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Rotate All

Schrödinger extension for KNIME Workbench version by Schrödinger

Rotates all structures into a new reference frame. The program initially aligns the first mobile structure onto the reference by running the structalign program and then applies the rotation matrix to all subsequent mobile structures.

Backend implementation

$SCHRODIGER/run rotate_all.py
The script rotate_all.py from mmshare-v*/python/common is used to implement this node.


Column containing reference structure
Select column in the input data table containing the reference structure
Column containing mobile structures
Select column in the input data table containing the mobile 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

Generate optimal pairwise alignment
Create a transformation matrix between the reference structure and each mobile structure and align. i.e. generate the optimal alignment for every pair of structures.
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Flow variable prefix keyword: RotateAll
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

Reference Structure in Maestro format
Mobile Structures in Maestro format

Output Ports

Aligned Structures in Maestro format


Standard output/error
Standard output/error

Best Friends (Incoming)

Best Friends (Outgoing)



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