Graph plots #186
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Graph plots #186
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a-r-j
approved these changes
Jul 2, 2022
Owner
|
LGTM, happy to merge. Could you quickly pull this up to head to incorporate the latest changes so tests can run? |
Contributor
Author
|
@a-r-j sure thing; although I'm not exactly sure how I would go about doing that. This is the first time i've submitted a PR sorry! Do you want me to re-commit to the already existing pull request? Or is there a simpler way? Cheers |
Merge for a-r-j#186
Codecov Report
@@ Coverage Diff @@
## master #186 +/- ##
==========================================
+ Coverage 40.27% 48.25% +7.98%
==========================================
Files 48 92 +44
Lines 2811 5326 +2515
==========================================
+ Hits 1132 2570 +1438
- Misses 1679 2756 +1077
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a-r-j
added a commit
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Jul 11, 2022
* update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Cam <[email protected]>
a-r-j
added a commit
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Jul 11, 2022
* refactor PDB download to support parallelisation * add tests for PDB download * refactor PDB download function call in getcontacts * add salt bridges and vdw interactions * use multiprocess downloading in torch datasets * add additional edge funcs * add residue_id to dfs and additional constants * update tests to account for residue id column * update dl func to check for obsolete PDBs * fix type error on paths * fix obsolete test * add bad pdb attr * add return to PDB download util * Merge master -> Patch (#190) * update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Cam <[email protected]> * patch torch geometric dataset and update changelog * black, isort * isort Co-authored-by: Cam <[email protected]>
a-r-j
added a commit
that referenced
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Jul 12, 2022
* refactor PDB download to support parallelisation * add tests for PDB download * refactor PDB download function call in getcontacts * add salt bridges and vdw interactions * use multiprocess downloading in torch datasets * add additional edge funcs * add residue_id to dfs and additional constants * update tests to account for residue id column * update dl func to check for obsolete PDBs * fix type error on paths * fix obsolete test * add bad pdb attr * add return to PDB download util * Merge master -> Patch (#190) * update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Cam <[email protected]> * patch torch geometric dataset and update changelog * black, isort * isort * add edge tests * remove unused workflow action * bump for 1.5.0 * add vdw clashes to constants Co-authored-by: Cam <[email protected]>
a-r-j
added a commit
that referenced
this pull request
Jul 14, 2022
* update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> * 1.5.0 patch3 (#189) * refactor PDB download to support parallelisation * add tests for PDB download * refactor PDB download function call in getcontacts * add salt bridges and vdw interactions * use multiprocess downloading in torch datasets * add additional edge funcs * add residue_id to dfs and additional constants * update tests to account for residue id column * update dl func to check for obsolete PDBs * fix type error on paths * fix obsolete test * add bad pdb attr * add return to PDB download util * Merge master -> Patch (#190) * update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Cam <[email protected]> * patch torch geometric dataset and update changelog * black, isort * isort Co-authored-by: Cam <[email protected]> * 1.5.0 patch3 (#191) * refactor PDB download to support parallelisation * add tests for PDB download * refactor PDB download function call in getcontacts * add salt bridges and vdw interactions * use multiprocess downloading in torch datasets * add additional edge funcs * add residue_id to dfs and additional constants * update tests to account for residue id column * update dl func to check for obsolete PDBs * fix type error on paths * fix obsolete test * add bad pdb attr * add return to PDB download util * Merge master -> Patch (#190) * update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Cam <[email protected]> * patch torch geometric dataset and update changelog * black, isort * isort * add edge tests * remove unused workflow action * bump for 1.5.0 * add vdw clashes to constants Co-authored-by: Cam <[email protected]> Co-authored-by: Cam <[email protected]>
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Fixes #15
Add capability to use
rsaanddim_[1-7]of the meiler embeddings as features by which the node size is scaled inprotein.visualisation.plotly_protein_structure_graph.Testing by plotting graph:
