Closed johnnytam100 closed 2 years ago
Hi, I'm sorry for reporting several situations at the same time. I met the same problem using the add_aromatic_interactions
add_aromatic_interactions
from graphein.protein.edges.distance import (add_peptide_bonds, add_hydrogen_bond_interactions, add_disulfide_interactions, add_ionic_interactions, add_aromatic_interactions, add_aromatic_sulphur_interactions, add_cation_pi_interactions ) new_edge_funcs = {"edge_construction_functions": [add_peptide_bonds, add_hydrogen_bond_interactions, add_disulfide_interactions, add_ionic_interactions, add_aromatic_interactions, add_aromatic_sulphur_interactions, add_cation_pi_interactions ] } config = ProteinGraphConfig(**new_edge_funcs) g = construct_graph(config=config, pdb_code="3ED8") p = plot_protein_structure_graph(G=g, angle=0, colour_edges_by="kind", colour_nodes_by="seq_position", label_node_ids=False) plt.suptitle("Protein graph with: peptide backbone, H-Bonds, \n Disulphide, ionic, aromatic, aromatic-sulphur and cation-pi interactions. \n Nodes coloured by sequence position, edges by type")
returned
DEBUG:graphein.protein.graphs:Deprotonating protein. This removes H atoms from the pdb_df dataframe DEBUG:graphein.protein.graphs:Detected 1134 total nodes INFO:graphein.protein.edges.distance:Found 372 hbond interactions. INFO:graphein.protein.edges.distance:Found 25 hbond interactions. INFO:graphein.protein.edges.distance:Found 10 disulfide interactions. INFO:graphein.protein.edges.distance:Found 983 ionic interactions. --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) [<ipython-input-8-183722266f5a>](https://localhost:8080/#) in <module>() 19 20 config = ProteinGraphConfig(**new_edge_funcs) ---> 21 g = construct_graph(config=config, pdb_code="3ED8") 22 p = plot_protein_structure_graph(G=g, angle=0, colour_edges_by="kind", colour_nodes_by="seq_position", label_node_ids=False) 23 plt.suptitle("Protein graph with: peptide backbone, H-Bonds, \n Disulphide, ionic, aromatic, aromatic-sulphur and cation-pi interactions. \n Nodes coloured by sequence position, edges by type") 4 frames [/usr/local/lib/python3.7/dist-packages/graphein/protein/utils.py](https://localhost:8080/#) in filter_dataframe(dataframe, by_column, list_of_values, boolean) 81 :rtype: pd.DataFrame 82 """ ---> 83 df = dataframe.copy() 84 df = df[df[by_column].isin(list_of_values) == boolean] 85 df.reset_index(inplace=True, drop=True) AttributeError: 'NoneType' object has no attribute 'copy'
And I checked my pandas version:
import pandas as pd print(pd.__version__)
1.3.5
May I know is it the problem with pandas version?
pandas
Originally posted by @johnnytam100 in https://github.com/a-r-j/graphein/issues/81#issuecomment-1045985671
Hi @johnnytam100 I’m going to check this out. I’ll close this and reopen the previous issue. Thanks for bringing it to my attention!
Hi, I'm sorry for reporting several situations at the same time. I met the same problem using the
add_aromatic_interactions
returned
And I checked my pandas version:
May I know is it the problem with
pandas
version?Originally posted by @johnnytam100 in https://github.com/a-r-j/graphein/issues/81#issuecomment-1045985671