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Add tensor parsing util #244

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merged 127 commits into from
Jan 30, 2023
Merged

Add tensor parsing util #244

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1e99c01
Add tensor parsing util
a-r-j Dec 9, 2022
7526d99
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 9, 2022
7f43d74
add missing arg comma
a-r-j Dec 9, 2022
33026a8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 9, 2022
b99f06f
Add backbone check util
a-r-j Dec 12, 2022
5cc92d9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 12, 2022
cf1c7f4
linting
a-r-j Dec 12, 2022
69693b9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 12, 2022
fa5d86d
add chain tensor
a-r-j Dec 17, 2022
b533786
add test for io utils
a-r-j Dec 18, 2022
e9d4f6a
fix loguru import
a-r-j Dec 18, 2022
b9c183d
add torchtyping dependency
a-r-j Dec 18, 2022
1d181b1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 18, 2022
1bb94e7
fix import message import
a-r-j Dec 18, 2022
f7c6141
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Dec 18, 2022
66bdfe5
add tests for angle utils
a-r-j Dec 19, 2022
83296ed
add tests for angle utils
a-r-j Dec 19, 2022
58584e8
add tests for tensor parsing
a-r-j Dec 21, 2022
8492a61
add tests for tensor parsing
a-r-j Dec 21, 2022
8059bcb
add sidechain atom groups
a-r-j Dec 21, 2022
059d188
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 21, 2022
c52acc4
add io tests
a-r-j Jan 2, 2023
8b9750b
add geometry tests
a-r-j Jan 2, 2023
4fca9bd
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 2, 2023
8b1a5e3
add geom ad sequence mnodules
a-r-j Jan 2, 2023
a882125
add test for inferring sequence from coordinates
a-r-j Jan 4, 2023
2e8de26
add einops as an optional dependecy
a-r-j Jan 4, 2023
f5526ed
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 4, 2023
5aa15b6
add sequence inference utils
a-r-j Jan 4, 2023
ac86009
add data testing utils
a-r-j Jan 4, 2023
2094264
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 4, 2023
dd1458b
add nan util
a-r-j Jan 4, 2023
ac34e9b
add angle computation utils
a-r-j Jan 4, 2023
c637049
add test for distmat reconstruction
a-r-j Jan 6, 2023
927d6de
wrap torch imports
a-r-j Jan 6, 2023
25227db
wrap imports
a-r-j Jan 6, 2023
355402d
wrap imports
a-r-j Jan 6, 2023
7f631ec
add representation utils
a-r-j Jan 6, 2023
9647bcd
wrap torch-dependent tests
a-r-j Jan 6, 2023
adcf47d
add edge tensor type
a-r-j Jan 6, 2023
20747ee
update changelog
a-r-j Jan 6, 2023
eb2cc05
add build params
a-r-j Jan 6, 2023
9d3d719
add updated angles script
a-r-j Jan 6, 2023
4d0912a
add graphein package test
a-r-j Jan 6, 2023
d9d87b1
wrap imports
a-r-j Jan 6, 2023
0157530
add plotting utils
a-r-j Jan 8, 2023
b0a08ff
push tensor utils
a-r-j Jan 8, 2023
6fd345d
update centering default args
a-r-j Jan 8, 2023
fc6947e
add reconstruction utils
a-r-j Jan 8, 2023
edf3421
add data objects
a-r-j Jan 8, 2023
3532196
add PyG dep
a-r-j Jan 9, 2023
0f5fde2
add PyG dep
a-r-j Jan 9, 2023
38672b2
add PyG dep
a-r-j Jan 9, 2023
fd14ff3
add PyG dep
a-r-j Jan 9, 2023
16a00e9
add PyG dep
a-r-j Jan 9, 2023
d8d3f79
add PyG dep
a-r-j Jan 9, 2023
0594758
add PyG dep
a-r-j Jan 9, 2023
d9eaf57
add PyG dep
a-r-j Jan 9, 2023
2e8e474
add pnerf
a-r-j Jan 9, 2023
bc0adab
update nx to numpy array to support 3.0
a-r-j Jan 9, 2023
ae0f483
fix kabsch test
a-r-j Jan 9, 2023
5004244
fix centering masking
a-r-j Jan 9, 2023
ebed037
remove nx.info - deprecated in nx 3.0
a-r-j Jan 9, 2023
cf3437f
rm gpickle reference - deprecated in nx 3.0
a-r-j Jan 9, 2023
4743b45
rm gpickle reference - deprecated in nx 3.0
a-r-j Jan 9, 2023
4c28f89
fix nx 3.0 adjacency issues
a-r-j Jan 9, 2023
e18bc62
fix for nx 3.0
a-r-j Jan 9, 2023
d93887c
ignore tensor tests for minimal build
a-r-j Jan 9, 2023
f069a87
ignore tensor tests for minimal build
a-r-j Jan 9, 2023
8919a5c
add additional docs
a-r-j Jan 11, 2023
b38ae4e
add additional testin utils
a-r-j Jan 11, 2023
2acd209
add docstrings to plot
a-r-j Jan 11, 2023
ebaf423
finish sequence docstrings
a-r-j Jan 11, 2023
ac17093
add notimplemented errors and todos
a-r-j Jan 11, 2023
aaf745a
finalise io
a-r-j Jan 11, 2023
9a96633
add tensor submodule to docs
a-r-j Jan 11, 2023
01f1161
add edges
a-r-j Jan 12, 2023
899ae4d
update license year
a-r-j Jan 12, 2023
ec8021a
add documented code
a-r-j Jan 12, 2023
fa1efb2
add documented code and edge funcs
a-r-j Jan 12, 2023
7ee4bf0
add updated tests
a-r-j Jan 12, 2023
986679c
update doc config
a-r-j Jan 12, 2023
64e4322
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 12, 2023
659cb5d
add additional constants
a-r-j Jan 12, 2023
62c82f4
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 12, 2023
bcb801e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 12, 2023
5db50f2
fix test
a-r-j Jan 13, 2023
bf427af
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 13, 2023
fdcb681
update changelog
a-r-j Jan 13, 2023
04b12a0
update readme
a-r-j Jan 13, 2023
1a051db
update docstrings
a-r-j Jan 13, 2023
9df4b8b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 13, 2023
b8ff8df
update docstrings
a-r-j Jan 13, 2023
f8d491a
update docstrings
a-r-j Jan 13, 2023
6b7e9ad
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 13, 2023
c31dd2e
bump license year
a-r-j Jan 14, 2023
6d6396b
fix angle dims
a-r-j Jan 14, 2023
682cb90
add noising and plotting
a-r-j Jan 14, 2023
012fd45
add node id to plots
a-r-j Jan 14, 2023
02ff7c0
add esmfold util
a-r-j Jan 14, 2023
7e7580a
add noise util
a-r-j Jan 14, 2023
494801d
Add structural metrics (#245)
a-r-j Jan 20, 2023
1530153
add dataloader
a-r-j Jan 25, 2023
ece5825
add folding utils
a-r-j Jan 26, 2023
f7a72eb
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 26, 2023
f467ee1
update readme
a-r-j Jan 27, 2023
62b68a1
add docs
a-r-j Jan 27, 2023
2936c1b
add tutorial notebooks
a-r-j Jan 27, 2023
68fa522
add fasta parsing util
a-r-j Jan 27, 2023
6661fe5
add data updates
a-r-j Jan 27, 2023
d47b733
fix df output
a-r-j Jan 27, 2023
5331854
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 27, 2023
b4f084d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 27, 2023
474e0c9
remove DL-dependent notebooks from minimal install test
a-r-j Jan 27, 2023
06026c4
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 27, 2023
ccc07e8
add watermark
a-r-j Jan 27, 2023
57b0a47
rm dataloaders from test
a-r-j Jan 27, 2023
6b10cfe
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 27, 2023
a10f9ff
fix typo in inc_dict attr
a-r-j Jan 27, 2023
533f127
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 27, 2023
50c789e
add doc dep install to build
a-r-j Jan 27, 2023
1b9c3d0
fix typo
a-r-j Jan 29, 2023
e861145
remove wildcard pyyaml version
a-r-j Jan 29, 2023
c9dde87
add try/except for atomic peptide bonds
a-r-j Jan 29, 2023
ed463a4
Merge branch 'master' into tensor_utils
a-r-j Jan 29, 2023
1c7447b
update tensor tutorial
a-r-j Jan 30, 2023
58829a0
Merge branch 'tensor_utils' of https://www.github.com/a-r-j/graphein …
a-r-j Jan 30, 2023
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pre-commit-ci[bot] committed Jan 27, 2023
commit 6b10cfef191e12d960c6d187a71b2de0e4b6d1e9
2 changes: 1 addition & 1 deletion .requirements/docs.in
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Expand Up @@ -11,4 +11,4 @@ sphinx-inline-tabs
sphinxext-opengraph
sphinxcontrib-gtagjs
ipython
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