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GunnerLab
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MCCE_Benchmarking
For benchmarking MCCE experiments viz experimental pKas or viz other MCCE experiments (A/B testing)
MIT License
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Testing MCCE_benchmarking without conda enviorment for MCCE4
#56
granepura
opened
4 months ago
0
Implement a "prerun step" using ProtInfo
#55
CatChenal
opened
4 months ago
0
Match `-wet` option to that in ProtInfo
#54
CatChenal
closed
4 months ago
0
Output tuple in "fit" key of pkas_stats dict even if failed fit.
#53
CatChenal
closed
5 months ago
0
Update docs and flowcharts
#51
CatChenal
closed
6 months ago
0
step3.py cannot run with the `--norun` flag
#50
CatChenal
closed
6 months ago
0
Fix pct_completed function
#49
CatChenal
closed
6 months ago
0
Implement a pre-run check function on user-provided pdbs
#48
CatChenal
closed
6 months ago
1
Update analysis on packaged data
#47
CatChenal
closed
6 months ago
0
Conformer-making level not an explicit command line option
#46
CatChenal
closed
5 months ago
2
Fix folder name truncation in pkanalysis collating functions
#45
CatChenal
closed
6 months ago
1
Use lower cases for folder names
#44
CatChenal
closed
7 months ago
0
No linked file as pdb source in 'bench_setup user_pdbs`
#43
CatChenal
closed
7 months ago
0
Missing `-e` option common to all steps
#42
CatChenal
closed
7 months ago
2
Transform 'norun' option to true flag for each step
#41
CatChenal
closed
7 months ago
0
Scheduling not working (see workaround)
#40
CatChenal
opened
7 months ago
1
Finalize crontab creation
#39
CatChenal
closed
7 months ago
0
Determine path parameters needed for successful scheduling either locally or on server
#38
CatChenal
closed
7 months ago
3
Revert crontab creation to using all args needed by bench_launchjob
#37
CatChenal
closed
7 months ago
0
Add report
#36
CatChenal
opened
7 months ago
0
Allow crontab creation with variable number of options
#35
CatChenal
closed
7 months ago
1
Entry point `bench_compare` finalization
#34
CatChenal
closed
7 months ago
0
Reference set prep
#33
CatChenal
opened
7 months ago
0
Redirect crontab errors to separate file
#32
CatChenal
closed
7 months ago
1
Create workflow docs for new EPs
#31
CatChenal
closed
7 months ago
1
Add comparison with refset in `bench_analyze expl_pkas`
#30
CatChenal
closed
7 months ago
0
Add comparison validation procedure
#29
CatChenal
closed
7 months ago
0
Remove pct_complete from analysis cli args
#28
CatChenal
closed
7 months ago
0
Progress report
#27
CatChenal
closed
7 months ago
1
Capture all out of bound messages in pK.out
#26
CatChenal
closed
7 months ago
0
Fix cli help display
#25
CatChenal
closed
7 months ago
0
Make cli arg -benchmarks_dir required
#24
CatChenal
closed
7 months ago
0
Fix logging
#23
CatChenal
closed
7 months ago
0
Remove ancillary files as part of data setup
#22
CatChenal
closed
7 months ago
0
Run script not copied
#21
CatChenal
closed
7 months ago
0
Remove setuptools-scm
#20
CatChenal
closed
4 months ago
1
Handle min_pct_complete different from 1
#19
CatChenal
closed
7 months ago
1
Make pkanalysis.py a cli
#18
CatChenal
closed
8 months ago
1
Create custom run script - MG
#17
CatChenal
closed
8 months ago
2
Create `bench_mcce_runs` end point for setting up & comparing two sets of mcce runs
#16
CatChenal
closed
7 months ago
2
Run pkanalysis on parse.e4 to output `matched_pka.csv` - MG
#15
CatChenal
closed
8 months ago
0
Add stats per residue type to analysis - MG
#14
CatChenal
closed
8 months ago
0
Add count of number of conformers in analysis - MG
#13
CatChenal
closed
8 months ago
0
Add function to parse the 'run' or 'progress' logs for time - MG
#12
CatChenal
closed
8 months ago
0
Implement logging in `pkanalysis.py` - MG
#11
CatChenal
closed
8 months ago
0
Re-run `parse.e4` reference dataset to obtain mfe info in `pK.out` - MG
#10
CatChenal
closed
8 months ago
0
Add '--xts' on step4 as part of default script - MG
#9
CatChenal
closed
8 months ago
0
Fix: automated scheduling
#8
CatChenal
closed
7 months ago
1
Setup new entry point, 'mcce_launch_job' for cron scheduling
#7
CatChenal
closed
8 months ago
0
Change options with action in `script_setup` sub-command
#6
CatChenal
closed
8 months ago
0
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