Generate Pairwise Matrix

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

Backend implementation

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.

Views

Log View

Log View

Workflows

• Clustering 1KNIME Hub
• Clustering 1KNIME Hub
• Clustering 1KNIME Hub
• Clustering 1-2KNIME Hub
• Clustering 1-2KNIME Hub
• Show all 20 workflows

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Developers