add findSurfaceResiduesListCharged.py #132
Conversation
|
Thanks @speleo3 , I forwarded the feedback to Teddy. He replied with some changes and a new file/API: https://pymolwiki.org/index.php/FindSurfaceCharge |
There was a problem hiding this comment.
Doesn't run properly if there are multiple objects in the selection (e.g. multiple objects in the workspace and you run the command without any provided arguments). Perhaps this should first detect the objects in the selection first and provide the charge for each object surface.
findSurfaceCharge.py
Outdated
| cmd.iterate(selName, "exposed.add((resv))", space=locals()) | ||
| cmd.delete(selName) | ||
|
|
||
| selNameRes = cmd.get_unused_name("exposed_res_") |
There was a problem hiding this comment.
unused variable?
findSurfaceCharge.py
Outdated
| cmd.iterate(allRes, "first.add((resv))", space=locals()) | ||
| cmd.delete(allRes) | ||
|
|
||
| selNameRes = cmd.get_unused_name("exposed_res_") |
There was a problem hiding this comment.
unused variable?
findSurfaceCharge.py
Outdated
|
|
||
| first=sorted(first)[0] #firstRes | ||
| #gets all charged amino acids on the surface | ||
| reslist= [] |
There was a problem hiding this comment.
reslist appended, but never used?
findSurfaceCharge.py
Outdated
| return selName | ||
|
|
||
|
|
||
| def findSurfaceCharge(pH=7.0, folded=True, selection="all", cutoff=2.5): |
There was a problem hiding this comment.
Might be helpful to also return the charge so that it's easier for the caller to obtain.
findSurfaceCharge.py
Outdated
| cutoff = float(cutoff) | ||
|
|
||
| selName = findSurfaceAtoms(selection, cutoff) | ||
|
|
||
| exposed = set() | ||
| cmd.iterate(selName, "exposed.add((resv))", space=locals()) | ||
| cmd.delete(selName) | ||
|
|
||
| selNameRes = cmd.get_unused_name("exposed_res_") | ||
|
|
||
| exposed=sorted(exposed) #list of exposed residues |
There was a problem hiding this comment.
readability: would probably pull out to another function
get_exposed_residues(selection: str, cutoff: float) -> set:or similar.
findSurfaceCharge.py
Outdated
| first = set() | ||
| allRes = findSurfaceAtoms(selection, 0) | ||
| cmd.iterate(allRes, "first.add((resv))", space=locals()) | ||
| cmd.delete(allRes) | ||
|
|
||
| selNameRes = cmd.get_unused_name("exposed_res_") | ||
|
|
||
| first=sorted(first)[0] #firstRes |
There was a problem hiding this comment.
readability: might be more readable to pull this out into its own func.
get_first_residue(selection: str) -> int:
There was a problem hiding this comment.
Looks OK to me.
Some optional improvements:
- add type hints
- auto-format code (yapf, black, ...)
- add module docstring which points to the wiki page
foldedargument is not really needed since the user can passcutoff=0
Tests would be nice, but I understand that there is no infrastructure in place in the repo.
|
Merged. As separate commit 4fcf977 since Github doesn't seem to specific commit author to someone else if one performs a squash merge. |
Adding this script on behalf of Teddy Warner from MIT.
Script page on the Wiki: https://pymolwiki.org/index.php/FindSurfaceResiduesListCharged