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train espaloma with MD simulation #1

Merged
merged 60 commits into from
Mar 12, 2024
Merged

train espaloma with MD simulation #1

merged 60 commits into from
Mar 12, 2024

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kntkb
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@kntkb kntkb commented Mar 7, 2024 •
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Description

Add features to train espaloma with reweighted observables obtained from MD simulations

Todos

Notable points that this PR has either accomplished or will accomplish.

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Status

  • Ready to go

kntkb added 30 commits February 9, 2024 15:25
@kntkb
use pint.UnitRegistry to convert units
ef04200
@kntkb
change units.py
b63147f
@kntkb
add implementation error for other systems in experiment.py
3176da2
@kntkb
add draft for train.py
12a749e
@kntkb
change logging info in espfit.utils.graphs.drop_and_merge_duplicates
47f00ce
@kntkb
first commit espfit/utils/sampler
f62bfd4
@kntkb
use pint.UnitRegistry to define units
cd23fff
@kntkb
remove espaloma train settings and add sampler settings to config.toml
91ac118
@kntkb
use local variables instead of instance attributes
08f4319
@kntkb
add train_weight method
cef6497
@kntkb
first commit test_app_train_sampler.py
d72a531
@kntkb
fix python to 3.11 and add pytest-cov in test_env.yaml
ab0a251
@kntkb
add space to indent lines
ed42b0c
@kntkb
Merge branch 'main' into feature/train_with_reweight
2918568
@kntkb
add space to indent line
f546b7f
@kntkb
convert unit string into openmm unit
628440f
@kntkb
create sampler system from toml file
245ab2c
@kntkb
allow creating multiple sampler systems
e4ecdf4
@kntkb
rename pdbfixer_min.pdb to target.pdb for nucleoside systems
04145ff
@kntkb
add reference fig, table information
1ada151
@kntkb
change output file name from pdbfixer_min.pdb to target.pdb
9d9bbe2
@kntkb
replace module.py with reweight.py
f337f55
@kntkb
rename experiment.py to analysis.py
585a685
@kntkb
add simulation settings to config
1e5b510
@kntkb
remove constraint and nonbonded method from instance variable
cf39f68
@kntkb
improve running sampler during espaloma training
eb234c0
@kntkb
update usage in README.md
56570cb
@kntkb
create new samplers during espaloma training
7db4dba
@kntkb
remove old comment
f7dbd7a
@kntkb
rename test_app_experiment.py to test_app_analysis.py
c6b0c3e
kntkb added 28 commits February 26, 2024 10:06
@kntkb
export loss per epoch to reporter.log
ff04682
@kntkb
use j-coupling names for keyname
43f7e99
@kntkb
add support to compute sampler loss
bdb1433
@kntkb
refactor reweight.py
095c873
@kntkb
fix SetupSampler.from_toml when args is not defined
09565a9
@kntkb
add pseudo code for get_effective_sampler_size
f70140f
@kntkb
clean up
52d32b5
@kntkb
fix docstring
6a0f43d
@kntkb
remove old comment
fd052d5
@kntkb
uncomment version
3ad0aa9
@kntkb
support minima conformer for each chunk when reshaping graphs
19f442f
@kntkb
fix report_loss to properly append loss data at each epoch
252012e
@kntkb
update docstring for reshape_conformation_size
5bf8717
@kntkb
update docstring in CustomGraphDataset
8d2871f
@kntkb
fix bug in training when restarting from existing checkpoint file
ee1503e
@kntkb
check output files after running test in test_train_sampler
c757c73
@kntkb
minor update
72946c4
@kntkb
remove mockcode.ipynb
9b9b963
@kntkb
average q_ref if different isomeric smiles are found in merging nonis…
58036dd 
…omeric molecules
@kntkb
add testsystems/nucleoside/target.pdb
5be247c
@kntkb
compare sorted number of conformers to prevent github CI failure
d53595a
@kntkb
add try-except to prevent UnassignedProperTorsionParameterException
41555f2
@kntkb
deprecate isomeric=False in drop_and_merge_duplicates
7164253
@kntkb
reflect changes in drop_duplicates in graphs.py
7490db5
@kntkb
use nonisomeric smiles to detect unique molecules
1c84410
@kntkb
fix bug in averaging partial charges for duplicate entries
cf5a36d
@kntkb
fix drop_and_merge_duplicates to drop_duplicates
0963d0f
@kntkb
fix drop_and_merge_duplicates to drop_duplicates
fb97040
@kntkb
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kntkb commented Mar 12, 2024

Test failures are due to missing openeye-toolkit license.

@kntkb kntkb merged commit 0284c10 into main Mar 12, 2024
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@kntkb