Batch FastROCS

Description

Overlays a FastROCS collection onto up to 10 shape or molecule queries and outputs a separate hit list for each query.

By default the best molecules from FastROCS are re-overlayed using ROCS and 25 random starts and up to 200 conformers of each molecule before being sent to the output hit list.

Most users should use the ‘FastROCS’ floe rather than this floe as it has more features. This floe is intended to be a replacement for the deprecated ‘Multi-Query Ligand-Based Virtual Screening with FastROCS and SubROCS’ for users who desire a separate hit for each query.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Query Dataset(s) (query_datasets): Dataset(s) with up to 10 query molecules and/or shape queries. A separate hit list will be created for each query.

  • 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

Outputs

Prefix Output Dataset Names with Query Title (prefix_output_dataset_names_with_query_title): If true the name/title of the associated query pre-appended to the names of all the output datasets listed below.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Hit List #1 Dataset (hit_list_1_dataset): Hit List for query 1. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #1

Hit List #2 Dataset (hit_list_2_dataset): Hit List for query 2. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #2

Hit List #3 Dataset (hit_list_3_dataset): Hit List for query 3. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #3

Hit List #4 Dataset (hit_list_4_dataset): Hit List for query 4. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #4

Hit List #5 Dataset (hit_list_5_dataset): Hit List for query 5. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #5

Hit List #6 Dataset (hit_list_6_dataset): Hit List for query 6. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #6

Hit List #7 Dataset (hit_list_7_dataset): Hit List for query 7. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #7

Hit List #8 Dataset (hit_list_8_dataset): Hit List for query 8. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #8

Hit List #9 Dataset (hit_list_9_dataset): Hit List for query 9. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #9

Hit List #10 Dataset (hit_list_10_dataset): Hit List for query 10. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query it is associated with.

  • Required

  • Type: dataset_out

  • Default: Hit List #10

Cluster Heads #1 Dataset (cluster_heads_1_dataset): Hit list for query #1 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #1 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #1 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #1

Cluster Heads #2 Dataset (cluster_heads_2_dataset): Hit list for query #2 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #2 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #2 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #2

Cluster Heads #3 Dataset (cluster_heads_3_dataset): Hit list for query #3 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #3 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #3 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #3

Cluster Heads #4 Dataset (cluster_heads_4_dataset): Hit list for query #4 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #4 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #4 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #4

Cluster Heads #5 Dataset (cluster_heads_5_dataset): Hit list for query #5 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #5 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #5 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #5

Cluster Heads #6 Dataset (cluster_heads_6_dataset): Hit list for query #6 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #6 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #6 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #6

Cluster Heads #7 Dataset (cluster_heads_7_dataset): Hit list for query #7 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #7 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #7 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #7

Cluster Heads #8 Dataset (cluster_heads_8_dataset): Hit list for query #8 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #8 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #8 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #8

Cluster Heads #9 Dataset (cluster_heads_9_dataset): Hit list for query #9 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #9 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #9 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #9

Cluster Heads #10 Dataset (cluster_heads_10_dataset): Hit list for query #10 that contains only one, top scoring, representative of each Bemis-Murcko core. This hit list is a subset of the ‘Hit List #10 Dataset’ that also includes the clustering information. This hit list is creating by filtering the ‘Hit List #10 Dataset’ for ‘Bemis Murcko Rank’=1 (see the parameter ‘Output Fields -> Bemis Murcko Rank Field’).

  • Required

  • Type: dataset_out

  • Default: Cluster Heads #10

Output Query Dataset #1 (output_query_dataset_1): This dataset holds a copy of the query used to generate Hit List 1. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #1

Output Query Dataset #2 (output_query_dataset_2): This dataset holds a copy of the query used to generate Hit List 2. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #2

Output Query Dataset #3 (output_query_dataset_3): This dataset holds a copy of the query used to generate Hit List 3. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #3

Output Query Dataset #4 (output_query_dataset_4): This dataset holds a copy of the query used to generate Hit List 4. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #4

Output Query Dataset #5 (output_query_dataset_5): This dataset holds a copy of the query used to generate Hit List 5. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #5

Output Query Dataset #6 (output_query_dataset_6): This dataset holds a copy of the query used to generate Hit List 6. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #6

Output Query Dataset #7 (output_query_dataset_7): This dataset holds a copy of the query used to generate Hit List 7. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #7

Output Query Dataset #8 (output_query_dataset_8): This dataset holds a copy of the query used to generate Hit List 8. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #8

Output Query Dataset #9 (output_query_dataset_9): This dataset holds a copy of the query used to generate Hit List 9. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #9

Output Query Dataset #10 (output_query_dataset_10): This dataset holds a copy of the query used to generate Hit List 10. Note if ‘Prefix Output Dataset Names with Query Title’ is True then the name of the output dataset specified here will be pre-appended with the name/title of the query.

  • Required

  • Type: dataset_out

  • Default: Output Query #10

Options

Hit List Size (hit_list_size): Number of top scoring molecules to output. This applies to all output hit lists if multiple queries are supplied

  • Type: integer

  • Default: 20000

Similarity Type (similarity_type): Type of similarity to use for FastROCS (and ROCS if ‘Refine with ROCS’ is ‘On’).

  • Type: string

  • Default: Tanimoto Combo

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

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]

Number of Random Starts (FastROCS) (number_of_random_starts_fastrocs): If specified fastROCS will use this number of random starts for each conformer overlay. If unspecified the default inertial starts will be used.

  • Type: integer

Refine with ROCS (refine_with_rocs): If ‘On’, the top scoring molecules from FastROCS will be re-overlaid and re-scored with ROCS, and these refined ROCS results will be output to the hit-lists in place of initial FastROCS results. if Off the top scoring FastROCS molecules will be output directly.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Refinement Max Confs (refinement_max_confs): Maximum number of conformers Omega will generate for the ROCS re-scoring step if chosen.

  • Type: integer

  • Default: 200

Number of Random Starts (ROCS) (rocs_number_of_random_starts): If ROCS rescoring is selected, ROCS uses this number of random starts for each conformer overlay. If unspecified the default inertial starts will be used.

  • Type: integer

  • Default: 25

Color Force Field Options

OEColorFF Type (oecolorff_type): FastROCS collections are prepared using the ImplicitMillsDean color force field. ‘None’ indicates that the prepared collections will be used as is, without modification. Shape queries are used as is, and their color features will not be modified. If a different color force field is selected it would be applied to the molecule queries, if ‘None’ is selected ImplicitMillsDean will be used.

  • Required

  • Type: string

  • Default: None

  • Choices: [‘ExplicitMillsDean’, ‘ImplicitMillsDeanNoRings’, ‘ExplicitMillsDeanNoRings’, ‘None’]

Custom Color Force Field File (cff_in): Custom Color Force Field (CFF) file to use in FastROCS and ROCS rescoring.

  • Type: file_in

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’]

Output Fields

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

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