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a-r-j
Protein Graph Library
> i see some comments on the parameters of function like below  And it seems your example code on doc about this function is not work anymore, I'm wondering...
Errors of adding the essential hydrogen bond interaction have been corrected. In particular, OE was divided into OE1 and OE2. Besides, OE1, OE2, OD1, OD2 and O were defined as...
**Describe the bug** For the Graphein - Atom Graph Tutorial (https://graphein.ai/notebooks/atom_graph_tutorial.html) Error is in this line: g = construct_graph(config=config, **pdb_path**="../examples/pdbs/3eiy.pdb") **pdb_path** should be changed to path **Expected behavior** A clear...
#### What does this implement/fix? Explain your changes Uses `cpdb` to parse PDB files for improved performance #### What testing did you do to verify the changes in this PR?...
#### Reference Issues/PRs Fixes Issue #353 Fixes Issue #354 #### What does this implement/fix? Explain your changes For Issue #353, this PR added a line to determine `dssp` version, which...
**Describe the bug** Hi Arian, great package! THe sidechain angle computation in the tensor submodule fails on non-standard residues. You've already handled this for `SEC`, it just needs to be...
When using the `ProteinGraphDataset` class, if a single graph fails construction in `construct_graphs_mp`, the graph will be passed to transformation functions as `None` and this will often cause them to...
The docs after following the link to [API Reference](https://graphein.ai/modules/graphein.ml.html#graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset) found on [this page](https://graphein.ai/notebooks/dataloader_tutorial.html#ProteinGraphDataset) are apparently missing.
I'm wondering if there's a way to create a graph using `residue` granularity (i.e. coords from the alpha-carbon; applying node features per in-sequence residue of the protein etc.) but use...
#### What does this implement/fix? Explain your changes This allows one to select PDB complex chains satisfying certain interface contact or hydrogen bonding constraints.
