Simplify AF2 structure retrieval #168
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a-r-j
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May 14, 2022
a-r-j
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Jun 30, 2022
* add RNA atomic edge funcs * add RNA 3D constants * add bpRNA parser * add Ryan's Nussinov algo implementation * add radius of gyration feature * add positional encoding of sequence * update docstrings and add interface subgraphs * docstring * rm unused import * add rich as a base requirement * update version string * black * add additional RNA tests * update rna docs * finalise RNA tutorial with 3D structures * merge * add edge funcs * add RNA graphs * add rna subgraphs * add rna features * update rna constants * resolve circular import * move edge funcs to submodule * make subgraphs editable downstream * set node size multiplier to a saner default * add smiles test file * use rich-click for cli, minor linting * add distance edges * add RNA visualisation * add nussinov test * use rich-click instead of click * add rna test structure * skip nussinov cell to avoid timeout * simplify af2 structure retrieval #168 * add plddt colouring for AF2 * linting * bugfixes for AF2 * add edge distance func * add graph feats to docs * add fully connected and distance window edges * remove erroneous import * add molecule features * add conformer generation and fragment graphs * update top level init with version and loguru logging * update changelog * black, isort * add loguru as dependency * fix edge construction funcs * fix rdkit util tests * fix tests * fix tests * try converting everything to tensor * fix edge distance func * fix conversion * add zinc & chembl utils * add molecule modelling tutorial.ipynb * add smilite dependency * fix notebook test * remove tests for molecule tutorial * update requirements * isort * add sequence homology splitting * update docs * rollback nx version * fix blast * fix blast * add antibody tutorial * update notebook for docs * fix dataset readme tables * add notebooks * update notebooks and docs * remove antibody_dev example * add line graph * update rna tests * update CLI * update ML utils * add dynamics features * add degree oh * fix naming * add naming changes to RNA * update molecule utils * update chain graph tutorial * update intersphinx mappings * isort * black * fix test * skip inconsistent mol test * skip zinc tests * add skip to ppi graph test if HGNC unavailable * remove debug cell * pin nx version * remove nx version pin * pin mpl chord dependency * proper HETATM handling * add pyg visualisation * resolve dataframe handling * update to tutorial for df handling * restore plddt vis * pin scipy version for plots * unpin scipy dependency * skip API calls in tutorials * update changelog * update version to 1.5.0rc1
a-r-j
added a commit
that referenced
this issue
Jun 30, 2022
* add RNA atomic edge funcs * add RNA 3D constants * add bpRNA parser * add Ryan's Nussinov algo implementation * add radius of gyration feature * add positional encoding of sequence * update docstrings and add interface subgraphs * docstring * rm unused import * add rich as a base requirement * update version string * black * add additional RNA tests * update rna docs * finalise RNA tutorial with 3D structures * merge * add edge funcs * add RNA graphs * add rna subgraphs * add rna features * update rna constants * resolve circular import * move edge funcs to submodule * make subgraphs editable downstream * set node size multiplier to a saner default * add smiles test file * use rich-click for cli, minor linting * add distance edges * add RNA visualisation * add nussinov test * use rich-click instead of click * add rna test structure * skip nussinov cell to avoid timeout * simplify af2 structure retrieval #168 * add plddt colouring for AF2 * linting * bugfixes for AF2 * add edge distance func * add graph feats to docs * add fully connected and distance window edges * remove erroneous import * add molecule features * add conformer generation and fragment graphs * update top level init with version and loguru logging * update changelog * black, isort * add loguru as dependency * fix edge construction funcs * fix rdkit util tests * fix tests * fix tests * try converting everything to tensor * fix edge distance func * fix conversion * add zinc & chembl utils * add molecule modelling tutorial.ipynb * add smilite dependency * fix notebook test * remove tests for molecule tutorial * update requirements * isort * add sequence homology splitting * update docs * rollback nx version * fix blast * fix blast * add antibody tutorial * update notebook for docs * fix dataset readme tables * add notebooks * update notebooks and docs * remove antibody_dev example * add line graph * update rna tests * update CLI * update ML utils * add dynamics features * add degree oh * fix naming * add naming changes to RNA * update molecule utils * update chain graph tutorial * update intersphinx mappings * isort * black * fix test * skip inconsistent mol test * skip zinc tests * add skip to ppi graph test if HGNC unavailable * remove debug cell * pin nx version * remove nx version pin * pin mpl chord dependency * proper HETATM handling * add pyg visualisation * resolve dataframe handling * update to tutorial for df handling * restore plddt vis * pin scipy version for plots * unpin scipy dependency * skip API calls in tutorials * update changelog * update version to 1.5.0rc1
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Is your feature request related to a problem? Please describe.
Now that biopandas 0.4.0 is out (:partying_face:) we can simplify graph construction from AF2 by simply adding a
uniprot_idarg tographein.protein.graphs.construct_graph()instead of doing the gymnastics of downloading a structure and feeding it in manually.The text was updated successfully, but these errors were encountered: