Skip to content

add empty molecule filter #15

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

Merged
sfluegel05 merged 2 commits into from
Jul 22, 2026
Merged

add empty molecule filter #15

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
57d8b89
add empty molecule filter
sfluegel05 Jul 22, 2026
dc08b71
add description
sfluegel05 Jul 22, 2026
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
6 changes: 4 additions & 2 deletions chebi_utils/sdf_extractor.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -160,12 +160,14 @@ def extract_molecules(filepath: str | Path) -> pd.DataFrame:
df["mol"] = [_parse_molblock(mb, cid) for mb, cid in zip(molblocks, chebi_ids, strict=False)]
df["chebi_id"] = df["chebi_id"].apply(_chebi_id_to_str)

# exclude records without a valid mol, but keep the same columns for consistency
# exclude records without a valid molecule
df = df[df["mol"].notna()]
# some molecule records are valid, but have no atoms (e.g. CHEBI:192499 in v251, cf. https://github.com/ebi-chebi/ChEBI/issues/4915)
df = df[[mol.GetNumAtoms() > 0 for mol in df["mol"]]]

return df


if __name__ == "__main__":
df = extract_molecules("data/chebi.sdf.gz")
df = extract_molecules("chebi.sdf.gz")
print(df.head())
Loading