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Prime Minimization

Schrödinger extension for KNIME Workbench version by Schrödinger

Minimize molecules using Prime. Note that Prime uses OPLS 2000 for the receptor/protein and OPLS 2001 for the ligand.

Backend implementation

scripts/refinestructCLI.py run by cmdRunner.py
The script refinestructCLI.py is passed to cmdRunner.py to implement this node.


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

Include Log in output
Include the Prime log file as a column in the output data table
Part of Protein to minimize (optional ASL)
Optional ASL expression that represents the part of the Protein to be minimized
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Flow variable prefix keyword: PrimeMini
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.

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.

Input Ports

Molecules in Maestro format

Output Ports

Minimized molecules in Maestro format

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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