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MDCATH #337

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Merged

RaulPPelaez merged 58 commits intotorchmd:maintorchmd/torchmd-net:mainfrom AntonioMirarchi:mdcath_dataloaderAntonioMirarchi/torchmd-net:mdcath_dataloaderCopy head branch name to clipboardJul 29, 2024

+417-1

Commits

Commits on Mar 28, 2024

• new mdcath dataset

  AntonioMirarchi

  committed
  936fc02

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• add mdcath init

  AntonioMirarchi

  committed
  05d298c

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• Merge branch 'main' of https://github.com/AntonioMirarchi/torchmd-net into mdcath_dataloader

  AntonioMirarchi

  committed
  5548e6c

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• improve memory usage avoiding to run out of memory

  AntonioMirarchi

  committed
  0dd872f

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• remove debug print

  AntonioMirarchi

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  6a75b02

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• to black

  AntonioMirarchi

  committed
  bec8144

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Commits on Apr 4, 2024

• change raw dir to self.root

  AntonioMirarchi

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  00380dd

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• add solid_ss to filter while processing

  AntonioMirarchi

  committed
  153c2b1

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• Merge branch 'torchmd:main' into mdcath_dataloader

  AntonioMirarchi

  authored
  3626751

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• Merge branch 'mdcath_dataloader' of https://github.com/AntonioMirarchi/torchmd-net into mdcath_dataloader

  AntonioMirarchi

  committed
  7536c30

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• compute dataset size

  AntonioMirarchi

  committed
  0b4ab67

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• add solid_ss to documentation

  AntonioMirarchi

  committed
  8482127

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• fix self.solid_ss

  AntonioMirarchi

  committed
  949a53f

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Commits on Apr 5, 2024

• fix replica for loop indentation

  AntonioMirarchi

  committed
  788d6fb

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• add possibility to get pdb list from file

  AntonioMirarchi

  committed
  104dfa9

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• fix filtering on numResidues and numAtoms, could be None

  AntonioMirarchi

  committed
  e555277

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• remove comment

  AntonioMirarchi

  committed
  7652c4c

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• remove preload dataset feature

  AntonioMirarchi

  committed
  c9a1903

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Commits on Apr 8, 2024

• fix process specific group, return and skipframes

  AntonioMirarchi

  committed
  2eab7ea

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• fix setup idx and get function

  AntonioMirarchi

  committed
  519ee6a

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Commits on Apr 30, 2024

• Merge branch 'main' of https://github.com/AntonioMirarchi/torchmd-net into mdcath_dataloader

  AntonioMirarchi

  committed
  a54d934

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• allow zero num workers in dataloader

  AntonioMirarchi

  committed
  68ba140

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• remove unused module

  AntonioMirarchi

  committed
  6fb7c4b

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• use read_direct from h5py

  AntonioMirarchi

  committed
  1bd39a0

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• update get function

  AntonioMirarchi

  committed
  c374ec8

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• fix setup idx

  AntonioMirarchi

  committed
  180535f

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• append more info to to_download dict, according to new setup idx

  AntonioMirarchi

  committed
  89df1cc

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• update file name

  AntonioMirarchi

  committed
  71059c8

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• add pytest for mdcath dataset

  AntonioMirarchi

  committed
  2ab24c9

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Commits on May 17, 2024

• fix memory occupancy due to attrs assertion in get

  AntonioMirarchi

  committed
  160fb61

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• remove preload_dataset_limit attr

  AntonioMirarchi

  committed
  8629621

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• update source file name

  AntonioMirarchi

  committed
  30e39a6

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Commits on May 31, 2024

• Merge branch 'main' into mdcath_dataloader

  AntonioMirarchi

  committed
  3ab4406

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• source file string defined as Instance variable

  AntonioMirarchi

  committed
  104348c

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• fix memory leak

  AntonioMirarchi

  committed
  481255b

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• small change

  AntonioMirarchi

  committed
  d63d081

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• remove unused instance

  AntonioMirarchi

  committed
  78ef15a

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• get also detailed info from get function

  AntonioMirarchi

  committed
  e27e8d8

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• fix self.source_file initialization

  AntonioMirarchi

  committed
  7145547

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• Merge branch 'mdcath_dataloader' of https://github.com/AntonioMirarchi/torchmd-net into mdcath_dataloader

  AntonioMirarchi

  committed
  6f68d62

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• update

  AntonioMirarchi

  committed
  4f6fd29

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Commits on Jul 10, 2024

• Merge branch 'main' of https://github.com/AntonioMirarchi/torchmd-net into mdcath_dataloader

  AntonioMirarchi

  committed
  9687f6f

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• Merge branch 'mdcath_dataloader' of https://github.com/AntonioMirarchi/torchmd-net into mdcath_dataloader

  AntonioMirarchi

  committed
  7b576c1

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Commits on Jul 19, 2024

• update to allcaps

  AntonioMirarchi

  committed
  0d0ee06

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• reorder and update code

  AntonioMirarchi

  committed
  6134086

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• Merge branch 'main' of https://github.com/AntonioMirarchi/torchmd-net into mdcath_dataloader

  AntonioMirarchi

  committed
  41b681a

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• Merge branch 'mdcath_dataloader' of https://github.com/AntonioMirarchi/torchmd-net into mdcath_dataloader

  AntonioMirarchi

  committed
  6e090e4

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• fix class name in test

  AntonioMirarchi

  committed
  262f8ad

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• undo on persistent workers

  AntonioMirarchi

  committed
  723164f

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• persistent_workers to False

  AntonioMirarchi

  committed
  fc56169

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Commits on Jul 20, 2024

• fix self.pdb_list in init

  AntonioMirarchi

  committed
  c0d39b7

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• fix source file name in unit test

  AntonioMirarchi

  committed
  1d04f6e

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• add unit test for pdb_list in mdcath

  AntonioMirarchi

  committed
  2b4dd43

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Commits on Jul 22, 2024

• rename arg skipFrames to skip_frames

  AntonioMirarchi

  committed
  7148b61

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• update skip_frames in mdcathtest

  AntonioMirarchi

  committed
  45f7f57

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Commits on Jul 29, 2024

• avoid error due to temperatures list, force str dtype

  AntonioMirarchi

  committed
  92d5f08

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• undo

  AntonioMirarchi

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  c12a2bd

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• force str dtype in temperatures list

  AntonioMirarchi

  committed
  f5c2d46

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