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Residue Scanning

Schrödinger extension for KNIME Workbench version 21.1.156.202102141445 by Schrödinger

Bioluminate residue scanning: Mutates and refines residues and proteins
For complete documentation, click the Help button ("?") in the "Residue Scanning" panel opened by "Settings..."

Backend implementation

$SCHRODINGER/run residue_scanning_gui.py and $SCHRODINGER/run residue_scanning_backend.py
residue_scanning_gui.py is used for dialog and residue_scanning_backend.py is used for node

Options

Column containing input structures
Select column in the input data table containing the structures
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
Opens the residue_scanning_gui.py to analyze the input and configure the node.
Note: Currently, the settings for the "Chains" drop-down (when "Stability and Affinity" is selected) and all the options in "Advanced..." dialog are not saved.
Include log in output
Includes the log file as a separate column in the output table
Number of subjobs
If not selected, total number of processors will be used as subjobs count
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: ResidueScanning
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 the flow variable.

To add a new option without a value, specify the option_name and the value as _on_ through the flow variable.

To override an existing option's value, 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.

To pick the value from a column in the input table, specify the option_name and the value as :column_name: through the flow variable. Any column other than String, Integer and Double types will be written to a file and the file name is added as the option value.

Note: This node adds a new parameter flow variable 'backend' so that downstream node can access the backend used by this node.

Input Ports

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Molecules in Maestro format

Output Ports

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Molecules in Maestro format with calculated energies

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.3

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Developers

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