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Modify graphs.py to handle insertions when {'insertions': True} #223

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merged 12 commits into from
Dec 8, 2022
Merged

Modify graphs.py to handle insertions when {'insertions': True} #223

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8845e85
update conversion
Oct 18, 2022
f9bfc95
fix coord issues
Oct 18, 2022
b4e150a
update graphs.py to handle insertions
Oct 24, 2022
ade2cb2
Merge branch 'master' into insertion
a-r-j Oct 31, 2022
a75b207
fix affedcted test
a-r-j Nov 2, 2022
d807dd8
accomodate insertion in hbond donor and acceptor
a-r-j Nov 2, 2022
2aeeaa4
update changelog
a-r-j Nov 2, 2022
707e6e5
Merge branch 'master' into insertion
a-r-j Nov 9, 2022
98dbe17
Merge branch 'master' into insertion
a-r-j Dec 7, 2022
cec18d6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 7, 2022
a45316e
Add control flow for insertion labelling
a-r-j Dec 7, 2022
2693ecd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 7, 2022
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[pre-commit.ci] auto fixes from pre-commit.com hooks 
for more information, see https://pre-commit.ci
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pre-commit-ci[bot] committed Dec 7, 2022
commit cec18d6a660cc90f2160d66ab5c1c44c2a6cba1c
1 change: 0 additions & 1 deletion graphein/protein/edges/distance.py
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Expand Up @@ -316,7 +316,6 @@ def add_disulfide_interactions(
)



def add_hydrogen_bond_interactions(
G: nx.Graph, rgroup_df: Optional[pd.DataFrame] = None
):
Expand Down
4 changes: 2 additions & 2 deletions graphein/protein/features/nodes/amino_acid.py
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Expand Up @@ -208,7 +208,7 @@ def hydrogen_bond_donor(
try:
features = HYDROGEN_BOND_DONORS[res][atom]
except KeyError:
try: # Handle insertions
try: # Handle insertions
atom = node_id[-2]
features = HYDROGEN_BOND_DONORS[res][atom]
except KeyError:
Expand Down Expand Up @@ -254,7 +254,7 @@ def hydrogen_bond_acceptor(
try:
features = HYDROGEN_BOND_ACCEPTORS[res][atom]
except KeyError:
try: # Handle insertions
try: # Handle insertions
atom = node_id[-2]
features = HYDROGEN_BOND_ACCEPTORS[res][atom]
except KeyError:
Expand Down
8 changes: 6 additions & 2 deletions graphein/protein/graphs.py
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Expand Up @@ -383,7 +383,9 @@ def sort_dataframe(df: pd.DataFrame) -> pd.DataFrame:
:return: Sorted protein dataframe.
:rtype: pd.DataFrame
"""
return df.sort_values(by=["chain_id", "residue_number", "atom_number", "insertion"])
return df.sort_values(
by=["chain_id", "residue_number", "atom_number", "insertion"]
)


def assign_node_id_to_dataframe(
Expand Down Expand Up @@ -584,7 +586,9 @@ def calculate_centroid_positions(
:rtype: pd.DataFrame
"""
centroids = (
atoms.groupby(["residue_number","chain_id","residue_name", "insertion"])
atoms.groupby(
["residue_number", "chain_id", "residue_name", "insertion"]
)
.mean()[["x_coord", "y_coord", "z_coord"]]
.reset_index()
)
Expand Down