Similarity Matrix (from Molecules)

Options

Include Molecule

Whether the molecule should be included in the output

Include Input

Whether all columns in the input should be included in the output

Fingerprint Type

Valid methods:

• linear
• maccs
• radial
• molprint2D
• torsion
• pairwise
• triplet
• dendritic

Note: Atom type is not used to generate finger prints when the "maccs" method is selected.

Precision

Select fingerprint precision:

• 1024 (10-bit)
• 2048 (11-bit)
• 4096 (12-bit)
• 32-bit (default)
• 64-bit

Selecting 64-bit reduces collisions of "on" bits, but doubles the space required to store each key. Selecting 1024, 2048 and 4096 increases the chance of feature collisions.

Atom type

Atom typing scheme. Must be an integer value between 1 and 10 or C or E.

Omit bits that are set by less than percentage

Omit bits that are set by more than percentage

Omit bits only set in single molecule

Omit bits set in all molecules

Reduce precision of fingerprints by specified number of bits

Only used with 32-bit precision. Reduces precision of fingerprints by specified number of bits. It increases the chance of feature collisions. For example, a value of 22 will reduce each single precision key (32 bits) into a range of 1024 (10 bits).

Scaling

Rescale binary fingerprint data to real.

Metric types

Valid metrics:

• buser
• cosine
• dice
• dixon
• euclidean
• hamann
• hamming
• kulczynski
• matching
• McConnaughey
• minmax
• patterDifference
• pearson
• petke
• rogersTanimoto
• shape
• simpson
• size
• soergel
• tanimoto
• tversky
• variance
• yule

Maximum number of fingerprints to load in memory at a time

Ignore any scaled fp values

Tversky alpha parameter

Tversky beta parameter

Gaussian parameter to make output matrix sparse

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: CanvasFPMatrix
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

Std output/error of FPGen 1

Std output/error of FPGen 1

Std output/error of FPGen 2

Std output/error of FPGen 2

Std output/error of FPMatrix

Std output/error of FPMatrix

Workflows

• Database analysis 1KNIME Hub
• Database analysis 1KNIME Hub
• Database analysis 1KNIME Hub
• Database analysis 1-2KNIME Hub
• Database analysis 1-2KNIME Hub
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