Code

Updates for version 1.1.0#15

Code

Merged

NiklasGebauer merged 39 commits intoatomistic-machine-learning:mainatomistic-machine-learning/schnetpack-gschnet:mainfrom NiklasGebauer:schnetpack-gschnet-1.1.0Copy head branch name to clipboardJul 2, 2024

+2,692-146

Commits

Commits on Aug 2, 2023

• add transform with trajectory sampling strategy that starts from predefined substructure; add transform to randomly sample a (possibly disconnected) substructure; add experiment config that uses ne…

  Show description for 9efbf9f
  NiklasGebauer

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  9efbf9f

• changed default substructure size to 50%

  NiklasGebauer

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  846be3e

• black reformatting

  NiklasGebauer

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  b562567

• improve readability

  NiklasGebauer

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  cf9c81b

• improve readability

  NiklasGebauer

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  80a78eb

Commits on Nov 2, 2023

• add generate function that can start from substructures and uses no origin token (i.e. the generation function for models trained with BuildAtomsTrajectoryFromSubstructure)

  NiklasGebauer

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  4e5c16c

• remove unused argument sort_idx_i

  NiklasGebauer

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  e948288

• add configs and cli functionality for generation of molecules starting from given substructures

  NiklasGebauer

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  feb6b92

Commits on Feb 15, 2024

• add heuristic to choose next atom by distance to focus

  NiklasGebauer

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  d75c935

Commits on Feb 19, 2024

• fix n_tokens return value in generate function

  NiklasGebauer

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  5e4f5a3

Commits on Mar 15, 2024

• refactor heuristics for choosing next atom for placement in BuildAtomsTrajectoryFromSubstructure and fix typo in sample_atom_placement_trajectory that would lead to a crash if starting from substru…

  Show description for c3d53cc
  NiklasGebauer

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  c3d53cc

Commits on Apr 12, 2024

• fix docstring for model argument 'average_type_distributions'

  NiklasGebauer

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  f8e7388

Commits on Apr 29, 2024

• Store distance unit used during training in model and transfer it to db metadata when generating molecules. Also, store boolean 'average_type_distribution' of model as buffer which is checkpointed …

  Show description for 29a8077
  NiklasGebauer

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  29a8077

• add transform for computing the number of heavy atoms in a molecule

  NiklasGebauer

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  57c070b

• add transform for computing the number of heavy atoms in a molecule

  NiklasGebauer

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  97d8398

Commits on May 2, 2024

• add validity check with rdDetermineBonds from rdkit

  NiklasGebauer

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  2821acd

Commits on May 27, 2024

• store more settings in metadata with generated molecules

  NiklasGebauer

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  2d42970

• adapt identification of stereoisomerism, always store isomeric smiles, bump required rdkit version

  NiklasGebauer

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  6e84a4e

Commits on May 28, 2024

• add transform for total number of atoms

  NiklasGebauer

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  a1b8e03

• fix comment

  NiklasGebauer

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  39dbbbe

Commits on Jun 3, 2024

• edit docstrings

  NiklasGebauer

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  1a3c793

• add option to write filtered db of valid molecules

  NiklasGebauer

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  b7f6f17

Commits on Jun 6, 2024

• fix bug in splitting with num_train=1 num_val=1

  NiklasGebauer

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  a1039f2

• store calculated neighborlists in connectivity check

  NiklasGebauer

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  77af61f

• add automatic computation of subset for training data base if split file is provided

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  3873395

Commits on Jun 7, 2024

• delete template data config

  NiklasGebauer

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  363c078

• add comment

  NiklasGebauer

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  0e376e7

• add custom resolver to automatically compute refresh rate that updates every 20 percent of each epoch (i.e. 5 times per epoch)

  NiklasGebauer

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  7294635

• add new config groups, clean up experiment template config, move list of callbacks to individual config

  NiklasGebauer

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  853fd43

• remove model parameters from template config

  NiklasGebauer

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  1593af0

• add automatic calculation of maximum distance and number of bins in the predicted distance distributions based on the chosen cutoffs

  NiklasGebauer

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  19f8391

• rename scripts for training and generation, add them to PATH in setup

  NiklasGebauer

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  4714680

• set default parameter for early stopping patience to 25

  NiklasGebauer

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  9c00d2d

Commits on Jun 8, 2024

• add config file for trainer, update template config

  NiklasGebauer

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  8a6cebf

Commits on Jun 9, 2024

• update model default parameters and model docs

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  6abd87e

• remove separate val and test workers argument from custom_data_cached config

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  d7cd823

Commits on Jun 10, 2024

• update config structure for molecule generation

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  a440b56

Commits on Jul 2, 2024

• update experiment configs

  NiklasGebauer

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  29915e2

• Merge branch 'main' of https://github.com/atomistic-machine-learning/schnetpack-gschnet

  NiklasGebauer

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  0de455f