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 Similarity
Tags : Graphsim Virtual Screening Plus Graphsim Plus
Python Name : multi_query_2d_similarity

Parameters

Inputs

  • Query Molecules Query molecules for the 2D Tanimoto calculation.
    Type : data_source
    Required : True
    Python 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_source
    Required : True
    Python Name : input_molecules

Outputs

  • Output Dataset Output dataset to write to
    Type : dataset_out
    Required : True
    Default : Multi Query 2D Similarity Results
    Python 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 : boolean
    Required : True
    Default : True
    Choices :True, False
    Python 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 : integer
    Required : True
    Default : 100000
    Min Value : 1
    Python Name : hit_list_size
  • Fingerprint Type The type of fingerprint to use in the Tanimoto calculation
    Type : string
    Required : True
    Default : Circular
    Choices :Circular, Path, Tree
    Python 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 : boolean
    Required : False
    Default : True
    Choices :True, False
    Python 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 : decimal
    Required : False
    Python 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 : decimal
    Required : False
    Python 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::mol
    Required : False
    Python 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::mol
    Required : False
    Python 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::float
    Required : True
    Default : 2D Tanimoto
    Python 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::string
    Required : False
    Default : Fingerprint Type
    Python 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::string
    Required : False
    Default : Best Query SMILES
    Python 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::string
    Required : False
    Default : Best Query Title
    Python Name : best_query_title_field