Code

train espaloma with MD simulation#1

Code

Merged

kntkb merged 60 commits intomainchoderalab/espfit:mainfrom feature/train_with_reweightchoderalab/espfit:feature/train_with_reweightCopy head branch name to clipboardMar 12, 2024

+1,615-1,468

Commits

Commits on Feb 9, 2024

• use pint.UnitRegistry to convert units

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  committed
  ef04200

Commits on Feb 12, 2024

• change units.py

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  b63147f

• add implementation error for other systems in experiment.py

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  3176da2

• add draft for train.py

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  12a749e

Commits on Feb 15, 2024

• change logging info in espfit.utils.graphs.drop_and_merge_duplicates

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  47f00ce

• first commit espfit/utils/sampler

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  f62bfd4

• use pint.UnitRegistry to define units

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  cd23fff

• remove espaloma train settings and add sampler settings to config.toml

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  91ac118

• use local variables instead of instance attributes

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  08f4319

• add train_weight method

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  cef6497

• first commit test_app_train_sampler.py

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  d72a531

Commits on Feb 16, 2024

• fix python to 3.11 and add pytest-cov in test_env.yaml

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  ab0a251

• add space to indent lines

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  ed42b0c

• Merge branch 'main' into feature/train_with_reweight

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  2918568

• add space to indent line

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  f546b7f

Commits on Feb 19, 2024

• convert unit string into openmm unit

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  628440f

• create sampler system from toml file

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  245ab2c

• allow creating multiple sampler systems

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  e4ecdf4

• rename pdbfixer_min.pdb to target.pdb for nucleoside systems

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  04145ff

• add reference fig, table information

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  1ada151

• change output file name from pdbfixer_min.pdb to target.pdb

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  9d9bbe2

Commits on Feb 21, 2024

• replace module.py with reweight.py

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  f337f55

• rename experiment.py to analysis.py

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  585a685

• add simulation settings to config

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  1e5b510

• remove constraint and nonbonded method from instance variable

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  cf39f68

• improve running sampler during espaloma training

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  eb234c0

• update usage in README.md

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  56570cb

• create new samplers during espaloma training

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  7db4dba

• remove old comment

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Commits on Feb 22, 2024

• rename test_app_experiment.py to test_app_analysis.py

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  c6b0c3e

• fix minor bug to pass all tests

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  7d67a3b

Commits on Feb 23, 2024

• run sampler using on-the-fly espaloma model created during training

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  cbcd343

Commits on Feb 26, 2024

• export loss per epoch to reporter.log

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  ff04682

Commits on Feb 28, 2024

• use j-coupling names for keyname

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  43f7e99

• add support to compute sampler loss

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  bdb1433

Commits on Mar 4, 2024

• refactor reweight.py

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  095c873

Commits on Mar 5, 2024

• fix SetupSampler.from_toml when args is not defined

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  09565a9

• add pseudo code for get_effective_sampler_size

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  f70140f

• clean up

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  52d32b5

Commits on Mar 6, 2024

• fix docstring

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  6a0f43d

• remove old comment

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  fd052d5

• uncomment version

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  3ad0aa9

• support minima conformer for each chunk when reshaping graphs

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  19f442f

• fix report_loss to properly append loss data at each epoch

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  252012e

• update docstring for reshape_conformation_size

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  5bf8717

• update docstring in CustomGraphDataset

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  8d2871f

• fix bug in training when restarting from existing checkpoint file

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  ee1503e

• check output files after running test in test_train_sampler

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  c757c73

• minor update

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  72946c4

• remove mockcode.ipynb

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  9b9b963

Commits on Mar 7, 2024

• average q_ref if different isomeric smiles are found in merging nonisomeric molecules

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  58036dd

• add testsystems/nucleoside/target.pdb

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  5be247c

Commits on Mar 8, 2024

• compare sorted number of conformers to prevent github CI failure

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  d53595a

• add try-except to prevent UnassignedProperTorsionParameterException

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  41555f2

• deprecate isomeric=False in drop_and_merge_duplicates

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  7164253

Commits on Mar 9, 2024

• reflect changes in drop_duplicates in graphs.py

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  7490db5

• use nonisomeric smiles to detect unique molecules

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  1c84410

Commits on Mar 10, 2024

• fix bug in averaging partial charges for duplicate entries

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  cf5a36d

Commits on Mar 12, 2024

• fix drop_and_merge_duplicates to drop_duplicates

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  0963d0f

• fix drop_and_merge_duplicates to drop_duplicates

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  fb97040