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Generate Pairwise Matrix

Schrödinger Nodes for Suite2018-1 version 0.0.1.7B27VcMf4_L7A58S5A8G55JS by Schrödinger

Calculate a pairwise distance matrix from binary molecular fingerprints generated by the fingerprint Generation node.

Backend implementation

utilities/canvasFPMatrix
canvasFPMatrix is used to implement this node.

Options

Save output binary matrix file to disc
This option should be selected when using large amounts of data.
Metric types
Valid metrics:
  • buser
  • cosine
  • dice
  • dixon
  • euclidean
  • hamann
  • hamming
  • kulczynski
  • matching
  • McConnaughey
  • minmax
  • patternDifference
  • pearson
  • petke
  • rogersTanimoto
  • shape
  • simpson
  • size
  • soergel
  • tanimoto
  • tversky
  • variance
  • yule
Maximum number of fingerprints to load in memory at a time
Default is 5000.
Ignore any scaled fp values
Use binary values in all cases.
Tversky alpha parameter
To be used with the Tversky metric: default set to 0.5
Tversky beta parameter
To be used with the Tversky metric: default set to 0.5
Flatten: Gaussian parameter
Gaussian parameter to make output matrix sparse. Only applicable to similarity metrics (buser, cosine, dice, hamann, kulczynski, matching, mcConnaughey, modifiedTanimoto, pearson, petke, rogersTanimoto, simpson, tanimoto, tversky, and yule).
Parameter flow variables
Any valid option for proplister.py can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: GeneratePWMatrix
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

Input Ports

Molecular fingerprints in binary format

Output Ports

Pairwise distance matrix in binary format

Views

Standard output
Standard output
Log View
Log View

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Update Site

To use this node in KNIME, install Schrödinger Nodes for Suite2018-1 from the following update site:

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