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Add "Retrospective" tab to dashboard #121

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merged 34 commits into from
Jun 15, 2021
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eac01b3
create basic outline for new tab
Dec 8, 2020
eb15091
create basic retrospective analysis tab
glass-w Dec 14, 2020
7be597e
change index skeleton for retrospective analysis
glass-w Dec 14, 2020
34b305d
set new column skeleton and use compound ID only
glass-w Dec 15, 2020
89f50a0
add skeleton function for extracting relatives
glass-w Dec 16, 2020
d740ae0
move function, update schema, test html, tidy up
glass-w Dec 17, 2020
ba32fae
add simple arsenic plots WIP
glass-w Dec 17, 2020
46d8dbc
change func name, add microstate check, tidy plots
glass-w Dec 17, 2020
4ccdc0f
wrangle exp values to fewer decimal places
glass-w Dec 18, 2020
94eed6f
fix plot, minor fixes
glass-w Dec 18, 2020
02a4f15
fix analysis.json formatting
glass-w Dec 18, 2020
addd3e4
format with black, update tab and plots
glass-w Dec 18, 2020
c31f0b8
fix formatting
glass-w Dec 18, 2020
45b2961
fix column format
glass-w Dec 18, 2020
c438652
use 0.1 error
glass-w Jan 11, 2021
54f1a8f
Merge branch 'sprint-5' into retro-tab
glass-w Jan 11, 2021
63d03fd
add plotly
glass-w Jan 12, 2021
fe76b7d
Bugfixes galore!
jchodera Jan 13, 2021
11b6724
Merge branch 'retro-tab' of https://github.com/choderalab/covid-moons…
jchodera Jan 13, 2021
2513495
Add reliable transformations plot to retrospective tab.
jchodera Jan 13, 2021
f2ea714
format with Black
glass-w Jan 13, 2021
b52279d
Handle InsufficientDataError
jchodera Jan 24, 2021
ba64518
Merge branch 'retro-tab' of https://github.com/choderalab/covid-moons…
jchodera Jan 24, 2021
585b87d
Accelerate analysis of incomplete transformations by skipping RUNs
jchodera Jan 24, 2021
2a72392
Accept _ in PostEra compound IDs
jchodera Jan 27, 2021
d3e3a88
Suppress nonpolar hydrogens by default
jchodera Jan 29, 2021
db1474d
Bugfix for sorting on webpages
jchodera Jan 30, 2021
1a4d290
Fix regex when multiple microstate suffixes are in use
jchodera Jan 30, 2021
cfb2604
Some cleanup
jchodera Jan 31, 2021
c30b862
Compress ZIP files
jchodera Feb 6, 2021
d44a60c
Correctly strip hydrogens from PDB files
jchodera Feb 6, 2021
18f6ba8
Small fixes and notes
dotsdl Jun 15, 2021
cea6944
Modifications in light of feedback from @glass-w, @jchodera
dotsdl Jun 15, 2021
8c0d75f
Merge branch 'master' into retro-tab
dotsdl Jun 15, 2021
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add simple arsenic plots WIP
glass-w committed Dec 17, 2020
commit ba32faea1c5f0d0487d80eba6f424b77f647a61d
44 changes: 44 additions & 0 deletions fah_xchem/analysis/plots.py
Original file line number Diff line number Diff line change
@@ -19,6 +19,45 @@
TransformationAnalysis,
)
from .constants import KT_KCALMOL
from arsenic import plotting


def plot_retrospective(
transformations: List[TransformationAnalysis],
output_dir: str,
filename: str = 'retrospective.png',
):

import networkx as nx
import os

graph = nx.DiGraph()

for analysis in transformations:
transformation = analysis.transformation

if analysis.binding_free_energy is None:
continue

print(transformation)

# Only interested if the compounds have an experimental DDG
if analysis.exp_ddg is not None:

graph.add_edge(
transformation.initial_microstate,
transformation.final_microstate,
exp_DDG=analysis.exp_ddg,
exp_dDDG=0.0, # TODO get error
calc_DDG=analysis.binding_free_energy.point,
calc_dDDG=analysis.binding_free_energy.stderr,
)

plotting.plot_DDGs(graph, filename=os.path.join(output_dir, filename))






def plot_work_distributions(
@@ -683,6 +722,11 @@ def generate_plots(

# Summary plots

plot_retrospective(
output_dir=output_dir,
transformations=series.transformations
)

with save_summary_plot(
name="relative_fe_dist",
):