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Shape Screening

Schrödinger extension for KNIME Workbench version by Schrödinger

Screens one or more files or a Phase database against a shape query. Each conformer of a given molecule is aligned to the query in various ways, and a similarity is computed based on approximate hard sphere overlapping volumes. The conformer and alignment yielding the highest shape similarity for a given molecule is written to the alignments file <jobname>_align.maegz, with the shape similarity property r_phase_Shape_Sim.
If GPU is selected in the python panel, then it runs shape screening on the GPU. In this case, it screens a shape data file against one or more shape queries.

Backend implementation

$SCHRODINGER/shape_screen or $SCHRODINGER/shape_screen_gpu


Column containing shape query
Select the column containing the shape query (either Maestro or SD type)
Screen structures in
Select the Screen source from three options: File, Input Structures or Phase Database
Column containing structures to screen
Select the column containing structures to be screened (either Maestro or SD type). Enabled only if "Input Structures" is selected.
File name
Browse to a structure file or Phase Database. Enabled only if File or Phase Database is selected. If GPU mode is selected in python panel, choose a Shape data file (*.bin)
Output hitlist only
Outputs a text cell with the contents of the similarity values.
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

On clicking "Settings" button, this node brings up the "Shape Screening" Python panel for configuration.
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Flow variable prefix keyword: ShapeScreen
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

Shape query (in Maestro or Sdf Format)
Structures to screen (in Maestro or Sdf Format)

Output Ports

Screening results (in Maestro, Sdf or Text)


Log output of Phase Shape
Log output of Phase Shape

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:


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