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Protein_ligand graph support & junction tree feature #164

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Reference Issues/PRs

What does this implement/fix? Explain your changes

Issue #162 a preliminary version of implementation, comments not edited, a couple of points need to be discussed including multiple TODOs and the choice of rdkit or pdb dataframe for ligand. Basic structures and features work out fine, but may need more testing.

What testing did you do to verify the changes in this PR?

for protein_ligand graph, tests/protein_ligand/test_graphs, right now only basic features are tested, see protein_ligand/config.py

for junction tree feature, tests/molecule/test_graphs, only basic usage is tested

@yuanqidu
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Review & discussion needed :D

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LGTM, but I think there's some refactoring to do to avoid duplication

@@ -20,6 +20,12 @@
compute_edges,
import_message,
)
from graphein.utils.junction_tree.jt_utils import (
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I think we can move these utils to graphein.molecule.utils

@@ -227,3 +233,37 @@ def construct_graph(
g = annotate_edge_metadata(g, config.edge_metadata_functions)

return g

def construct_junction_tree(
smiles: Optional[str] = None,
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I think using an RDKit mol as the input makes this function more general (this way we can call it for mols parsed from SDF, PDB, Mol2 etc).

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I also don't think the input should be optional

try:
from .visualisation import plot_chord_diagram
except ImportError:
pass
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We should use the import message util from graphein.utils.utils.import_message

from graphein.utils.config import PartialMatchOperator, PathMatchOperator


class DSSPConfig(BaseModel):
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Unneeded, can import

executable: str = "mkdssp"


class GetContactsConfig(BaseModel):
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Unneeded, can import

@@ -0,0 +1,979 @@
"""Functions for plotting protein graphs and meshes."""
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Can probably avoid duplication

return atomic_df


def deprotonate_structure(df: pd.DataFrame) -> pd.DataFrame:
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Can probably a void a lot of duplication here

@@ -0,0 +1,1832 @@
# %%
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Can avoid duplication

log = logging.getLogger(__name__)


def compute_distmat(coords: np.ndarray) -> np.ndarray:
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can avoid duplication

else:
g.add_edge(n1, n2, kind={"junction_tree"})

return g
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needs newline

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sonarcloud bot commented May 9, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

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sonarcloud bot commented Jul 6, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

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sonarcloud bot commented Aug 23, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

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2 participants