Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

WatFinder - findClusterCenters() extension #1967

Merged
merged 7 commits into from
Oct 30, 2024
Merged

WatFinder - findClusterCenters() extension #1967

Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
9fa736c
extension of findClusterCenters() functionality
karolamik13 Oct 6, 2024
63ece76
findClusterCenters() improvement - HOH is added to water selection
karolamik13 Oct 6, 2024
ae788f4
fix indents
jamesmkrieger Oct 7, 2024
7d5a566
use any water in findClusterCenters
jamesmkrieger Oct 7, 2024
1b7c3cf
reorder to use else for nonwater
jamesmkrieger Oct 7, 2024
d1aaecd
changes to more general selection for oxygen [findClusterCenters()]
karolamik13 Oct 7, 2024
c17d92b
Merge branch 'prody:main' into interactions
karolamik13 Oct 11, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 10 additions & 4 deletions prody/proteins/waterbridges.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ def auto(it=count()):

from prody import LOGGER, SETTINGS
from prody.atomic import Atom, Atomic, AtomGroup
from prody.atomic.flags import DEFAULTS
from prody.ensemble import Ensemble
from prody.measure import calcAngle, calcDistance
from prody.measure.contacts import findNeighbors
Expand Down Expand Up @@ -1297,7 +1298,7 @@ def findClusterCenters(file_pattern, **kwargs):
:type file_pattern: str

:arg selection: selection string
by default water and name OH2 is used
by default 'water and name "O.*"' is used
:type selection: str

:arg distC: distance to other molecules
Expand All @@ -1317,7 +1318,7 @@ def findClusterCenters(file_pattern, **kwargs):
import glob
import numpy as np

selection = kwargs.pop('selection', 'water and name OH2')
selection = kwargs.pop('selection', 'water and name "O.*"')
distC = kwargs.pop('distC', 0.3)
numC = kwargs.pop('numC', 3)
filename = kwargs.pop('filename', None)
Expand All @@ -1333,8 +1334,13 @@ def findClusterCenters(file_pattern, **kwargs):
removeResid = []
removeCoords = []
for ii in range(len(coords_all)):
sel = coords_all.select('water within '+str(distC)+' of center',
center=coords_all.getCoords()[ii])
if 'water' in selection.split() or np.any([water in selection.split() for water in DEFAULTS['water']]):
sel = coords_all.select('water within '+str(distC)+' of center',
center=coords_all.getCoords()[ii])
else:
sel = coords_all.select(str(selection)+' within '+str(distC)+' of center',
center=coords_all.getCoords()[ii])

if sel is not None and len(sel) <= int(numC):
removeResid.append(coords_all.getResnums()[ii])
removeCoords.append(list(coords_all.getCoords()[ii]))
Expand Down
Loading