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MDCATH #337

Merged
merged 58 commits into from
Jul 29, 2024
Merged

MDCATH #337

merged 58 commits into from
Jul 29, 2024

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AntonioMirarchi
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This pull request introduces the MDCATH class, which extends torch_geometric.data.Dataset to facilitate the processing and handling of the mdCATH dataset, available on Hugging Face.

Key Features:

  • The MDCATH class processes the mdcath_source.h5 file, efficiently filtering domains and trajectories based on the specified filter arguments.
  • Users can customize the filtering criteria by passing specific arguments to the class, allowing for targeted data selection

@AntonioMirarchi
new mdcath dataset
936fc02
@AntonioMirarchi
add mdcath init
05d298c
@AntonioMirarchi
Merge branch 'main' of https://github.com/AntonioMirarchi/torchmd-net …
5548e6c 
…into mdcath_dataloader
@AntonioMirarchi
improve memory usage avoiding to run out of memory
0dd872f
@AntonioMirarchi
remove debug print
6a75b02
@AntonioMirarchi
to black
bec8144
@AntonioMirarchi
change raw dir to self.root
00380dd
@AntonioMirarchi
add solid_ss to filter while processing
153c2b1
@AntonioMirarchi
Merge branch 'torchmd:main' into mdcath_dataloader
3626751
@AntonioMirarchi
Merge branch 'mdcath_dataloader' of https://github.com/AntonioMirarch…
7536c30 
…i/torchmd-net into mdcath_dataloader
@AntonioMirarchi
compute dataset size
0b4ab67
@AntonioMirarchi
add solid_ss to documentation
8482127
@AntonioMirarchi
fix self.solid_ss
949a53f
@AntonioMirarchi
fix replica for loop indentation
788d6fb
@AntonioMirarchi
add possibility to get pdb list from file
104dfa9
@AntonioMirarchi
fix filtering on numResidues and numAtoms, could be None
e555277
@AntonioMirarchi
remove comment
7652c4c
@AntonioMirarchi
remove preload dataset feature
c9a1903
@AntonioMirarchi
fix process specific group, return and skipframes
2eab7ea
@AntonioMirarchi
fix setup idx and get function
519ee6a
@AntonioMirarchi
Merge branch 'main' of https://github.com/AntonioMirarchi/torchmd-net …
a54d934 
…into mdcath_dataloader
@AntonioMirarchi
allow zero num workers in dataloader
68ba140
@AntonioMirarchi
remove unused module
6fb7c4b
@AntonioMirarchi
use read_direct from h5py
1bd39a0
@AntonioMirarchi
update get function
c374ec8
@AntonioMirarchi
fix setup idx
180535f
@AntonioMirarchi
append more info to to_download dict, according to new setup idx
89df1cc
@AntonioMirarchi
update file name
71059c8
@AntonioMirarchi
add pytest for mdcath dataset
2ab24c9
@AntonioMirarchi
fix memory occupancy due to attrs assertion in get
160fb61
@AntonioMirarchi
source file string defined as Instance variable
104348c
@AntonioMirarchi
fix memory leak
481255b
@AntonioMirarchi
small change
d63d081
@AntonioMirarchi
remove unused instance
78ef15a
@AntonioMirarchi
get also detailed info from get function
e27e8d8
@AntonioMirarchi
fix self.source_file initialization
7145547
@AntonioMirarchi
Merge branch 'mdcath_dataloader' of https://github.com/AntonioMirarch…
6f68d62 
…i/torchmd-net into mdcath_dataloader
@AntonioMirarchi
update
4f6fd29
@AntonioMirarchi
Merge branch 'main' of https://github.com/AntonioMirarchi/torchmd-net …
9687f6f 
…into mdcath_dataloader
@AntonioMirarchi
Merge branch 'mdcath_dataloader' of https://github.com/AntonioMirarch…
7b576c1 
…i/torchmd-net into mdcath_dataloader
@AntonioMirarchi
update to allcaps
0d0ee06
@AntonioMirarchi
reorder and update code
6134086
@AntonioMirarchi
Merge branch 'main' of https://github.com/AntonioMirarchi/torchmd-net …
41b681a 
…into mdcath_dataloader
@AntonioMirarchi
Merge branch 'mdcath_dataloader' of https://github.com/AntonioMirarch…
6e090e4 
…i/torchmd-net into mdcath_dataloader
@AntonioMirarchi
fix class name in test
262f8ad
@AntonioMirarchi
undo on persistent workers
723164f
@AntonioMirarchi
persistent_workers to False
fc56169
@AntonioMirarchi
fix self.pdb_list in init
c0d39b7
@AntonioMirarchi
fix source file name in unit test
1d04f6e
@AntonioMirarchi
add unit test for pdb_list in mdcath
2b4dd43
@AntonioMirarchi
rename arg skipFrames to skip_frames
7148b61
@AntonioMirarchi
update skip_frames in mdcathtest
45f7f57
@RaulPPelaez
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Looks great Antonio. Is it ready to merge?

@AntonioMirarchi
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Yes, ready to merge! I added a small change to force temperatures list to contain only str in order to avoid h5 reading errors when int values are passed using the yaml.

@RaulPPelaez
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Looks great. Great work Antonio!

@RaulPPelaez RaulPPelaez merged commit 6dea4b6 into torchmd:main Jul 29, 2024
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@RaulPPelaez RaulPPelaez RaulPPelaez approved these changes

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@AntonioMirarchi @RaulPPelaez