Multi Query 2D Similarity
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Product-based/GraphSim
Role-based/Computational Chemist
Solution-based/Virtual-screening/DB Search/2D Similarity and SubSearch
Task-based/Virtual Screening - Ligand-Based
Description
For a set of input molecules computes the highest 2D Tanimoto similarity to any query molecule. Users can optionally filter these molecules by the computed Tanimoto. The floe can then either output all the input molecules or optionally create a hit list of top scoring molecules.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Query Molecules (query_molecules): Query molecules for the 2D Tanimoto calculation.
Required
Type: data_source
Input Molecules (input_molecules): Dataset(s) with molecules to screen. For each molecule the 2D Tanimoto to all the query molecules will be calculated and the molecule will be assigned a 2D Tanimoto equal to the highest Tanimoto to any query.
Required
Type: data_source
Outputs
Output Dataset (output_dataset): Output dataset to which to write.
Required
Type: dataset_out
Default: Multi Query 2D Similarity Results
Options
Enable Hit List (enable_hit_list): If set to ‘On’ the output will be a sorted list of the top scoring molecules by 2D Tanimoto. If set to ‘Off’ all molecule will be directly outputted to the output dataset unsorted.
Required
Type: boolean
Default: True
Choices: [True, False]
Hit List Size (hit_list_size): Size of the output hit list. If ‘Enable Hit List’ is ‘Off’ this parameter will have no effect.
Required
Type: integer
Default: 100000
Fingerprint Type (fingerprint_type): The type of fingerprint to use in the Tanimoto calculation
Required
Type: string
Default: Circular
Choices: [‘Circular’, ‘Path’, ‘Tree’]
Use Virtual Screening Fingerprint Variant (use_virtual_screening_fingerprint_variant): If ‘On’ the virtual screening variant of the selected fingerprint will be used. The virtual screening variant treats certain functional group identically regardless of there pKa state. E.g. protonated and unprotonated carboxylic acids.
Type: boolean
Default: True
Choices: [True, False]
Options: Filtering
Filter Tanimotos Higher Than (filter_tanimotos_higher_than): If this parameter is set, any molecule with a Tanimoto higher than this value will be discarded.
Type: decimal
Filter Tanimotos Lower Than (filter_tanimotos_lower_than): If this parameter is set, any molecule with a Tanimoto lower than this value will be discarded.
Type: decimal
Input Fields
Molecule Field (molecule_field): Field on the input records containing the molecule to process. If unspecified the primary molecule field will be used.
Type: field_parameter::mol
Query Molecule Field (query_molecule_field): Field on the input query records containing the query molecules. If unspecified the primary molecule field will be used.
Type: field_parameter::mol
Output Fields
Tanimoto Field (tanimoto_field): Field on the output records the computed Tanimoto of each molecule will be stored in.
Required
Type: field_parameter::float
Default: 2D Tanimoto
Fingerprint Type Field (fingerprint_type_field): Field on the output records with the name of the fingerprint type used to calculate the Tanimoto. Creation of this field can be suppressed by clearing the default value of this parameter.
Type: field_parameter::string
Default: Fingerprint Type
Best Query SMILES Field (best_query_smiles_field): Field on the output records containing the SMILES of the query molecule with the highest Tanimoto to the input molecule. Creation of this field can be suppressed by clearing the default value of this parameter.
Type: field_parameter::string
Default: Best Query SMILES
Best Query Title Field (best_query_title_field): Field on the output records containing the title of the query molecule with the highest Tanimoto to the input molecule. Creation of this field can be suppressed by clearing the default value of this parameter.
Type: field_parameter::string
Default: Best Query Title
Development
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]
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’]