Batch FastROCS
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
This floe overlays a FastROCS collection onto ten or fewer 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 Plus 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 Floe 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 supplies several pregenerated vendor molecule collections in Organization Data. The Prepare Giga Collections or Giga Dock 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 is 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 created 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 created 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 created 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 created 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 created 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 created 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 created 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 created 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 created 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 created 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.
Required
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 Tanimoto’, ‘Shape Ref Tversky’, ‘Shape Fit Tversky’]
Refine with ROCS (refine_with_rocs): If On, the top scoring molecules from FastROCS will be re-overlaid and rescored 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]
GPU Hardware
FastROCS Instance Type (fastrocs_instance_type): The instances excluded by default are 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 3–4 times more than SPOT instances, but they 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