used as queries.

WARNING: using ‘all’ or ‘limit’ can significantly increase the cost of the floe.

  • Type: string

  • Default: first10

  • Choices: [‘fail’, ‘active’, ‘first10’, ‘limit’, ‘all’]

Options: FastROCS

Number of FastROCS Random Starts (number_of_fastrocs_random_starts): If specified FastROCS will used the specified number of random starting orientations for each conformer being overlayed with FastROCS. If unspecified the default 4 inertial starts will be used. Compute time (i.e., cost) scales roughly linearly with the number of starts.

  • Type: integer

Shape Only FastROCS Overlay (shape_only_fastrocs_overlay): If set to ‘On’ FastROCS will overlay molecules using shape only ignoring color. If set to ‘Off’ FastROCS will overlay molecules using shape&color. Note that this parameters affects the overlay process, but not the scoring (e.g., the overlay can be done with shape while the scoring is done with shape and color). Also note that if either Fit or Referency Tversky scoring is selected (see ‘FastROCS Similarity Type’ parameter) the overlay will be done with shape only ignoring the setting of this flag.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Options: Re-scoring

Number of Molecules to Re-score (number_of_molecules_to_re_score): The number of top scoring molecules from FastROCS that will be sent to any of the enabled post-processing methods (ROCS and/or Docking). Note that the outputted hit lists will still be of the size specified by the ‘Hit List Size’ parameter, which is generally smaller than this number. Maximum allowed value 100,000,000. Minimum allowed value is 100,000.

  • Type: integer

  • Default: 100000

ROCS Re-scoring Mode (rocs_re_scoring_mode): Type of ROCS re-scoring to do on the top scoring molecule from FastROCS if ‘Shape Query(s) for ROCS Re-scoring (Optional)’ is not specified (if it is specified this parameter is ignored and ROCS rescoring will be done with the shape query(s)). ‘Off’ : Turns of ROCS re-scoring of the top FastROCS Molecules. ‘Best FastROCS Query’: Overlay molecules onto the query FastROCS selected as the best query for the molecule. ‘All Queries’: Overlay molecules onto all queries and output the best overlay. WARNING: ‘All Queries’ mode can result in significant compute costs if there are many queries and molecules to re-score.

  • Type: string

  • Default: Best FastROCS Query

  • Choices: [‘Off’, ‘Best FastROCS Query’, ‘All Queries’]

Number of ROCS Re-scoring Random Starts (number_of_rocs_re_scoring_random_starts): If specified ROCS re-scoring will used the specified number of random starting orientations for each conformer being overlayed. If unspecified the default 4 inertial starts will be used. Compute time scales roughly linearly with the number of starts.

  • Type: integer

ROCS Re-scoring Shape Query Similarity Type (rocs_re_scoring_shape_query_similarity_type): Similarity type to use in the ROCS Re-scoring step when shape queries for ROCS re-scoring have been set with the ‘Inputs -> Shape Query(s) for ROCS Re-scoring (Optional)’ parameter. This parameter is ignored if ‘Inputs -> Shape Query(s) for ROCS Re-scoring (Optional)’ is not set.

  • Type: string

  • Default: Tanimoto Combo

  • Choices: [‘Tanimoto Combo’, ‘Ref Tversky’, ‘Fit Tversky’, ‘Shape Tanimoto’, ‘Shape Ref Tversky’, ‘Shape Fit Tversky’]

Dock Re-scoring Mode (dock_re_scoring_mode): Docking method to use to dock the top scoring molecules from FastROCS when design units are supplied to the floe (see ‘Design Unit(s) Optional’ parameter). ‘Fred’ is the default structure based scoring method. ‘Hybrid’ biases the the docking towards poses that overlay the crystallographic ligand (the design unit(s) must have a bound ligand). ‘FastFred’ is a faster variant of ‘Fred’ (typically ~2x faster) that samples less and uses a simpler scoring function in the initial stages of docking. This parameter also determines how the ‘best design unit’ is selected when multiple design units are supplied to the floe. For ‘Fred’ and ‘FastFred’ mode ‘best design unit’ is the design unit with the best docking score, and for ‘Hybrid’ the ‘best design unit’ is the design unit with the most similar bound ligand. With multiple design units ‘Hybrid’ is a much more computationally efficient because each molecule is only docked once to the design unit with the most similar bound ligand, while ‘Fred’ and ‘FastFred’ modes dock each molecule to all the design units to determine which one gives the lowest score.

  • Type: string

  • Default: Fred

  • Choices: [‘Fred’, ‘Hybrid’, ‘Fast Fred’]

Consensus Max Pareto Rank (consensus_max_pareto_rank): When re-scoring with both docking and rocs each molecule will get a pareto dominance rank based on the docking score and rocs similarity. Molecules with a pareto dominance rank higher than this number will be filtered out of the consensus hit lists. Minimum allowed value 0. Maximum allowed value 10.

  • Type: integer

  • Default: 4

Options: Novelty

Novelty Fingerprint Type (novelty_fingerprint_type): Type of fingerprint to use to identify molecules that are 2D dissimilar to the query molecule in 2D space.

  • Type: string

  • Default: Circular

  • Choices: [‘Circular’, ‘Path’, ‘Tree’]

Novelty Pareto Max Rank (novelty_pareto_max_rank): In the pareto consensus for novelty this is the maximum pareto domiance rank that will be allowed. Setting this to higher values will cause more molecule to appear in the FastROCS and ROCS novelty hit lists. Max value 10

  • Type: integer

  • Default: 10

GPU Hardware

FastROCS Instance Type (fastrocs_instance_type): The instances excluded by default are known to be not cost effective for FastROCS.

  • Type: string

  • Default: !cdns,!g4dn.metal,!g5.12xlarge,!g5.24xlarge,!g5.48xlarge,!g4dn.12xlarge,!g3s.,!p3.

Spot instance policy for FastROCS GPU Instance. (spot_instance_policy_for_fastrocs_gpu_instance): To run on SPOT instances use the default setting of ‘preferred’. To run on ON-DEMAND instances set the value to ‘prohibited’. ON-DEMAND instances typically cost x3-4 more than SPOT instances, but are more available than SPOT instances when overall demand for GPUs on AWS is high.

  • Type: string

  • Default: Preferred

  • Choices: [‘Allowed’, ‘Preferred’, ‘NotPreferred’, ‘Prohibited’, ‘Required’]

Input Fields

Input Query Mol Field (input_query_mol_field): Field on the input query dataset(s) with the query molecules. If unspecified the primary (i.e., default) molecule field will be used.

  • Type: field_parameter::mol

Input Shape Query Field (input_shape_query_field): Field on the input query dataset(s) with the shape query to search against. If unspecified each record will be searched for a single shape query.

  • Type: field_parameter

Query Design Unit Field (query_design_unit_field): Field on the query dataset(s) passed to ‘Input Query Dataset(s)’ holding a design unit with a ligand to use as the query. If unspecified the floe will use whatever design unit it can find on any field of each record, provided the record does not have multiple fields with design units.

  • Type: field_parameter

Dock Design Unit Field (dock_design_unit_field): Field on the datasets passed to ‘Design Unit(s) (Optional)’) that contains the design unit(s) to dock to. If unspecified the floe will use whatever design unit it can find on any field of each record, provided the record does not have multiple fields with design units.

  • Type: field_parameter

Dock Receptor Field (dock_receptor_field): Field on the datasets passed to ‘Design Unit(s) (Optional)’) that contains and old style receptor molecule to dock to. If unspecified the primary molecule field will be used.

  • Type: field_parameter::mol

Output Fields

Overlay Molecule Field (overlay_molecule_field): Field on the output records that will hold the structure of the molecule overlayed by ROCS or FastROCS.

  • Type: field_parameter::mol

  • Default: Overlay Molecule

Tanimoto Combo Field (tanimoto_combo_field): Output field with the Tanimoto Combo. This field will only be created if the score type is FastROCS Similarity Type is Tanimoto Combo. The value in this field is a duplicate of the value in Combo Similarity.

  • Type: field_parameter::float

  • Default: Tanimoto Combo

Tanimoto Color Field (tanimoto_color_field): Output field with the Color Tanimoto. This field will only be created if the score type is FastROCS Similarity Type is Tanimoto Combo. The value in this field is a duplicate of the value in Color Similarity.

  • Type: field_parameter::float

  • Default: Color Tanimoto

Tanimoto Shape Field (tanimoto_shape_field): Output field with the Shape Tanimoto. This field will only be created if the score type is FastROCS Similarity Type is Tanimoto Combo. The value in this field is a duplicate of the value in Shape Similarity.

  • Type: field_parameter::float

  • Default: Shape Tanimoto

Tversky Combo Field (tversky_combo_field): Output field with the Tversky Combo. This field will only be created if the score type is FastROCS Similarity Type is Fit Tversky or Ref Tversky. The value in this field is a duplicate of the value in Combo Similarity.

  • Type: field_parameter::float

  • Default: Tversky Combo

Tversky Color Field (tversky_color_field): Output field with the Color Tversky. This field will only be created if the score type is FastROCS Similarity Type is Fit Tversky or Ref Tversky. The value in this field is a duplicate of the value in Color Similarity.

  • Type: field_parameter::float

  • Default: Color Tversky

Tversky Shape Field (tversky_shape_field): Output field with the Shape Tversky. This field will only be created if the score type is FastROCS Similarity Type is Fit Tversky or Ref Tversky. The value in this field is a duplicate of the value in Shape Similarity.

  • Type: field_parameter::float

  • Default: Shape Tversky

Best Query Field (best_query_field): Output field for the query with the highest similarity to the fit molecule.

  • Type: field_parameter::mol

  • Default: Query

Best Query ID Field (best_query_id_field): Output field for the ID of the query with the highest similarity to the molecule. This identifier will also appear in the dataset specified by the ‘Output Query Dataset’ parameter.

  • Type: field_parameter::int

  • Default: Query ID

Best Query Link Field (best_query_link_field): Output field for a link to the query with the highest similarity to the molecule. The link will point to the query in the dataset specified by the ‘Output Query Dataset’ parameter.

  • Type: field_parameter::link

  • Default: Query Link

Bemis Murcko Field (bemis_murcko_field): Output field for the Bemis Murcko core SMILES.

  • Type: field_parameter::string

  • Default: Bemis Murcko

Bemis Murcko ID Field (bemis_murcko_id_field): Output Field with an integer ID of the Bemis Murcko core. All molecules with the same Bemis Murcko core SMILES will have the same ID, and those with different Bemis Murcko core SMILES will have different IDs. The IDs starts at 1 and increments by 1 each time a new Bemis Murcko core is seen. Thus this integer ID identifier depends on the order the records are passed unlike the Bemis Murcko core SMILES itself.

  • Type: field_parameter::int

  • Default: Bemis Murcko ID

Bemis Murcko Rank Field (bemis_murcko_rank_field): Integer Field with the rank of the molecule within its Bemis Murcko family (i.e., the rank the molecule would have if the if the hit list contained only the molecules with the same Bemis Murcko core SMILES)

  • Type: field_parameter::int

  • Default: Bemis Murcko Rank

Hetero Bemis Murcko Field (hetero_bemis_murcko_field): Output field for the Hetero Bemis Murcko core SMILES.

  • Type: field_parameter::string

  • Default: Hetero Bemis Murcko

Hetero Bemis Murcko ID Field (hetero_bemis_murcko_id_field): Output Field with an integer ID of the Hetero Bemis Murcko core. All molecules with the same Hetero Bemis Murcko core SMILES will have the same ID, and those with different Hetero Bemis Murcko core SMILES will have different IDs. The IDs starts at 1 and increments by 1 each time a new Hetero Bemis Murcko core is seen. Thus this integer ID identifier depends on the order the records are passed unlike the Hetero Bemis Murcko core SMILES itself.

  • Type: field_parameter::int

  • Default: Hetero Bemis Murcko ID

Hetero Bemis Murcko Rank Field (hetero_bemis_murcko_rank_field): Integer Field with the rank of the molecule within its Hetero Bemis Murcko family (i.e., the rank the molecule would have if the if the hit list contained only the molecules with the same Hetero Bemis Murcko core SMILES)

  • Type: field_parameter::int

  • Default: Hetero Bemis Murcko Rank

Docked Molecule Field (docked_molecule_field): Output field for the docked molecule. This field will only be created on the output records if design units are supplied to this floe.

  • Type: field_parameter::mol

  • Default: Docked Molecule

Docked Score Field (docked_score_field): Output field for the score of the docked molecule. This field will only be created on the output records if design units are supplied to this floe.

  • Required

  • Type: field_parameter::float

  • Default: Chemgauss4

Design Unit ID Field (design_unit_id_field): Output field for the ID of the design unit the molecule scores best in. This field will only be created on the output records if design units are supplied to this floe.

  • Type: field_parameter::int

  • Default: Design Unit ID

Design Unit Link Field (design_unit_link_field): Output field for a Link to the design unit the molecule scores best in. This field will only be created on the output records if design units are supplied to this floe.

  • Type: field_parameter::link

  • Default: Design Unit Link

Steric Score Field (steric_score_field): Output field for the steric score component of the docked molecule. This field will only be created on the output records if design units are supplied to this floe and this parameter is specified.

  • Type: field_parameter::float

Clash Score Field (clash_score_field): Output field for the clash score component of the docked molecule. This field will only be created on the output records if design units are supplied to this floe and this parameter is specified.

  • Type: field_parameter::float

Protein Desolv Score Field (protein_desolv_score_field): Output field for the protein desolvation score component of the docked molecule. This field will only be created on the output records if design units are supplied to this floe and this parameter is specified.

  • Type: field_parameter::float

Ligand Desolv Score Field (ligand_desolv_score_field): Output field for the ligand desolvation score component of the docked molecule. This field will only be created on the output records if design units are supplied to this floe and this parameter is specified.

  • Type: field_parameter::float

Ligand Desolv HB Score Field (ligand_desolv_hb_score_field): Output field for the ligand desolvation hydrogen bond score component of the docked molecule. This field will only be created on the output records if design units are supplied to this floe and this parameter is specified.

  • Type: field_parameter::float

Hydrogen Bond Score Field (hydrogen_bond_score_field): Output field for the hydrogen bond score component of the docked molecule. This field will only be created on the output records if design units are supplied to this floe and this parameter is specified.

  • Type: field_parameter::float

Consensus Pareto Dominance Rank Field (consensus_pareto_dominance_rank_field): Integer field on the output record holding the pareto dominance rank of the record.

  • Required

  • Type: field_parameter::int

  • Default: Pareto Rank

Highest 2D Tanimoto (highest_2d_tanimoto): Output field for each molecules highest 2D Tanimoto to any query. This Tanimoto value is used to generate the FastROCS and ROCS novelty output hit lists

  • Required

  • Type: field_parameter::float

  • Default: 2D Tanimoto

Most 2D Similar Query SMILES Field (most_2d_similar_query_smiles_field): Output field holding the SMILES of the query molecule with the highest Tanimoto to the output molecule.

  • Type: field_parameter::string

  • Default: Most 2D Similar Query SMILES

Most 2D Similar Query Title Field (most_2d_similar_query_title_field): Output field holding the Title of the query molecule with the highest Tanimoto to the output molecule.

  • Type: field_parameter::string

  • Default: Most 2D Similar Query Title

Fingerprint Type Field (fingerprint_type_field): Output field holding the name of the type of fingerprint used in the 2D calculation. This field will only be added to the output if a value is entered for this parameter.

  • Type: field_parameter::string

Development

Re-score Max Confs (re_score_max_confs): Maximum number of conformers Omega will generate for the re-scoring step, both ROCS and Docking.This value shouldn’t be set below 200 if the run will do Docking Re-scoring.

  • Type: integer

  • Default: 200

FastROCS&ROCS Sort Field (fastrocsrocs_sort_field): Sort field for the ROCS and FastROCS Hit List.

  • Required

  • Type: field_parameter::float

  • Default: ROCS and FastROCS Sort Field

Re-score Shard Size (re_score_shard_size): The target number of records in a shard.

0 indicates to run up to the max_shard_bytes limit per shard

  • Required

  • Type: integer

  • Default: 500

Raw Resized Shard Size (raw_resized_shard_size): The target number of records in a shard.

0 indicates to run up to the max_shard_bytes limit per shard

  • Required

  • Type: integer

  • Default: 1000

Memory (MB) for Re-scoring Cubes (memory_mb_for_re_scoring_cubes): The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.

  • Type: decimal

  • Default: 4096

FastROCS Max Parallel (fastrocs_max_parallel): The maximum number of concurrently running copies of this Cube

  • Type: integer

  • Default: 1000

Min Shard Download Timeout (min_shard_download_timeout): Minimum timeout for the smart shard to records cubes

  • Required

  • Type: integer

  • Default: 2

Max Shard Download Timeout (max_shard_download_timeout): Maximum timeout for the smart shard to records cubes

  • Required

  • Type: integer

  • Default: 21600.0

Session Retry Dict for Shard Download (session_retry_dict_for_shard_download_): Session retry dict for the smart shard to records cubes

  • Type: string

  • Default: [‘429:1000’, ‘460:1000’, ‘500:1000’, ‘502:1000’, ‘503:1000’, ‘504:1000’]

Shard Download Attempts (shard_download_attempts): Download attempts for the smart shard to records cubes

  • Type: integer

  • Default: 1

FastROCS download Retry Timeout (fastrocs_download__retry_timeout): Sets the retry timeout (sec) on the cube_session OrionSession for this cube. If unspecified parallel cubes will uses a value of 600 and serial cubes will use a value of 7200.

  • Type: integer

  • Default: 60

FastROCS Upload Retry Timeout (fastrocs_upload_retry_timeout): Sets the retry timeout on the OrionSession used to create and upload the output shards. If unspecified the orionclient default will be used.

  • Type: integer

  • Default: 180

FastROCS Download Attempts (fastrocs_download_attempts): Number of attempts to make when downloading a shard

  • Type: integer

  • Default: 1

FastROCS Upload Attempts (fastrocs_upload_attempts): Number of attempts to make when uploading a shard

  • Type: integer

  • Default: 3

Min Shard Upload Timeout (min_shard_upload_timeout): Minimum timeout for the smart records to record shard cubes

  • Required

  • Type: integer

  • Default: 2

Max Shard Upload Timeout (max_shard_upload_timeout): Maximum timeout for the smart records to record shard cubes

  • Required

  • Type: integer

  • Default: 21600.0

Session Retry Dict for Shard Upload (session_retry_dict_for_shard_upload_): Session retry dict for the smart records to record shard cubes

  • Type: string

  • Default: [‘429:1000’, ‘460:1000’, ‘500:1000’, ‘502:1000’, ‘503:1000’, ‘504:1000’]

Shard Upload Attempts (shard_upload_attempts): Download attempts for the smart record to record shard cubes

  • Type: integer

  • Default: 3

Serial Cube Retry Timeout (serial_cube_retry_timeout): Sets the retry timeout (sec) on the cube_session OrionSession for this cube. If unspecified parallel cubes will uses a value of 600 and serial cubes will use a value of 7200.

  • Type: integer

FastROCS Output Shard Min Size (fastrocs_output_shard_min_size): The desired size of the output shards will in general be the number of records to output divided by the number of threads. This parameter sets a minimum value on the desired shard size.

  • Type: integer

  • Default: 10000

Hit List Instance Type (hit_list_instance_type): The type of instance that this cube needs to be run on

  • Type: string

  • Default: r5,r6,r7

Number of upload shard CPUs (number_of_upload_shard_cpus): Number of CPUs on FastROCS cube to use to upload shards

  • Type: integer

Log FastROCS Times and Disk Usage (log_fastrocs_times_and_disk_usage): If On timing information will be sent to the log as the cube runs.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Re-score cube instance type (re_score_cube_instance_type): The type of instance that this cube needs to be run on

  • Type: string

Shape Only (shape_only): If ‘On’ the overlap will only be in terms of shape (i.e., no color contribution)

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Max Optimization Steps (max_optimization_steps): Maximum number of optimization steps to use per conformer overlay.

  • Type: integer

  • Default: 200

Catch exceptions (catch_exceptions): If Off exception handling will be disabled for this cube.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Catch exceptions (parallel_catch_exception_methods): Specifies which methods of a parallel cube an exception will be caught and emitted to the exception port if the port is connected. If the exception port is connected to an exception handler this will stop the floe

  • Type: string

  • Default: [‘begin’]

  • Choices: [‘begin’, ‘process’, ‘end’]

Enable cube timing report (time_all_cubes): If true this cube will emit timing information to the timing_data port.

  • Type: boolean

  • Default: True

  • Choices: [True, False]