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Add new helper functions to PDBManager #322

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merged 14 commits into from
May 25, 2023
Merged

Add new helper functions to PDBManager #322

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3d8e17a
Add name parsing function to PDBDataset API
May 23, 2023
94c9fae
Merge branch 'master' of https://github.com/amorehead/graphein
May 23, 2023
99e329c
Add new helper functions for working with non-protein molecule types …
May 23, 2023
72573e6
Update variable names and default values
May 24, 2023
a035384
Update syntax
May 24, 2023
c07bea1
Restore .gitignore
May 24, 2023
361b940
Restore .gitignore
May 24, 2023
efc2d3d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 24, 2023
a6c4a6e
Handle edge case
May 24, 2023
9831fc3
Merge branch 'master' of https://github.com/amorehead/graphein
May 24, 2023
768f15f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 24, 2023
6b1879e
Handle edge cases in export function
May 25, 2023
c5d7d6e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 25, 2023
e527f74
update changelog
a-r-j May 25, 2023
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17 changes: 9 additions & 8 deletions graphein/ml/datasets/pdb_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1778,7 +1778,7 @@ def merge_pdb_chain_groups(self, group: DataFrameGroupBy) -> pd.DataFrame:

def select_pdb_by_criterion(
self, pdb: PandasPdb, field: str, field_values: List[Any]
) -> PandasPdb:
) -> Optional[PandasPdb]:
"""Filter a PDB using a field selection.

:param pdb: The PDB object to filter by a field.
Expand All @@ -1789,18 +1789,18 @@ def select_pdb_by_criterion(
the PDB.
:type field_values: List[Any]

:return: The filtered PDB object.
:rtype: PandasPdb
:return: The filtered PDB object or instead `None` to signify
that no atoms within the PDB object were found after filtering.
:rtype: Optional[PandasPdb], optional
"""
for key in pdb.df:
if field in pdb.df[key]:
filtered_pdb = pdb.df[key][
pdb.df[key][field].isin(field_values)
]
if "ATOM" in key:
assert (
len(filtered_pdb) > 0
), "Filtered DataFrame must contain atoms."
if "ATOM" in key and len(filtered_pdb) == 0:
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I may be being a little pedantic here but I see two possible edge cases with this:

  1. Sometimes protein atoms are stored as HETATMs (typically modified residues but this kind of bad practice does happen as an abuse of the PDB format to suit some niche way to store structure data)
  2. Similarly, what if the desired selection is actually the HETATM data? Protein-nucleic acid complexes or protein-peptide complexes may store the ligand as a HETATM

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@amorehead amorehead May 25, 2023 •
edited

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No problem. Points 1 and 2 didn't come to my mind when I originally implemented this, and I kept expanding on it until now. In light of these points, I think it makes more sense to avoid skipping such DataFrames altogether. It will then be the user's responsibility to "vet" the exported PDB files for these kinds of edge cases in their selected PDBs. Better yet, we can simply issue a warning to users that no "standard" atoms were found post-filtering. However, we would then still export the PDB complex as requested.

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I've modified this logic to only issue a warning in such an edge case now.

log.warning("Filtered DataFrame does not contain any atoms. Skipping DataFrame...")
return None
pdb.df[key] = filtered_pdb
return pdb

Expand Down Expand Up @@ -1891,7 +1891,8 @@ def write_out_pdb_chain_groups(
pdb, "chain_id", chains
)
# export selected chains within the same PDB file
pdb_chains.to_pdb(str(output_pdb_filepath))
if pdb_chains:
pdb_chains.to_pdb(str(output_pdb_filepath))

def write_df_pdbs(
self,
Expand Down