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 and minimum cost per query.

Details

Title : Batch FastROCS
Tags : Large Scale Floes Screening Virtual fastrocs rocs batch
Python Name : #03_batch_fastrocs

Parameters

Inputs

  • Query Dataset(s) Dataset(s) with up to 10 query molecules and/or shape queries. A separate hit list will be created for each query.
    Type : data_source
    Required : True
    Python Name : query_datasets
  • 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.
    Type : collection_source
    Required : True
    Python Name : fastrocs_input_collection

Outputs

  • 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.
    Type : boolean
    Required : True
    Default : True
    Choices :True, False
    Python Name : prefix_output_dataset_names_with_query_title
  • 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.
    Type : dataset_out
    Required : True
    Default : Hit List #1
    Python Name : hit_list_1_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.
    Type : dataset_out
    Required : True
    Default : Hit List #2
    Python Name : hit_list_2_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.
    Type : dataset_out
    Required : True
    Default : Hit List #3
    Python Name : hit_list_3_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.
    Type : dataset_out
    Required : True
    Default : Hit List #4
    Python Name : hit_list_4_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.
    Type : dataset_out
    Required : True
    Default : Hit List #5
    Python Name : hit_list_5_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.
    Type : dataset_out
    Required : True
    Default : Hit List #6
    Python Name : hit_list_6_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.
    Type : dataset_out
    Required : True
    Default : Hit List #7
    Python Name : hit_list_7_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.
    Type : dataset_out
    Required : True
    Default : Hit List #8
    Python Name : hit_list_8_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.
    Type : dataset_out
    Required : True
    Default : Hit List #9
    Python Name : hit_list_9_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.
    Type : dataset_out
    Required : True
    Default : Hit List #10
    Python Name : hit_list_10_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #1
    Python Name : cluster_heads_1_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #2
    Python Name : cluster_heads_2_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #3
    Python Name : cluster_heads_3_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #4
    Python Name : cluster_heads_4_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #5
    Python Name : cluster_heads_5_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #6
    Python Name : cluster_heads_6_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #7
    Python Name : cluster_heads_7_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #8
    Python Name : cluster_heads_8_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #9
    Python Name : cluster_heads_9_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’).
    Type : dataset_out
    Required : True
    Default : Cluster Heads #10
    Python Name : cluster_heads_10_dataset
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #1
    Python Name : output_query_dataset_1
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #2
    Python Name : output_query_dataset_2
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #3
    Python Name : output_query_dataset_3
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #4
    Python Name : output_query_dataset_4
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #5
    Python Name : output_query_dataset_5
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #6
    Python Name : output_query_dataset_6
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #7
    Python Name : output_query_dataset_7
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #8
    Python Name : output_query_dataset_8
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #9
    Python Name : output_query_dataset_9
  • 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.
    Type : dataset_out
    Required : True
    Default : Output Query #10
    Python Name : output_query_dataset_10

Options

  • Hit List Size Number of top scoring molecules to output. This applies to all output hit lists if multiple queries are supplied
    Type : integer
    Required : True
    Default : 20000
    Range : 100 to 50000
    Python Name : hit_list_size
  • Similarity Type Type of similarity to use for FastROCS (and ROCS if ‘Refine with ROCS’ is ‘On’).
    Type : string
    Required : False
    Default : Tanimoto Combo
    Choices :Tanimoto Combo, Ref Tversky, Fit Tversky, Shape Tanimoto, Shape Ref Tversky, Shape Fit Tversky
    Python Name : similarity_type
  • 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.
    Type : boolean
    Required : True
    Default : True
    Choices :True, False
    Python Name : refine_with_rocs

GPU Hardware

These parameters control the AWS instance type the FastROCS Cube will use. There is in general no reason to adjust these. They are exposed because overall demand for GPU instances on AWS has occasionally been very high and this has led to extremely long run times for this floe as it waits for GPU instances in some circumstances.

  • FastROCS Instance Type The instances excluded by default are known to be not cost effective for FastROCS.
    Type : string
    Required : False
    Default : !cdns,!g4dn.metal,!g5.12xlarge,!g5.24xlarge,!g5.48xlarge,!g4dn.12xlarge,!g3s.,!p3.
    Python Name : fastrocs_instance_type
  • 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
    Required : False
    Default : Preferred
    Choices :Allowed, Preferred, NotPreferred, Prohibited, Required
    Python Name : spot_instance_policy_for_fastrocs_gpu_instance

Output Fields

These parameters allow the user to change the default output fields this floe creates in the output datasets and/or collections. Note that parameters identifying a molecule field are special. If a molecule field is left empty the floe writes the molecule to the primary (i.e., default) molecule field of the record. The primary molecule of a dataset can be identified in the UI by looking for star on its field badge. CAUTION: If these parameters are modified the modifications must also be applied to the input fields of downstream floes that read fields written by this floe. If the downstream floe does not support specifying the input field then they may not work properly with the output of this floe if these settings are modified.

  • 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
    Required : False
    Default : Tanimoto Combo
    Python Name : tanimoto_combo_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
    Required : False
    Default : Color Tanimoto
    Python Name : tanimoto_color_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
    Required : False
    Default : Shape Tanimoto
    Python Name : tanimoto_shape_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
    Required : False
    Default : Tversky Combo
    Python Name : tversky_combo_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
    Required : False
    Default : Color Tversky
    Python Name : tversky_color_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
    Required : False
    Default : Shape Tversky
    Python Name : tversky_shape_field
  • Bemis Murcko Field Output field for the Bemis Murcko core SMILES.
    Type : field_parameter::string
    Required : False
    Default : Bemis Murcko
    Python Name : bemis_murcko_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
    Required : False
    Default : Bemis Murcko ID
    Python Name : bemis_murcko_id_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
    Required : True
    Default : Bemis Murcko Rank
    Python Name : bemis_murcko_rank_field
  • Hetero Bemis Murcko Field Output field for the Hetero Bemis Murcko core SMILES.
    Type : field_parameter::string
    Required : False
    Default : Hetero Bemis Murcko
    Python Name : hetero_bemis_murcko_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
    Required : False
    Default : Hetero Bemis Murcko ID
    Python Name : hetero_bemis_murcko_id_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
    Required : False
    Default : Hetero Bemis Murcko Rank
    Python Name : hetero_bemis_murcko_rank_field