(protein) termini patching #374
Conversation
- with the -ter flag, add modifications read from the force field to the n and c termini
… remove terminal modifications
- updated m3 command to include -ter - new m3/prot.itp with correct parameters
There was a problem hiding this comment.
We're on the right track here. What do you think about making this a general modifications processor. I would parese a stirng of potential modifcations with the same syntax as used for splitting ligands etc. like so:
-mods <resname>#<resid>:modification_name
Of course we are lazy people so we keep the terminal patch for proteins. But I suggest that the ter flag takes to potential values such that you can toggle between charged and neutral.
In your apply_modifications processor, you want to loop over the list of modifications taken from the input and call parse_residue_spec(resspec) from annotate_ligands. This returns a dict of resids and resnames. So then you can go and loop over the meta-molecule to do the modifications. You may want to check of both resid and resname are given that they match.
For the protein terminal case you basically keep doing what you're doing, but simply take the highest/lowest resid.
There was a problem hiding this comment.
@csbrasnett looks pretty good; I've some detail comments which I think should be easy to fix
There was a problem hiding this comment.
I've left some comments about a potential strategy to set the correct default values for the terminal modifications.
There are two edge-cases where this strategy will fail:
-
If a non-protein residue has an atom named BB. I think we should simply add protein resnames to the modification dict and check those. You can make a variable like in the ff file
protein_resnames = 'ALA|LYS|...'and then when applying we simply check if the resnames match. Since Vermouth generates avermouth.molecule.Choiceobject you need to do the check usingChoice.match. Calling @pckroon for some advise of comparing resnames using choice objects. -
When a protein itp is provided to begin with. Like in the case of PEGylated proteins. However, these nodes have a special attribute
from_itpat the meta_molecule level. Thus we can simply check if this attribute exists and if it does we do not patch.
Both checks I would add to apply modification and not to patch termini. If you need help or have questions let me know. Thanks for taking care of this.
Use |
- removed -ter flag from polyply - -ter flag is not necessary anymore because apply_modifications.py will automatically add protein termini to the resspec if no modifications are given - the modifications in the resspec will then only be applied if the target residue is in fact a protein residue
|
I think this addresses everything now, let me know your thoughts. One point of concern - when I was looking at doing a test for the final missing part of the codecov report, I can't see a 'from_itp' key in the node dictionary for the test molecules, even though they have been? Looking at meta_molecule.py I'm not sure how/where this is added anyway? |
There was a problem hiding this comment.
@csbrasnett only minor comments; and I want to wait for PR #381 to be merged because that brings a required bug fix to the template generation workflow.
with the -ter flag, add modifications read from the force field to the n and c termini