Code

train espaloma with MD simulation#1

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

Commits

Commits on Feb 9, 2024

• use pint.UnitRegistry to convert units

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Commits on Feb 12, 2024

• change units.py

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• add implementation error for other systems in experiment.py

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• add draft for train.py

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Commits on Feb 15, 2024

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

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• first commit espfit/utils/sampler

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• use pint.UnitRegistry to define units

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

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• use local variables instead of instance attributes

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• add train_weight method

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• first commit test_app_train_sampler.py

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Commits on Feb 16, 2024

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

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• add space to indent lines

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• Merge branch 'main' into feature/train_with_reweight

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• add space to indent line

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Commits on Feb 19, 2024

• convert unit string into openmm unit

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• create sampler system from toml file

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• allow creating multiple sampler systems

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

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• add reference fig, table information

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

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Commits on Feb 21, 2024

• replace module.py with reweight.py

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• rename experiment.py to analysis.py

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• add simulation settings to config

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• remove constraint and nonbonded method from instance variable

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• improve running sampler during espaloma training

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• update usage in README.md

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• create new samplers during espaloma training

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• 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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• fix minor bug to pass all tests

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Commits on Feb 23, 2024

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

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Commits on Feb 26, 2024

• export loss per epoch to reporter.log

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Commits on Feb 28, 2024

• use j-coupling names for keyname

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• add support to compute sampler loss

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Commits on Mar 4, 2024

• refactor reweight.py

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Commits on Mar 5, 2024

• fix SetupSampler.from_toml when args is not defined

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• add pseudo code for get_effective_sampler_size

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• clean up

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Commits on Mar 6, 2024

• fix docstring

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• remove old comment

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• uncomment version

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• support minima conformer for each chunk when reshaping graphs

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• fix report_loss to properly append loss data at each epoch

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• update docstring for reshape_conformation_size

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• update docstring in CustomGraphDataset

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• fix bug in training when restarting from existing checkpoint file

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• check output files after running test in test_train_sampler

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• minor update

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• remove mockcode.ipynb

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Commits on Mar 7, 2024

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

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• add testsystems/nucleoside/target.pdb

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Commits on Mar 8, 2024

• compare sorted number of conformers to prevent github CI failure

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• add try-except to prevent UnassignedProperTorsionParameterException

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• deprecate isomeric=False in drop_and_merge_duplicates

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Commits on Mar 9, 2024

• reflect changes in drop_duplicates in graphs.py

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• use nonisomeric smiles to detect unique molecules

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Commits on Mar 10, 2024

• fix bug in averaging partial charges for duplicate entries

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Commits on Mar 12, 2024

• fix drop_and_merge_duplicates to drop_duplicates

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• fix drop_and_merge_duplicates to drop_duplicates

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