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Canvas Fingerprint Generation

Schrödinger Nodes for Suite2018-1 version 0.0.1.7B27VcMf4_L7A58S5A8G55JS by Schrödinger

Generate molecular fingerprints

Backend implementation

utilities/canvasFPGen
canvasFPGen is used to implement this node.

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.

Input Ports

Molecules in Maestro, SMILES or SD format

Output Ports

Molecular fingerprints in Binary format
Molecules that failed to generate a fingerprint

Views

Standard output of Fingerprint Generation
Standard output of Finger Print Generation

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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