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Compute FlexS Alignments

BioSolveIT Plugins version 2.12.0.0001047 by BioSolveIT GmbH

This node performs FlexS 3D alignments. The approach used here is to have a query molecule which is used as a so-called reference, and a molecule data stream (library) at the input ports. The library molecules will be aligned onto the reference molecule and the aligned conformations will be sent to the output port.

The node is an interface to trigger external FlexS runs that perform 3D molecular alignments. The path to the external FlexS executable has to be configured in
File -> Preferences -> KNIME -> BioSolveIT Settings -> FlexS
Please mind: FlexS has to be licensed and installed separately.
The easiest way to install FlexS is to install the BioSolveIT KNIME binary package for FlexS.
See http://www.biosolveit.de/FlexS/ for more details.

Options

Select the column containing the query molecule
The molecule provided in this column is used as a template for the 3D alignment. If the input table contains more than one column with a compatible type, you can choose which column should be taken. The column has to be in SDF or Mol2 format with 3D coordinates. Please note that currently only the molecule is used.
Select the column containing the library molecule(s)
The molecules provided in this column are aligned with the query molecule. If the input table contains more than one column with a compatible type, you can choose which column should be taken. Compatible types are SDF or Mol2 format with 3D coordinates.
Number of poses per molecule
Choose the number of alignment poses you want to generate per library molecule.
Type of output
Here you can select what type of output should be generated:

Pose: The output table only contains the library molecule poses.
Score: The output table only contains the score of the poses.
Score + Pose: The output table contains both score and poses.
Result Table: The output table contains a detailed results table including score contributions.
Result Table + Pose: The output table contains a detailed results table and the poses.
Append all data columns of library table.
Select append all additional data columns of your input table to the output table.
Use remote computing via SSH
Select run FlexS on a remote server. Please set up your remote computing settings in the FlexS global settings using
File -> Preferences -> KNIME -> BioSolveIT Settings -> FlexS
Keep debug files and show the log after the run
This setting keeps all temporary files and opens an edtior to show the output of the external program. This setting is very helpful for debugging.
TAB: Script
Here you can customize your FlexS alignment script. Please modify it only if you are sure you know what you are doing. You can use the following variables in your script:

@job_library_size - The Library size. It is currently set fixed to the count of incoming molecules.
@nof_poses - The number of poses as defined in the Settings tab.
@queryfile - The incoming reference molecule. This must be in Mol2 format and must contain partial charges. Only the first row will be used.
@libraryfile - The incoming molecule. It must be in Mol2 format and must contain partial charges.
@resultfile - The computed results table. This will be created by FlexS.
@posesfile - The computed poses file. This will be created by FlexS.

Input Ports

Query: Input table with at least one column containing a molecule in Mol2 (preferably with partial charges) or SDF format with 3D coordinates. Please note that currently only the first molecule will be used.
Library: Input table with at least one column containing a molecule in Mol2 (perferably with partial charges) or SDF format with 3D coordinates.

Output Ports

Alignments: Output table that contains the 3D Alignments.
Errors: The rows of the incoming table which could not be aligned for any reason.

Best Friends (Incoming)

Best Friends (Outgoing)