Multi Query 2D Similarity
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.
Details
Title : Multi Query 2D SimilarityTags : Graphsim Virtual Screening Plus Graphsim PlusPython Name : multi_query_2d_similarity
Parameters
Inputs
Query Molecules Query molecules for the 2D Tanimoto calculation.Type : data_sourceRequired : TruePython Name : query_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.Type : data_sourceRequired : TruePython Name : input_molecules
Outputs
Output Dataset Output dataset to write toType : dataset_outRequired : TrueDefault : Multi Query 2D Similarity ResultsPython Name : output_dataset
Options
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.Type : booleanRequired : TrueDefault : TrueChoices :True, FalsePython Name : enable_hit_list Hit List Size Size of the output hit list. If ‘Enable Hit List’ is ‘Off’ this parameter will have no effect.Type : integerRequired : TrueDefault : 100000Min Value : 1Python Name : hit_list_size Fingerprint Type The type of fingerprint to use in the Tanimoto calculationType : stringRequired : TrueDefault : CircularChoices :Circular, Path, TreePython Name : fingerprint_type 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 : booleanRequired : FalseDefault : TrueChoices :True, FalsePython Name : use_virtual_screening_fingerprint_variant
Options: Filtering
Filter Tanimotos Higher Than If this parameter is set, any molecule with a Tanimoto higher than this value will be discarded.Type : decimalRequired : FalsePython Name : filter_tanimotos_higher_than Filter Tanimotos Lower Than If this parameter is set, any molecule with a Tanimoto lower than this value will be discarded.Type : decimalRequired : FalsePython Name : filter_tanimotos_lower_than
Input Fields
These parameters specify the fields on the input datasets and/or collections these floes read data from. Note that parameters identifying a molecule field are special. If left empty the floe will read the molecule from the primary (i.e., default) molecule field on the input record. The primary molecule of a dataset can be identified in the UI by looking for star on its field badge.
Molecule Field Field on the input records containing the molecule to process. If unspecified the primary molecule field will be used.Type : field_parameter::molRequired : FalsePython Name : 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::molRequired : FalsePython Name : query_molecule_field
Output Fields
This parameter specified the names fields that will be added to the output records.
Tanimoto Field Field on the output records the computed Tanimoto of each molecule will be stored in.Type : field_parameter::floatRequired : TrueDefault : 2D TanimotoPython Name : tanimoto_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::stringRequired : FalseDefault : Fingerprint TypePython Name : fingerprint_type_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::stringRequired : FalseDefault : Best Query SMILESPython Name : best_query_smiles_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::stringRequired : FalseDefault : Best Query TitlePython Name : best_query_title_field