add automated toppar generation for unknown small molecules#1476
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rvhonorato merged 53 commits intomainfrom Feb 27, 2026
Merged
add automated toppar generation for unknown small molecules#1476rvhonorato merged 53 commits intomainfrom
rvhonorato merged 53 commits intomainfrom
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Sorted it out (: |
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February 25, 2026 13:01
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amjjbonvin
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Very nice! Works perfectly on my side
Would it be possible to also compile the prodrg exec for aarch64-linux?
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A very nice addition!
Works fine on my side - will should do some benchmarking on a protein-ligand dataset to check the performance (the shape docking set is a good one for this).
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Checklist
CHANGELOG.mdis updated to incorporate new changesSummary of the Pull Request
This PR adds a new
libligandwith the purpose of handling small molecules, in this case specifically the creation.topand.paramfiles using PRODRG.Currently when the user does not input
ligand_param/top_fnameand the input contains any unknown hetatms, there are just deleted during sanitization. I am not sure if this is the desired behaviour or not, but assuming it is - I added a new boolean parameter calledautotopparto ensure this pathway of removing unknown atoms can be preserved.So to trigger the automated generation, the user needs to set
autotoppar=trueand if this parameter is defined together withligand_param/top_fname,ligand_param/top_fnametakes priority.The automated topology/param generation of small molecules is done via
prodrg- shipped as a binary with the code after this PR. I also added two sanitization methods to removeNBONdsfrom the parameters generated by prodrg as they can interfer with haddock ones, and also found that prodrg will sometimes add a:to the topology which breaks CNS syntax - so there is another method to clean it.And needles to say this only applies to things that are not known by haddock, which is defined in
haddock.core.supported_molecules.When we automate the toppar generation, what means is that we are effectively setting the
ligand_param/top_fnamefor the user. This is easily done in the module that generates it, but this value needs to be propagated so that modules downstream on the workflow can also access it. To deal with this behaviour I added a new logic inlibworkflowto handle this propagation.Related Issue
#1475
Additional Info
We currently only have prodrg binaries for
x86_64-linuxandarm64-darwin- when we have others they should also be added here, but we need to handle this elsewhere, please look here: https://github.com/haddocking/prodrgrun_prodrgwill fail graciously ifautotoppar=truein an unsupported architecture.