Add pbc kwarg to Contacts #2646

ss62171 · 2020-03-25T20:36:40Z

Changes made in this Pull Request:

Added a kwargs boolean option 'is_box' whether to take PBC into account or not.

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

fiona-naughton · 2020-03-29T12:39:51Z

package/MDAnalysis/analysis/contacts.py

@@ -424,18 +424,28 @@ def __init__(self, u, select, refgroup, method="hard_cut", radius=4.5,
        self.select = select
        self.grA = u.select_atoms(select[0])
        self.grB = u.select_atoms(select[1])
-
+        self.is_box = self.fraction_kwargs.get('is_box')


The name is_box isn't particularly intuitive; something like pbc would be better.

Also, since it is only used in __init__ and not in the fraction_contacts methods where fraction_kwargs is passed, it'd make more sense to directly include as an argument of __init__ rather than through kwargs. This would also make it easier to include in the docs here.

fiona-naughton · 2020-03-29T13:04:35Z

testsuite/MDAnalysisTests/analysis/test_contacts.py

+        sel1 = "(resname ARG LYS) and (name NH* NZ)"
+        sel2 = "(resname ASP GLU) and (name OE* OD*)"
+        acidic = u.select_atoms(sel2)
+        basic = u.select_atoms(sel1)


You could focus the test on a particular pair we know is split across the periodic boundary, to make it easier to directly check the distances measured are what we expect given PBC.

fiona-naughton · 2020-03-29T13:07:22Z

testsuite/MDAnalysisTests/analysis/test_contacts.py

+
+        q.r0 = np.array(q.r0).squeeze()
+        r.r0 = np.array(r.r0).squeeze()
+        assert_array_equal(q.r0,r.r0)


We expect the distance to be different with or without consideration of the periodic boundaries, so this test is currently failing; maybe you could compare directly with what we expect the values to be instead?

ss62171 · 2020-03-29T17:51:47Z

@fiona-naughton @orbeckst can you please review these changes?

lilyminium · 2020-03-29T21:51:11Z

Just FYI, distance_array will take a box=None argument.

ss62171 · 2020-03-29T22:09:17Z

Just FYI, distance_array will take a box=None argument.

@lilyminium I didn't get this. Can you please clarify :)

codecov · 2020-03-29T22:09:30Z

Codecov Report

Merging #2646 into develop will decrease coverage by 0.04%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #2646      +/-   ##
===========================================
- Coverage    91.01%   90.96%   -0.05%     
===========================================
  Files          174      174              
  Lines        23595    23314     -281     
  Branches      3082     3083       +1     
===========================================
- Hits         21474    21207     -267     
+ Misses        1498     1487      -11     
+ Partials       623      620       -3

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/contacts.py	`100.00% <100.00%> (ø)`
package/MDAnalysis/auxiliary/base.py	`88.19% <0.00%> (-0.74%)`	⬇️
package/MDAnalysis/coordinates/chain.py	`87.37% <0.00%> (-0.59%)`	⬇️
package/MDAnalysis/coordinates/TRZ.py	`83.46% <0.00%> (-0.38%)`	⬇️
package/MDAnalysis/coordinates/base.py	`93.46% <0.00%> (-0.36%)`	⬇️
package/MDAnalysis/coordinates/DMS.py	`88.23% <0.00%> (-0.34%)`	⬇️
package/MDAnalysis/coordinates/GMS.py	`85.41% <0.00%> (-0.30%)`	⬇️
package/MDAnalysis/coordinates/INPCRD.py	`90.62% <0.00%> (-0.29%)`	⬇️
package/MDAnalysis/coordinates/GSD.py	`86.95% <0.00%> (-0.28%)`	⬇️
package/MDAnalysis/coordinates/TXYZ.py	`90.10% <0.00%> (-0.22%)`	⬇️
... and 37 more

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fiona-naughton

A couple comments.

Following @lilyminium's comment, you could set a value box based on pbc (ie. None or dimensions, as appropriate) and run distance_array with that, rather than needing an if/else every time.

fiona-naughton · 2020-03-31T03:41:17Z

package/MDAnalysis/analysis/contacts.py

@@ -392,6 +392,9 @@ def __init__(self, u, select, refgroup, method="hard_cut", radius=4.5,
        method : string | callable (optional)
            Can either be one of ``['hard_cut' , 'soft_cut', 'radius_cut']`` or a callable
            with call signature ``func(r, r0, **kwargs)`` (the "Contacts API").
+        pbc : bool (optional)
+            Uses periodic boundary conditions to calculate distances if set to ``True``; the
+             default is ``False``.


I would set the default to True instead, since this is probably what most users would expect the behaviour to be

fiona-naughton · 2020-03-31T03:46:41Z

package/MDAnalysis/analysis/contacts.py

@@ -461,7 +479,8 @@ def _new_selections(u_orig, selections, frame):
    """create stand alone AGs from selections at frame"""
    u = MDAnalysis.Universe(u_orig.filename, u_orig.trajectory.filename)
    u.trajectory[frame]
-    return [u.select_atoms(s) for s in selections]
+    temp_u = u.copy()


The idea of using copy() here would be to avoid having to reload a universe from the filenames - you can copy u_orig directly.

can I fix this in another pull request?

fiona-naughton · 2020-03-31T03:55:58Z

testsuite/MDAnalysisTests/analysis/test_contacts.py

+        average_contacts_r = np.mean(r.timeseries[:, 1])
+        average_contacts_q = np.mean(q.timeseries[:, 1])
+
+        assert not average_contacts_q == average_contacts_r


A test like this isn't ideal as inequality could be due to any number of things going wrong. I'd find a specific value(s) you expect to be returned and check against that - say by measuring the expected distances with and without PBC in another program or directly using distance_array

lilyminium · 2020-03-31T19:23:27Z

you could set a value box based on pbc (ie. None or dimensions, as appropriate) and run distance_array with that, rather than needing an if/else every time.

Yep, thanks for clarifying @fiona-naughton. However the box dimensions will change for every frame in an NPT ensemble so it might be better to set a box getting function to use in _single_frame instead e.g.

if pbc:
    self._get_box = lambda ts: ts.dimensions
else:
    self._get_box = lambda ts: None

and call it with box=self._get_box(self._ts). This is less readable than if/else-ing though.

ss62171 · 2020-03-31T19:48:51Z

@lilyminium thanks for clarifying and providing better way to implement this :)

ss62171 · 2020-04-02T19:57:03Z

@fiona-naughton any other changes needed?

ss62171 · 2020-04-06T22:16:46Z

@lilyminium can you please review this.

lilyminium

Please also update CHANGELOG and add a .. versionchanged to the docstring of Contacts.

lilyminium · 2020-04-08T07:04:21Z

testsuite/MDAnalysisTests/analysis/test_contacts.py

+                        refgroup=(acidic, basic), radius=6.0, pbc=pbc)
+        r.run()
+        if pbc:
+            expected = [1., 0.43138152, 0.3989021, 0.43824337, 0.41948765,


Looks good @ss62171 -- personally I would change the test so that the expected values are also part of parametrize, e.g.

@pytest.mark.parametrize("pbc,expected", [ (True, [1., 0.43138152, 0.3989021, 0.43824337, 0.41948765, 0.42223239, 0.41354071, 0.43641354, 0.41216834, 0.38334858]), (False, [1., 0.42327791, 0.39192399, 0.40950119, 0.40902613, 0.42470309, 0.41140143, 0.42897862, 0.41472684, 0.38574822]) ])

A new push would also restart the Appveyor tests, which as far as I can tell have failed due to running out of time. I can't seem to restart these jobs individually without a commit -- @MDAnalysis/coredevs have any insight?

lilyminium · 2020-04-09T08:18:56Z

package/MDAnalysis/analysis/contacts.py

@@ -373,6 +373,8 @@ class Contacts(AnalysisBase):
    .. versionchanged:: 1.0.0
       ``save()`` method has been removed. Use ``np.savetxt()`` on
       :attr:`Contacts.timeseries` instead.
+    .. versionchanged:: 2.0.0


Thanks @ss62171, just one final thing -- this should be for version 1.0.0 which hasn't been released yet.

lilyminium · 2020-04-10T11:25:08Z

Thanks @ss62171, looks good to me! Are you happy with this @fiona-naughton?

ss62171 · 2020-04-18T15:37:33Z

@lilyminium any updates on this?

lilyminium · 2020-04-20T06:23:46Z

Sorry for the delay @ss62171, I've been busy. I've requested another review from @fiona-naughton and if she doesn't do so within 24 hours I'll presume that she is too and merge the PR.

Fiona's comments re: pbc=True kwarg name and default, and the test equality have been addressed; the copy() comment refers to now-removed code.

lilyminium · 2020-04-22T06:07:13Z

Thanks for your patience @ss62171, this will make Contacts analysis much nicer to use.

ss62171 added 2 commits March 26, 2020 01:46

Fixes MDAnalysis#2368: added option to calculate distances using PBC

921eb56

Added test to check distance calculated using PBC

d796742

fiona-naughton requested changes Mar 29, 2020

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test added

856344c

documented changes

05a442c

fiona-naughton previously requested changes Mar 31, 2020

View reviewed changes

added box_dim and test modified

c97cacc

added lambda func to get dimension of box

8b204d2

lilyminium requested changes Apr 8, 2020

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edit changelog and docstring of class

ee62918

lilyminium requested changes Apr 9, 2020

View reviewed changes

fixed typo

043819b

lilyminium approved these changes Apr 10, 2020

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lilyminium requested a review from fiona-naughton April 20, 2020 06:22

lilyminium changed the title ~~Contact~~ Add pbc kwarg to Contacts Apr 22, 2020

lilyminium merged commit 400f93c into MDAnalysis:develop Apr 22, 2020

fiona-naughton added the defect label Sep 26, 2023

fiona-naughton added the Component-Analysis label Sep 26, 2023

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Add pbc kwarg to Contacts #2646

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Add pbc kwarg to Contacts #2646

Add pbc kwarg to Contacts #2646

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