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

Jump to bottom

Two doctest fixes #4366

Merged
merged 8 commits into from
Dec 21, 2023
Merged

Two doctest fixes #4366

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
30c8bcc
Fixed errors in atomicdistances.py
ljwoods2 Dec 15, 2023
eadfff0
Removed unused import
ljwoods2 Dec 15, 2023
ad513dd
Fixed tests in overview.rst
ljwoods2 Dec 15, 2023
1cd5749
Added name to authors per PR feedback
ljwoods2 Dec 15, 2023
7f54629
Added username to CHANGELOG
ljwoods2 Dec 17, 2023
1840877
Added CHANGELOG entry describing PR
ljwoods2 Dec 17, 2023
6605d48
Merge branch 'develop' into two-doctest-fixes
ljwoods2 Dec 20, 2023
33ca37c
Merge branch 'develop' into two-doctest-fixes
RMeli Dec 21, 2023
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
44 changes: 21 additions & 23 deletions package/MDAnalysis/analysis/atomicdistances.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,53 +67,51 @@

We will calculate the distances between an atom group of atoms 101-105
and an atom group of atoms 4001-4005 with periodic boundary conditions.
To select these atoms:
To select these atoms: ::

>>> u = mda.Universe(GRO, XTC)
>>> ag1 = u.atoms[100:105]
>>> ag2 = u.atoms[4000:4005]

We can run the calculations using any variable of choice such as
``my_dists`` and access our results using ``my_dists.results``:
``my_dists`` and access our results using ``my_dists.results``: ::

>>> my_dists = ad.AtomicDistances(ag1, ag2).run()
>>> my_dists.results
array([[37.80813681, 33.2594864 , 34.93676414, 34.51183299, 34.96340209],
[27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345],
[23.27210749, 30.38714688, 32.48269361, 31.91444505, 31.84583838],
[18.40607922, 39.21993135, 39.33468192, 41.0133789 , 39.46885946],
[26.26006981, 37.9966713 , 39.14991106, 38.13423586, 38.95451427],
[26.83845081, 34.66255735, 35.59335027, 34.8926705 , 34.27175056],
[37.51994763, 38.12161091, 37.56481743, 36.8488121 , 35.75278065],
[37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816],
[38.76272761, 41.31816555, 38.81588421, 39.82491432, 38.890219 ],
[39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]])
[27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345],
[23.27210749, 30.38714688, 32.48269361, 31.91444505, 31.84583838],
[18.40607922, 39.21993135, 39.33468192, 41.0133789 , 39.46885946],
[26.26006981, 37.9966713 , 39.14991106, 38.13423586, 38.95451427],
[26.83845081, 34.66255735, 35.59335027, 34.8926705 , 34.27175056],
[37.51994763, 38.12161091, 37.56481743, 36.8488121 , 35.75278065],
[37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816],
[38.76272761, 41.31816555, 38.81588421, 39.82491432, 38.890219 ],
[39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]])

To do the computation without periodic boundary conditions, we can enter
the keyword argument ``pbc=False`` after ``ag2``. The result is different
in this case:
in this case: ::

>>> my_dists_nopbc = ad.AtomicDistances(ag1, ag2, pbc=False).run()
>>> my_dists_nopbc.results
array([[37.80813681, 33.2594864 , 34.93676414, 34.51183299, 34.96340209],
[27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345],
[23.27210749, 30.38714688, 32.482695 , 31.91444505, 31.84583838],
[18.40607922, 39.21992825, 39.33468192, 41.0133757 , 39.46885946],
[26.26006981, 37.99666906, 39.14990985, 38.13423708, 38.95451311],
[26.83845081, 34.66255625, 35.59335027, 34.8926705 , 34.27174827],
[51.86981409, 48.10347964, 48.39570072, 49.14423513, 50.44804292],
[37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816],
[56.39657447, 41.31816555, 38.81588421, 39.82491432, 38.890219 ],
[39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]])
[27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345],
[23.27210749, 30.38714688, 32.482695 , 31.91444505, 31.84583838],
[18.40607922, 39.21992825, 39.33468192, 41.0133757 , 39.46885946],
[26.26006981, 37.99666906, 39.14990985, 38.13423708, 38.95451311],
[26.83845081, 34.66255625, 35.59335027, 34.8926705 , 34.27174827],
[51.86981409, 48.10347964, 48.39570072, 49.14423513, 50.44804292],
[37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816],
[56.39657447, 41.31816555, 38.81588421, 39.82491432, 38.890219 ],
[39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]])

"""

import numpy as np

from MDAnalysis.lib.distances import calc_bonds


import warnings
import logging
from .base import AnalysisBase

Expand Down
2 changes: 1 addition & 1 deletion package/doc/sphinx/source/documentation_pages/overview.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ over time::
< DCDReader '/..../MDAnalysis/tests/data/adk_dims.dcd' with 98 frames of 3341 atoms (0 fixed) >

Finally, the :meth:`MDAnalysis.Universe.select_atoms` method generates a new
:class:`~MDAnalysis.core.groups.AtomGroup` according to a selection criterion
:class:`~MDAnalysis.core.groups.AtomGroup` according to a selection criterion::

>>> calphas = u.select_atoms("name CA")
>>> print(calphas)
Expand Down
Loading