vermouth-martinize
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marrink-lab
Describe and apply transformation on molecular structures and topologies
We (still) have some maintenance debt to repay. In particular, there are some processors that have no tests (as in 0), and a couple which only have sparse test coverage....
We inherited the current mapping dir structure from backwards. We should revisit this, and make it easier to find the mappings that can be applied for mapping e.g. universal to...
Currently only links can have choices (i.e. a link might apply to a molecule if the respective attribute matches one in the link choice list). However, it would be an...
>if I want the pdb to define it I do what? Hah! That's now impossible :') If you do '-cter none' you'll end up with a chemically nonsense, uncapped terminus....
https://github.com/marrink-lab/vermouth-martinize/blob/f33eb3d3c5724186267dca2e1f26dc4fb9b9d5cb/vermouth/pdb/pdb.py#L410-L412 Should be list of molecules.
It seems that the performance improvement in master has significantly slowed down the mutation processor. For a single mutation I go from 9s to 53s (!)
Currently, modifications can only act on residues where there are unexpected atoms (such as PTMs). However, in some cases it is desireable to only remove atoms. E.g. uncharged amine groups....
Running martinize2 with `-ff elnedyn22p` fails with an error about nodes not having a "chain" key during linking. I suspect that dummy beads are not populated appropriately during the mapping...
When atoms are missing in the input structure their nodes get created by repair_graph, but they are not given a position. We need a processor that takes a system, and...
I will likely not implement it in #41 where I planned to because the PR is already enormous. So I write it down here. We need to support secondary structures...
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Describe and apply transformation on molecular structures and topologies