Generate Pairwise Matrix (2 Inputs)

Calculate a pairwise distance matrix from two sets of binary molecular fingerprints generated by the fingerprint Generation node.
Note that if comparing two sets of molecules which differ in number, a non-square matrix will be created which cannot be used with any other KNIME node or Canvas function. The option to generate a table of similarity values should be selected in this case.

Backend implementation

utilities/canvasFPMatrix
canvasFPMatrix is used to implement this node.

Options

Output in table format
Output is a table of similarity values.
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: GeneratePWMatrix2
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

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Molecular fingerprints in binary format (1st input)
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Molecular fingerprints in binary format (2nd input)

Output Ports

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Pairwise distance matrix in binary format

Views

Log View
Log View

Workflows

Links

Developers

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