"get_contacts_config":
GetContactsConfig(
contacts_dir="../examples/contacts/",
pdb_dir="../examples/contacts/",
),
"dssp_config":
DSSPConfig(),
}
config = ProteinGraphConfig(**configs)
config.edge_construction_functions = [
salt_bridge,
hydrogen_bond,
van_der_waals,
pi_cation,
pi_stacking,
hydrophobic,
t_stacking,
]
# Test High-level API
# Iterate over rows to produce Graph, pickle graph and label
for row in tqdm(range(len(df))):
example = df.iloc[row]
file_path = f'pdbs/{example["Free PDB"]}.pdb'
contact_file = f'contacts/{example["Free PDB"]}_contacts.tsv'
g = construct_graph(config=config, pdb_code=example["Free PDB"])
print(g)
from graphein.protein.edges.distance import add_k_nn_edges
from graphein.protein.features.sequence.sequence import molecular_weight
configs = {
"granularity": "CA",
"keep_hets": False,
"insertions": False,
"verbose": False,
"get_contacts_config": GetContactsConfig(),
"dssp_config": DSSPConfig(),
"graph_metadata_functions": [molecular_weight],
}
config = ProteinGraphConfig(**configs)
config.edge_construction_functions = [
partial(add_k_nn_edges, k=3, long_interaction_threshold=0)
]
# Test High-level API
g = construct_graph(
config=config,
pdb_path="../examples/pdbs/3eiy.pdb",
)
"""
# Test Low-level API
raw_df = read_pdb_to_dataframe(
pdb_path="../../examples/pdbs/3eiy.pdb",
verbose=config.verbose,
)
processed_pdb_df = process_dataframe(
protein_df=raw_df,
# v, f, a = create_mesh(pdb_code="3eiy")
# m = convert_verts_and_face_to_mesh(v, f)
# plot_pointcloud(m, "Test")
# TEST PROTEIN STRUCTURE GRAPH PLOTTING
configs = {
"granularity": "atom",
"keep_hets": False,
"deprotonate": True,
"insertions": False,
"verbose": False,
}
config = ProteinGraphConfig(**configs)
config.edge_construction_functions = [
add_atomic_edges,
add_ring_status,
add_bond_order,
]
config.node_metadata_functions = [meiler_embedding, expasy_protein_scale]
g = construct_graph(
config=config, pdb_path="../examples/pdbs/3eiy.pdb", pdb_code="3eiy"
)
p = plotly_protein_structure_graph(
g,
30,
(1000, 2000),
colour_nodes_by="element_symbol",
colour_edges_by="kind",