Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix Protein initialisation #317 #318

Merged
merged 50 commits into from
May 11, 2023
Merged

Fix Protein initialisation #317 #318

merged 50 commits into from
May 11, 2023

Conversation

a-r-j
Copy link
Owner

@a-r-j a-r-j commented May 10, 2023

Reference Issues/PRs

#317

What does this implement/fix? Explain your changes

What testing did you do to verify the changes in this PR?

Pull Request Checklist

  • Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
  • Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
  • Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
  • Ran python -m py.test tests/ and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., python -m py.test tests/protein/test_graphs.py)
  • Checked for style issues by running black . and isort .

a-r-j and others added 30 commits April 17, 2023 02:53
@a-r-j
add PSW to nonstandard residues
176d884
@a-r-j
improve insertion and non-standard residue handling
fa89a37
@a-r-j
refactor chain selection
9855b9b
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
f143719 
for more information, see https://pre-commit.ci
@a-r-j
remove unused verbosity arg
3f3b3d9
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
09f05e5 
for more information, see https://pre-commit.ci
@a-r-j
fix chain selection in tests
b7475df
@a-r-j
Merge branch 'tensor_fixes' of https://www.github.com/a-r-j/graphein …
2e0a371 
…into tensor_fixes
@a-r-j
fix chain selection in tutorial notebook
d2c1808
@a-r-j
fix notebook chain selection
fc332c6
@a-r-j
fix chain selection typehint
4a67851
@a-r-j
Update changelog
5f648d2
@a-r-j
Add NLW to non-standard residues
ab26d78
@a-r-j
Merge branch 'tensor_fixes' of https://www.github.com/a-r-j/graphein …
a449bba 
…into tensor_fixes
@a-r-j
add .ent support
afc0f8b
@a-r-j
add entry for construction from dataframe
258c94d
@a-r-j
add missing stage arg
c9856ae
@a-r-j
improve obsolete mapping retrieving to include entries with no replac…
9e1191a 
…ement
@a-r-j
Merge branch 'master' into tensor_fixes
17c38ab
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
7bf4ff3 
for more information, see https://pre-commit.ci
@a-r-j
update changelog
5af9e06
@a-r-j
add transforms to foldcomp datasets
e00bdfb
@a-r-j
fix jaxtyping syntax
31018bc
@a-r-j
Merge branch 'tensor_fixes' of https://www.github.com/a-r-j/graphein …
6e26455 
…into tensor_fixes
@a-r-j
Merge branch 'master' into tensor_fixes
3681714
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
adbdbe1 
for more information, see https://pre-commit.ci
@a-r-j
Update changelog
50ac31b
@a-r-j
fix double application of transforms
088ae02
@a-r-j
improve foldcomp data loading performance
fb684af
@a-r-j
Merge branch 'tensor_fixes' of https://www.github.com/a-r-j/graphein …
a543a75 
…into tensor_fixes
a-r-j and others added 20 commits May 1, 2023 04:52
@a-r-j
Merge branch 'master' into tensor_fixes
a00e2be
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ccf0437 
for more information, see https://pre-commit.ci
@a-r-j
remove unused imports
7939a82
@a-r-j
remove unused imports
d72abf9
@a-r-j
linting
8b551c7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
86bedcf 
for more information, see https://pre-commit.ci
@a-r-j
Update changelog
685d3db
@a-r-j
add B factors to FC parsing output
bebc3c4
@a-r-j
Merge branch 'tensor_fixes' of https://www.github.com/a-r-j/graphein …
c973422 
…into tensor_fixes
@a-r-j
bugfix to alpha & kappa angle embedding
828af29
@a-r-j
Merge branch 'master' into tensor_fixes
c986df0
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
6c48878 
for more information, see https://pre-commit.ci
@a-r-j
update changelog
fc7657e
@a-r-j
handle selenocysteine in sidechain torsion angle computation
7192613
@a-r-j
Merge branch 'tensor_fixes' of https://www.github.com/a-r-j/graphein …
6a31729 
…into tensor_fixes
@a-r-j
fix protein data object initialisation #317
84fc3e4
@a-r-j
Merge branch 'master' into protein_obj
9dcc1c7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
f5d1f26 
for more information, see https://pre-commit.ci
@a-r-j
restore eq dunder
6269d25
@a-r-j
update changelog
d96d60f
@sonarcloud
Copy link

sonarcloud bot commented May 10, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@a-r-j a-r-j merged commit 3286dce into master May 11, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@a-r-j