WIP: multipucker

[hainm]

No description provided.

[PhiMykah]

@hainm I had some time so I started implementation of multipucker on the multipucker branch this on this fork. Before starting a pull request, I was curious about what to do with the frame_indices parameter with multipucker, and what tests to implement. I am unsure what tests I can perform that have expected results. Any other comments or suggestions are appreciated. Thank you!

[hainm]

I was curious about what to do with the frame_indices parameter with multipucker

Please see super_dispatch code. I think if frame_indices is not None, the code will slice the given traj
saying multipucker(traj, frame_indices=[1,3,5]) will return value fro only 3 frames.

[hainm]

and what tests to implement. I am unsure what tests I can perform that have expected results.

Traditionally we reuse the cpptraj's command in its testing folder to make sure to reproduce exact values

• You can make a new test file in this folder: https://github.com/Amber-MD/pytraj/tree/6d62181522d0ef8d35a41e3a78e52821046dd667/tests/test_analysis
• see this for example: https://github.com/Amber-MD/pytraj/blob/6d62181522d0ef8d35a41e3a78e52821046dd667/tests/test_analysis/test_pucker.py

Please let me know if you have other questions. Cheers.

[hainm]

@PhiMykah Please see cpptraj's command for multipucker here: https://github.com/Amber-MD/cpptraj/blob/master/test/Test_MultiPucker/RunTest.sh

(and find many tests for many others here: https://github.com/Amber-MD/cpptraj/tree/master/test)

[PhiMykah]

@hainm Hello! I am doing some multipucker testing, and currently I am having issues with running pyranoid puckertypes. I ran test_multipucker.py found here using unittest, and received the following error regarding the pyranoid test:

/.../source/pytraj/pytraj/all_actions.py:3207: ResourceWarning: unclosed file <_io.TextIOWrapper name=3 mode='r' encoding='utf-8'>
  c_dslist, _ = do_action(traj, command, c_action.Action_MultiPucker)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/.../source/pytraj/pytraj/all_actions.py:3207: ResourceWarning: unclosed file <_io.TextIOWrapper name=5 mode='r' encoding='utf-8'>
  c_dslist, _ = do_action(traj, command, c_action.Action_MultiPucker)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
..E
======================================================================
ERROR: test_multipucker_pyranoid (__main__.TestMultipucker.test_multipucker_pyranoid)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/.../source/pytraj/tests/test_analysis/test_multipucker.py", line 60, in test_multipucker_pyranoid
    data_pyranoid = pt.multipucker(traj=traj, name='Pyranoid',
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/.../source/pytraj/pytraj/utils/get_common_objects.py", line 314, in inner
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/.../source/pytraj/pytraj/all_actions.py", line 3207, in multipucker
    c_dslist, _ = do_action(traj, command, c_action.Action_MultiPucker)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/.../source/pytraj/pytraj/analysis/c_action/__init__.py", line 25, in do_action
    act = action_class(command=command, top=top, dslist=c_dslist)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "pytraj/analysis/c_action/c_action.pyx", line 84, in pytraj.analysis.c_action.c_action.Action.__init__
  File "/.../source/pytraj/pytraj/utils/decorators.py", line 59, in _inner
    return func(self, *args, **kwd)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "pytraj/analysis/c_action/c_action.pyx", line 180, in pytraj.analysis.c_action.c_action.Action.setup
RuntimeError: Failed to setup action. Use pytraj._verbose() to turn on the error report.

----------------------------------------------------------------------
Ran 3 tests in 0.012s

FAILED (errors=1)

I also have the pytraj verbose log. I am positive that it is likely the result of a syntactical issue, but I am unsure where to look for it, and what in particular is causing the setup action to fail. Any ideas? Thanks in advance for your help!

[hainm]

@PhiMykah I am testing your branch now...

[hainm]

@PhiMykah I found the issue. It's because of this

puckertype=['pyranoid','C1','C2','C3','C4','C5','05'],

In your code, '05' is zero and five. It should be "O" (as in Oxygen) and "5" (O5)

[PhiMykah]

In your code, '05' is zero and five. It should be "O" (as in Oxygen) and "5" (O5)

I see it now, Thank you! I had a feeling it was something with syntax 😅