Shape Screening

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

Options

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

Settings...

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.
Usage:
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)

Popular Predecessors

Popular Successors

Views

Log output of Phase Shape: Log output of Phase Shape

Workflows

Developers

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.1.135.v202402072122

On NodePit since: 2023-12-06

Last update: 2024-04-19

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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