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Add tensor parsing util #244

Merged
merged 127 commits into from
Jan 30, 2023
Merged

Add tensor parsing util #244

merged 127 commits into from
Jan 30, 2023

Commits on Dec 9, 2022

  1. Add tensor parsing util

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  3. add missing arg comma

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    a-r-j authored Dec 9, 2022
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Commits on Dec 12, 2022

  1. Add backbone check util

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  3. linting

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Commits on Dec 17, 2022

  1. add chain tensor

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Commits on Dec 18, 2022

  1. add test for io utils

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  2. fix loguru import

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    a-r-j committed Dec 18, 2022
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  3. add torchtyping dependency

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  5. fix import message import

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  6. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

    …into tensor_utils
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Commits on Dec 19, 2022

  1. add tests for angle utils

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  2. add tests for angle utils

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Commits on Dec 21, 2022

  1. add tests for tensor parsing

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  2. add tests for tensor parsing

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  3. add sidechain atom groups

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Commits on Jan 2, 2023

  1. add io tests

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  2. add geometry tests

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  3. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

    …into tensor_utils
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  4. add geom ad sequence mnodules

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Commits on Jan 4, 2023

  1. add test for inferring sequence from coordinates

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  2. add einops as an optional dependecy

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  4. add sequence inference utils

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  5. add data testing utils

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  6. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

    …into tensor_utils
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  7. add nan util

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  8. add angle computation utils

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Commits on Jan 6, 2023

  1. add test for distmat reconstruction

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  2. wrap torch imports

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  3. wrap imports

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  4. wrap imports

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  5. add representation utils

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  6. wrap torch-dependent tests

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  7. add edge tensor type

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  8. update changelog

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  9. add build params

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  10. add updated angles script

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  11. add graphein package test

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  12. wrap imports

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Commits on Jan 8, 2023

  1. add plotting utils

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  2. push tensor utils

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  3. update centering default args

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  4. add reconstruction utils

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  5. add data objects

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Commits on Jan 9, 2023

  1. add PyG dep

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  2. add PyG dep

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  3. add PyG dep

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  4. add PyG dep

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  5. add PyG dep

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  6. add PyG dep

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  7. add PyG dep

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  9. add pnerf

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  10. update nx to numpy array to support 3.0

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  11. fix kabsch test

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  12. fix centering masking

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  13. remove nx.info - deprecated in nx 3.0

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  14. rm gpickle reference - deprecated in nx 3.0

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  15. rm gpickle reference - deprecated in nx 3.0

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  16. fix nx 3.0 adjacency issues

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  17. fix for nx 3.0

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  18. ignore tensor tests for minimal build

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  19. ignore tensor tests for minimal build

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Commits on Jan 11, 2023

  1. add additional docs

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  2. add additional testin utils

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  3. add docstrings to plot

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  4. finish sequence docstrings

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  5. add notimplemented errors and todos

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  6. finalise io

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  7. add tensor submodule to docs

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Commits on Jan 12, 2023

  1. add edges

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  2. update license year

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  3. add documented code

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  4. add documented code and edge funcs

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  5. add updated tests

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  6. update doc config

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  8. add additional constants

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  9. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

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Commits on Jan 13, 2023

  1. fix test

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  2. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

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  3. update changelog

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  4. update readme

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  5. update docstrings

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  7. update docstrings

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  8. update docstrings

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Commits on Jan 14, 2023

  1. bump license year

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  2. fix angle dims

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  3. add noising and plotting

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  4. add node id to plots

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  5. add esmfold util

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  6. add noise util

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Commits on Jan 20, 2023

  1. Add structural metrics (#245) 

    * Add gdt metric

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Commits on Jan 25, 2023

  1. add dataloader

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Commits on Jan 26, 2023

  1. add folding utils

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  2. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

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    a-r-j committed Jan 26, 2023
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Commits on Jan 27, 2023

  1. update readme

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    a-r-j authored Jan 27, 2023
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  2. add docs

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  3. add tutorial notebooks

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    a-r-j committed Jan 27, 2023
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  4. add fasta parsing util

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    a-r-j committed Jan 27, 2023
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  5. add data updates

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    a-r-j committed Jan 27, 2023
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  6. fix df output

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    a-r-j committed Jan 27, 2023
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  7. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

    …into tensor_utils
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  8. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  9. remove DL-dependent notebooks from minimal install test

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    a-r-j committed Jan 27, 2023
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  10. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

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  11. add watermark

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    a-r-j committed Jan 27, 2023
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  12. rm dataloaders from test

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  13. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  14. fix typo in inc_dict attr

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  15. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

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  16. add doc dep install to build

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    a-r-j authored Jan 27, 2023
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Commits on Jan 29, 2023

  1. fix typo

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    a-r-j committed Jan 29, 2023
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  2. remove wildcard pyyaml version

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    a-r-j committed Jan 29, 2023
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  3. add try/except for atomic peptide bonds

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  4. Merge branch 'master' into tensor_utils

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    a-r-j authored Jan 29, 2023
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Commits on Jan 30, 2023

  1. update tensor tutorial

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    a-r-j committed Jan 30, 2023
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  2. Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein … 

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