Skip to content

Improved, Best-like contact analysis (Issue #702) #708

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

Closed
jandom wants to merge 26 commits into from
Closed

Improved, Best-like contact analysis (Issue #702) #708

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
26 commits
Select commit Hold shift + click to select a range
755631c
Improved, Best-like contact analysis (Issue #702)
Feb 9, 2016
cd67662
Revert to changes to contacts.py
Feb 10, 2016
a55119a
Arguments refactored, numpy-style docs
Feb 10, 2016
093a091
Refactor universe identity check between groups, optional scipy.spars…
Feb 10, 2016
c6fe71e
Add test files to package, rename test class for contacts
Feb 10, 2016
2440ef7
Contact analysis: move the example to cookbook
Feb 11, 2016
9f67bb2
Correct typo in tests
Feb 11, 2016
e60e4d8
Fixed module import
Feb 11, 2016
876e2a5
Fixed module imports (ii)
Feb 11, 2016
d151610
Fixed imports (iii)
Feb 11, 2016
137426e
Single class that supports both cutoff and best-hummer contacts
Feb 12, 2016
b9d35d4
Clean-up docs, bzip conf files
Feb 12, 2016
216b040
Trying to make the new Contacts class as close to ContactAnalysis1 cl…
Feb 13, 2016
07e0238
Re-link to gro.bz2 files in setup.py
Feb 14, 2016
acc2f24
Moved all the remaining methods from ContactAnalysis1 to Contacts
Feb 15, 2016
e183fe6
Deprecate the old ContactAnalysis1 class
Feb 15, 2016
e18b55c
Corrected docs, moved things around - general feature cleanup
Feb 23, 2016
c743c58
Test and docstring cleanup
Feb 24, 2016
714dd64
improvements for distances
orbeckst Feb 24, 2016
d5e2995
doc string upgrades in analysis.contacts
orbeckst Feb 24, 2016
03980b9
added back ContactAnalysis
orbeckst Feb 24, 2016
a2a3379
Merge branch 'issue-702-contacts' of github.com:jandom/mdanalysis int…
orbeckst Feb 25, 2016
c82c185
Upated CHANGELOG, brought back the old ContactAnalysis class
Feb 25, 2016
2e7c4ee
Remove any self calls from load method, to make it nice and static
Feb 26, 2016
d8df641
Merge branch 'issue-702-contacts' of https://github.com/orbeckst/mdan…
Feb 26, 2016
395a41a
Merge branch 'orbeckst-issue-702-contacts' into issue-702-contacts
Feb 26, 2016
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
8 changes: 8 additions & 0 deletions package/CHANGELOG
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,14 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
??/??/16 jandom

* 0.15.0

Changes

* Generalized contact analysis class added. (Issue #702)

??/??/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo

Expand Down
2 changes: 1 addition & 1 deletion package/MDAnalysis/analysis/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ def _conclude(self):
"""
pass

def run(self):
def run(self, **kwargs):
Copy link
Member

@kain88-de kain88-de Feb 24, 2016

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Is the run function using the kwargs?

Copy link
Member

@orbeckst orbeckst Feb 24, 2016

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think the rationale was that run functions are always happy to take in kwars... but I think I can be easily swayed to say that we should only advertise what one particular run function needs (and I know that you're a proponent of explicit kwargs). So, yes, I come around to the idea to only put in those args that are really needed.

"""Perform the calculation"""
logger.info("Starting preparation")
self._prepare()
Expand Down
Loading