Protein_ligand graph support & junction tree feature #164
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… pr/yuanqidu/157
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Review & discussion needed :D |
graphein/molecule/graphs.py
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| @@ -20,6 +20,12 @@ | |||
| compute_edges, | |||
| import_message, | |||
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| from graphein.utils.junction_tree.jt_utils import ( | |||
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I think we can move these utils to graphein.molecule.utils
graphein/molecule/graphs.py
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| @@ -227,3 +233,37 @@ def construct_graph( | |||
| g = annotate_edge_metadata(g, config.edge_metadata_functions) | |||
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| return g | |||
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| 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 | ||
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| class DSSPConfig(BaseModel): |
| executable: str = "mkdssp" | ||
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| class GetContactsConfig(BaseModel): |
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| """Functions for plotting protein graphs and meshes.""" | |||
graphein/protein_ligand/graphs.py
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| return atomic_df | ||
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| def deprotonate_structure(df: pd.DataFrame) -> pd.DataFrame: |
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Can probably a void a lot of duplication here
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| # %% | |||
| log = logging.getLogger(__name__) | ||
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| def compute_distmat(coords: np.ndarray) -> np.ndarray: |
graphein/molecule/graphs.py
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| else: | ||
| g.add_edge(n1, n2, kind={"junction_tree"}) | ||
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| return g |
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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