Installation in Colab notebook about graphein HOT 8 CLOSED

from graphein.protein.visualisation import plot_protein_structure_graph

p = plot_protein_structure_graph(G=g, angle=0, colour_edges_by="kind", colour_nodes_by="element_symbol", label_node_ids=False, node_size_min=2, node_alpha=0.85, node_colour_map=plt.cm.tab10)
plt.suptitle("Atom-level graph. Nodes coloured by their Element")

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
[<ipython-input-7-c327719f0d21>](https://localhost:8080/#) in <module>()
      1 from graphein.protein.visualisation import plot_protein_structure_graph
      2 
----> 3 p = plot_protein_structure_graph(G=g, angle=0, colour_edges_by="kind", colour_nodes_by="element_symbol", label_node_ids=False, node_size_min=2, node_alpha=0.85, node_colour_map=plt.cm.tab10)
      4 plt.suptitle("Atom-level graph. Nodes coloured by their Element")

5 frames
[/usr/local/lib/python3.7/dist-packages/matplotlib/artist.py](https://localhost:8080/#) in _update_property(self, k, v)
   1000                 if not callable(func):
   1001                     raise AttributeError('{!r} object has no property {!r}'
-> 1002                                          .format(type(self).__name__, k))
   1003                 return func(v)
   1004 

AttributeError: 'Axes3D' object has no property 'auto_add_to_figure'

# Warning! This cell may crash a binder notebook as the pre-trained model download is rather large!
# NBVAL_SKIP
from graphein.protein.features.sequence.embeddings import esm_sequence_embedding, biovec_sequence_embedding

new_graph_annotation_funcs = {"graph_metadata_functions": [esm_sequence_embedding, biovec_sequence_embedding]}
config = ProteinGraphConfig(**new_graph_annotation_funcs)

g = construct_graph(config=config, pdb_code="3eiy")
print("ESM:", g.graph["esm_embedding_A"])
print("biovec:", g.graph["biovec_embedding_A"])

DEBUG:graphein.protein.graphs:Deprotonating protein. This removes H atoms from the pdb_df dataframe
DEBUG:graphein.protein.graphs:Detected 174 total nodes
Downloading: "https://github.com/facebookresearch/esm/archive/main.zip" to /root/.cache/torch/hub/main.zip
Downloading: "https://dl.fbaipublicfiles.com/fair-esm/models/esm1b_t33_650M_UR50S.pt" to /root/.cache/torch/hub/checkpoints/esm1b_t33_650M_UR50S.pt
Downloading: "https://dl.fbaipublicfiles.com/fair-esm/regression/esm1b_t33_650M_UR50S-contact-regression.pt" to /root/.cache/torch/hub/checkpoints/esm1b_t33_650M_UR50S-contact-regression.pt
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
[<ipython-input-15-fcdeef6b5567>](https://localhost:8080/#) in <module>()
      6 config = ProteinGraphConfig(**new_graph_annotation_funcs)
      7 
----> 8 g = construct_graph(config=config, pdb_code="3eiy")
      9 print("ESM:", g.graph["esm_embedding_A"])
     10 print("biovec:", g.graph["biovec_embedding_A"])

3 frames
[/usr/local/lib/python3.7/dist-packages/graphein/protein/features/sequence/embeddings.py](https://localhost:8080/#) in _load_biovec_model()
    203     """
    204 
--> 205     return biovec.models.load_protvec(
    206         os.fspath(
    207             Path(__file__).parent.parent

NameError: name 'biovec' is not defined