vermouth-martinize
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marrink-lab
Describe and apply transformation on molecular structures and topologies
This PR implements a temporary interactions dict instead of using the replace_interaction function in DoLinks. The benefit is that do-links does not iterate over the complete interactions list every time...
#434 quick-fixes #433, but @fgrunewald raised the good point that the true solution is to have all writers accept a file handle rather than a path. This way you could...
If no chain is provided in the PDB somehow we don't set the default A. Is that correct?
Apparently write itp get's the node indices from the order of the node-dict of a molecule not the actual key. This is actually problematic for example if you want to...
The selector used to select what is a protein is very limited and uses a hardcoded list of protein residues. I encountered limitations due to that while using specific names...
Not many people are using scfix with Martini3 proteins even though it improves side-chain conformations and dynamics. Perhaps it would be best to make this option default.
To streamline the code in places (especially with links) it would be good to have a ResidueID class, that combines the residue number, name and chain, and/or has a reference...
Apparently of the Model number exceeds 10000 the pdb reader fails without error and just returns an empty list. Not sure how much this is a PDB format thing, but...
``` [ link ] resname "DT|DG|DC|DA" [ bonds ] BB3 >BB1 1 0.35300 10000 {"group": "link"} [ angles ] BB2 BB3 >BB1 2 102.00000 150 {"group": "link"} BB3 >BB1 >BB2...
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Describe and apply transformation on molecular structures and topologies