Canvas Fingerprint Generation

Generate molecular fingerprints

Backend implementation

Options

Column containing input

Choose the input column to generate the molecular fingerprints

Column containing Smiles molecule names

Choose the input column that sets the molecules names (Only available when the input is Smiles)

Include additional molecule data fields in output fingerprints

Not available if input type is smiles.

Fingerprint Type

Valid methods:

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

Note: Atom type is not used 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/bond type

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

Filter bits by ON/OFF frequency

Discard bits that are ON in less than % of molecules

Discard bits that are ON in more than % of molecules

Discard bits that are only ON in single molecules

Discard bits that are ON in all molecules

Filter bits by information content

Retain the # most informative bits

keep only the # most informative bits across the chosen input set.

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).

Compress fingerprints

Use frequency-based compression to reduce required storage by approximately tenfold.

Scaling

Rescale binary fingerprint data to real.

Parameter flow variables

Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: CanvasFPGen
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 from command line, just specify the option_name and the value as _off_ through the flow variable.

Views

Standard output of Fingerprint Generation

Standard output of Finger Print Generation

Workflows

• Clustering 1KNIME Hub
• Clustering 1KNIME Hub
• Clustering 1KNIME Hub
• Clustering 1-2KNIME Hub
• Clustering 1-2KNIME Hub
• Show all 21 workflows

Links

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Developers