More improvements and fixes

[jamesmkrieger]

• Critical fix when using start frame - otherwise, it doesn't analyse enough frames
  For both trajectory and multi-model PDB

• added use_segname to getResidueName for use with calcBridgesResiduesHistogram

• made selectSurroundingBox select whole residues

Now, we should get sensible results

[karolamik13]

There is a problem with calcWaterBridgesTrajectory()

calcWaterBridgesTrajectory(coords_traj, trajectory, method='cluster')

@> Frame: 0
@> Frame: 1
@> Frame: 2
Process Process-2:
@> Frame: 3
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
Process Process-3:
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
Traceback (most recent call last):
NameError: free variable 'indices' referenced before assignment in enclosing scope
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
Process Process-4:
@> Frame: 4
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
Process Process-5:
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
NameError: free variable 'indices' referenced before assignment in enclosing scope
Traceback (most recent call last):
@> Frame: 5
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
NameError: free variable 'indices' referenced before assignment in enclosing scope
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
NameError: free variable 'indices' referenced before assignment in enclosing scope
Process Process-6:
Traceback (most recent call last):
Process Process-7:
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
NameError: free variable 'indices' referenced before assignment in enclosing scope
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
NameError: free variable 'indices' referenced before assignment in enclosing scope
@> Frame: 6
@> Frame: 7
@> Frame: 8
Process Process-8:
@> Frame: 9
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
@> Frame: 10
Process Process-9:
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
NameError: free variable 'indices' referenced before assignment in enclosing scope
Process Process-10:
@> Frame: 11
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
Process Process-11:
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
NameError: free variable 'indices' referenced before assignment in enclosing scope
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
NameError: free variable 'indices' referenced before assignment in enclosing scope
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
NameError: free variable 'indices' referenced before assignment in enclosing scope
Process Process-12:
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
Process Process-13:
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
NameError: free variable 'indices' referenced before assignment in enclosing scope
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 575, in analyseFrame
atoms_copy = atoms_copy[indices]
NameError: free variable 'indices' referenced before assignment in enclosing scope
@> Frame: 12
@> Frame: 13
@> Frame: 14
..

[jamesmkrieger]

Ah ok. I need to set indices as None if there’s no selection. Thanks

[karolamik13]

I have a similar error as previously.

calcWaterBridgesTrajectory(coords_traj, trajectory, method='cluster')
@> Frame: 0
@> Frame: 1
@> Frame: 2
@> Frame: 3
@> Frame: 4
@> Frame: 5
Process Process-3:
Process Process-2:
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/atomic/atomgroup.py", line 220, in getitem
index = int(index)
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/atomic/atomgroup.py", line 220, in getitem
index = int(index)
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'
Process Process-4:

During handling of the above exception, another exception occurred:

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/atomic/atomgroup.py", line 220, in getitem
index = int(index)
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
Process Process-5:
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'
File "/home/karolamik/anaconda3/envs/prody/lib/python3.9/site-packages/ProDy-2.4.1-py3.9-linux-x86_64.egg/prody/proteins/waterbridges.py", line 576, in analyseFrame
atoms_copy = atoms_copy[indices]

During handling of the above exception, another exception occurred:
...

I have such problems with two systems with MD, but when I am running your script "example.py" for 4a0v, it looks good.

python example.py
@> Atom group was loaded in 0.47s.
@> DCD file contains 4 coordinate sets for 707044 atoms.
@> DCD file was parsed in 0.04 seconds.
@> 32.37 MB parsed at input rate 902.61 MB/s.
@> 4 coordinate sets parsed at input rate 111 frame/s.

running 1 times with 4 frames for 1 subunit
@> Frame: 0
@> Frame: 1
@> Frame: 2
@> Frame: 3
@> 7 water bridges detected using method chain for frame 0
@> 710 water bridges detected using method chain for frame 1
@> 679 water bridges detected using method chain for frame 2
@> 705 water bridges detected using method chain for frame 3

timing is 0.307 minutes total, or 4.606 seconds/frame

running 1 times with 4 frames for 4 subunits
@> Frame: 0
@> Frame: 1
@> Frame: 2
@> Frame: 3
@> 34 water bridges detected using method chain for frame 0
@> 2180 water bridges detected using method chain for frame 1
@> 2138 water bridges detected using method chain for frame 3
@> 2157 water bridges detected using method chain for frame 2

timing is 0.963 minutes total, or 14.449 seconds/frame

[karolamik13]

I tested two cases with MD trajectories, all WatFinder functions from the ProDy website tutorial, and your script for TriC/CCT. Everything is working fine.

[jamesmkrieger]

ok, now it's working for savePDBWaterBridgesTrajectory too!

[karolamik13]

I tested all main functionalities of WatFinder (two cases with MDs (case study 2 and 4), general WatFinder tutorial, example.py from James, and calculations for TriC/CCT (case study 5 provided by James).
Everything looks good.