Molecule Aligner (FlexS)

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.

FlexS has to be licensed separately, see http://www.biosolveit.de/FlexS/ for more details.

Options

Library column

Name of the column containing the molecules that should be aligned. Allowed formats are sdf or mol2. 3d coordinates are required.

Reference molecule column

Name of the column containing the reference molecule. Allowed formats are sdf or mol2. 3d coordinates are required.

Similarity threshold

Only those library molecules exceeding the similarity threshold will be piped into the results. If you want to retrieve all possible results, set this value to zero.

Number of alignments

Specify the maximum number of generated aligned molecules per input molecule.

Append all data columns of the library table

Select this if you want to append all data columns of your input table to the output table.

Keep debug files and show the log after the run

This setting keeps all temporary files and opens an editor to show the output of the external program. This setting is very helpful for debugging.

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