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fp.to_dataframe(return_atoms=True,drop_empty=True) still slow #112

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ReneHamburger1993 opened this issue Apr 3, 2023 · 1 comment · Fixed by #113
Closed

fp.to_dataframe(return_atoms=True,drop_empty=True) still slow #112

ReneHamburger1993 opened this issue Apr 3, 2023 · 1 comment · Fixed by #113

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@ReneHamburger1993
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Hi,

I have 25k frames that I analyzed and it took ~5min to get the full atomid DataFrame with my selections.

I traced it down to the grouping including the "empty" columns.

If we remove them before grouping it gets much faster.

1000 frames: 10s -> ~2s
25k frames: ~300s -> 60s

Though its a factor of 5 faster now.
I will open a PR with my optimization.

Kind regards
René
ReneHamburger1993 referenced this issue in ReneHamburger1993/ProLIF Apr 3, 2023
@ReneHamburger1993
Update utils.py
d9cf65a 
PR to fix [https://github.com/chemosim-lab/ProLIF/issues/112](#112)
ReneHamburger1993 added a commit to ReneHamburger1993/ProLIF that referenced this issue Apr 3, 2023
@ReneHamburger1993
Fix chemosim-lab#112
54b6535 
drop cols containing None before grouping. Speeds the function up in my case: ~x5
when called as `fp.to_dataframe(return_atoms=True,drop_empty=True)`
@ReneHamburger1993 ReneHamburger1993 mentioned this issue Apr 3, 2023
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@cbouy
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cbouy commented Apr 5, 2023

Hi René and thanks a lot for reporting this and contributing, I'll try to have a look at your PR this week.

Best,
Cédric

@cbouy cbouy closed this as completed in #113 Apr 5, 2023
cbouy added a commit that referenced this issue Apr 5, 2023
@ReneHamburger1993 @cbouy
Rene hamburger1993 patch 1 (#113)
e2497c1 
* Fix #112

drop cols containing None before grouping. Speeds the function up: ~x5
when called as `fp.to_dataframe(return_atoms=True, drop_empty=True)`

---------

Co-authored-by: Cédric Bouysset <[email protected]>
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Rene hamburger1993 patch 1 ReneHamburger1993/ProLIF
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@cbouy @ReneHamburger1993