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FlexPepDock Concatenation

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FlexPepDock Concatenation


Thanks in advance for all those who help out with this issue. Using the FlexPepDock application, I have generated multiple decoys.silent files (binary) during docking. Multiple decoys.silent files were generated as I used a small cluster of 20 processors where each processor generated its own decoys_X.silent file. Now that I have successfully performed these docks, I would like to concatenate all of the decoys.silent files into a single decoys.silent file for analysis. Is it possible to simply use the method below...

cat decoys_1.silent decoys_2.silent decoys_3.silent > decoys.silent

However, I recall using a different and more complicated script when concatenating silent files in the LigandDock application.


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Mon, 2014-08-11 07:39

How you combine silent files depends on the type of silent file you use.

Ligand docking used a format called "AtomTreeDiff", which required a specialist program to combine the structures.

I'm guessing that the silent files that you have from FlexPepDock are of the "protein" or "binary" silent file format. These formats are set up for simple concatenation - that is, using the commandline you propose should work. Alternatively, we have programs which will do the combination for you. For example, the combine_silent application:

combine_silent.linuxgccrelease -in:file:silent decoys_1.silent decoys_2.silent decoys_3.silent -out:file:silent decoys.silent

The benefit of this is you can control the output file format (e.g. by adding "-out:file:silent_struct_type binary") or only extract and combine certain structures, by using the "-in:file:tags" option.

For the simple use cases, though, the "cat" approach works just fine.

Tue, 2014-08-12 08:24

Thanks rmorreti! Your response was very helpful.

Wed, 2014-08-13 10:06