Code

Add support for 3D RNA Graphs#165

Code

Merged

a-r-j merged 111 commits intomastera-r-j/graphein:masterfrom rna3da-r-j/graphein:rna3dCopy head branch name to clipboardJun 30, 2022

+745,405-20,719

Commits

Commits on Apr 27, 2022

• add RNA atomic edge funcs

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• add RNA 3D constants

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• add bpRNA parser

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• add Ryan's Nussinov algo implementation

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Commits on May 1, 2022

• add radius of gyration feature

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• add positional encoding of sequence

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• update docstrings and add interface subgraphs

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• docstring

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• rm unused import

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• add rich as a base requirement

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• update version string

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Commits on May 2, 2022

• black

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Commits on May 7, 2022

• add additional RNA tests

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Commits on May 12, 2022

• update rna docs

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• Merge branch 'master' into rna3d

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• finalise RNA tutorial with 3D structures

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• merge

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• resolve merge conflict

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• add edge funcs

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• add RNA graphs

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• add rna subgraphs

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• add rna features

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• update rna constants

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• resolve circular import

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• move edge funcs to submodule

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• make subgraphs editable downstream

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• set node size multiplier to a saner default

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• add smiles test file

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• use rich-click for cli, minor linting

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Commits on May 13, 2022

• add distance edges

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• add RNA visualisation

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• add nussinov test

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• use rich-click instead of click

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• add rna test structure

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Commits on May 14, 2022

• skip nussinov cell to avoid timeout

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• simplify af2 structure retrieval #168

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• add plddt colouring for AF2

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• linting

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• bugfixes for AF2

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• add edge distance func

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• add graph feats to docs

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Commits on May 15, 2022

• Merge branch 'master' into rna3d

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• add fully connected and distance window edges

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• Merge branch 'rna3d' of https://www.github.com/a-r-j/graphein into rna3d

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• remove erroneous import

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• add molecule features

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• add conformer generation and fragment graphs

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• update top level init with version and loguru logging

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• update changelog

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• black, isort

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• add loguru as dependency

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• fix edge construction funcs

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Commits on May 16, 2022

• fix rdkit util tests

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• fix tests

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• fix tests

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• try converting everything to tensor

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• fix edge distance func

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• fix conversion

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Commits on May 17, 2022

• add zinc & chembl utils

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• add molecule modelling tutorial.ipynb

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• add smilite dependency

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• fix notebook test

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Commits on May 19, 2022

• remove tests for molecule tutorial

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• update requirements

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• isort

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• add sequence homology splitting

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• update docs

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• rollback nx version

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• fix blast

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• fix blast

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• add antibody tutorial

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• update notebook for docs

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• fix dataset readme tables

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• add notebooks

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• update notebooks and docs

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Commits on May 20, 2022

• remove antibody_dev example

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Commits on May 24, 2022

• Merge branch 'master' into rna3d

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• add line graph

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• Merge branch 'rna3d' of https://www.github.com/a-r-j/graphein into rna3d

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Commits on May 27, 2022

• update rna tests

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• update CLI

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• update ML utils

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• add dynamics features

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• add degree oh

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• fix naming

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• add naming changes to RNA

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• update molecule utils

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• update chain graph tutorial

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• update intersphinx mappings

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• isort

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• black

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• fix test

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Commits on May 28, 2022

• skip inconsistent mol test

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• skip zinc tests

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• add skip to ppi graph test if HGNC unavailable

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• remove debug cell

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• pin nx version

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Commits on Jun 21, 2022

• Merge branch 'master' into rna3d

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• remove nx version pin

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• pin mpl chord dependency

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Commits on Jun 23, 2022

• proper HETATM handling

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• add pyg visualisation

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Commits on Jun 24, 2022

• resolve dataframe handling

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• update to tutorial for df handling

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• restore plddt vis

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• merge

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• pin scipy version for plots

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Commits on Jun 27, 2022

• unpin scipy dependency

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Commits on Jun 28, 2022

• skip API calls in tutorials

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Commits on Jun 30, 2022

• update changelog

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• update version to 1.5.0rc1

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