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Add mmcif compatibility to mdanalysis library #57

Merged
merged 16 commits into from
Nov 24, 2021
Merged

Add mmcif compatibility to mdanalysis library #57

merged 16 commits into from
Nov 24, 2021

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joaomcteixeira
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Add mmcif compatibility to mdanalysis library.

See MDAnalysis/mdanalysis#2367 (comment)

@joaomcteixeira joaomcteixeira added the enhancement New feature or request label Nov 23, 2021
@joaomcteixeira joaomcteixeira self-assigned this Nov 23, 2021
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codecov-commenter commented Nov 23, 2021

Codecov Report

Merging #57 (6072acf) into master (ed69930) will not change coverage.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff            @@
##            master       #57   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           21        22    +1     
  Lines         1122      1136   +14     
  Branches        84        85    +1     
=========================================
+ Hits          1122      1136   +14     
Impacted Files Coverage Δ
src/taurenmd/libs/libmda.py 100.00% <100.00%> (ø)
src/taurenmd/libs/libmdt.py 100.00% <100.00%> (ø)
src/taurenmd/libs/libopenmm.py 100.00% <100.00%> (ø)

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@joaomcteixeira
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The feature is working perfectly when the client runs. Also, it works when importing manually from a script, for example:

import subprocess

cmd = 'taurenmd report tests/data/pcnaA_frame0.cif tests/data/pcnaA.dcd'

p = subprocess.run(cmd.split(), capture_output=True)
print(p)

from taurenmd.libs.libmda import load_universe

load_universe('tests/data/pcnaA_frame0.cif', 'tests/data/pcnaA.dcd')

But can't make it work in the test cases in tests_libmda.py...

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codeclimate bot commented Nov 24, 2021

Code Climate has analyzed commit b5c0ff4 and detected 0 issues on this pull request.

View more on Code Climate.

@joaomcteixeira joaomcteixeira merged commit 08f0f33 into master Nov 24, 2021
@joaomcteixeira joaomcteixeira deleted the mmcif branch November 24, 2021 22:29
joaomcteixeira added a commit that referenced this pull request Nov 24, 2021
Merge pull request #57

Add mmcif compatibility to mdanalysis library
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2 participants