Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Correct the judgment of hydrogen bonds #370

Open
wants to merge 10 commits into
base: master
Choose a base branch
from
Open

Correct the judgment of hydrogen bonds #370

Changes from 1 commit
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
fb1d42d
Update distance.py
Linsastar Mar 2, 2024
4a9320b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 2, 2024
26c90bc
Fixed filtering of atoms that may form hydrogen bonds
Linsastar Mar 4, 2024
b717cf5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 4, 2024
d064829
Modified the code for judging hydrogen bonds
Linsastar Mar 4, 2024
6d3f706
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 4, 2024
c53e688
Update distance.py
Linsastar Mar 4, 2024
a5a4a6a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 4, 2024
b244c37
Corrected hydrogen bond determination, now hydrogen bonds on the main…
Linsastar Mar 16, 2024
c8d591c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
60 changes: 30 additions & 30 deletions graphein/protein/edges/distance.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -334,8 +334,30 @@ def add_disulfide_interactions(


def add_hydrogen_bond_interactions(
G: nx.Graph, rgroup_df: Optional[pd.DataFrame] = None
G: nx.Graph, rgroup_df: Optional[pd.DataFrame] = None
):
rgroup_df = G.graph["raw_pdb_df"]
HBOND_ATOMS = [
"ND1", # histidine
"ND2", # asparagine
"NE", # arginine
"NE1", # tryptophan
"NE2", # glutamate, histidine
"NH1", # arginine
"NH2", # arginine
"NZ", # lysine
"OD1", # asparagine, aspartic
"OD2", # aspartic
"OE1", # glutamate
"OE2", # glutamate
"OG", # serine
"OG1", # threonine
"OH", # tyrosine, threonine, serine
"SD", # methionine
"SG", # cysteine
"N", # backbone
"O", # backbone
]
DONORS_ATOM: List[str] = [
"ND2", # asparagine
"NE", # arginine
Expand All @@ -361,32 +383,11 @@ def add_hydrogen_bond_interactions(
]
"""Add all hydrogen-bond interactions."""
# For these atoms, find those that are within 3.5A of one another.
if rgroup_df is None:
rgroup_df = G.graph["rgroup_df"]
# if rgroup_df is None:
# rgroup_df = G.graph["rgroup_df"]
Copy link
Owner

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

What is the purpose of not using the supplied rgroup_df?

Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes, you're right. I commented out the code like that just to facilitate debugging and determine the hydrogen bonds on the main chain.

rgroup_df = filter_dataframe(rgroup_df, "node_id", list(G.nodes()), True)
HBOND_ATOMS = [
"ND1", # histidine
"ND2", # asparagine
"NE", # arginine
"NE1", # tryptophan
"NE2", # glutamate, histidine
"NH1", # arginine
"NH2", # arginine
"NZ", # lysine
"OD1", # asparagine, aspartic
"OD2", # aspartic
"OE1", # glutamate
"OE2", # glutamate
"OG", # serine
"OG1", # threonine
"OH", # tyrosine, threonine, serine
"SD", # methionine
"SG", # cysteine
"N", # backbone
"O",
]

hbond_df = filter_dataframe(rgroup_df, "atom_name", HBOND_ATOMS, True)

if len(hbond_df.index) > 0:
distmat = compute_distmat(hbond_df)
interacting_atoms = get_interacting_atoms(3.5, distmat)
Expand All @@ -404,20 +405,19 @@ def add_hydrogen_bond_interactions(
for r1, r2 in get_edges_by_bond_type(G, "hbond"):
# print(G.nodes.data())
condition1 = (
G.nodes[r1]["atom_type"] in ACCEPTORS_ATOM
and G.nodes[r2]["atom_type"] in DONORS_ATOM
G.nodes[r1]["atom_type"] in ACCEPTORS_ATOM
and G.nodes[r2]["atom_type"] in DONORS_ATOM
)
condition2 = (
G.nodes[r2]["atom_type"] in ACCEPTORS_ATOM
and G.nodes[r1]["atom_type"] in DONORS_ATOM
G.nodes[r2]["atom_type"] in ACCEPTORS_ATOM
and G.nodes[r1]["atom_type"] in DONORS_ATOM
)
is_ionic = condition1 or condition2
if not is_ionic:
G.edges[r1, r2]["kind"].remove("hbond")
if len(G.edges[r1, r2]["kind"]) == 0:
G.remove_edge(r1, r2)


def add_ionic_interactions(
G: nx.Graph, rgroup_df: Optional[pd.DataFrame] = None
):
Expand Down