Minor sanity fixes

pyproject.toml

@@ -30,7 +30,6 @@ dev = [
     "biopython>=1.85",
     "playwright>=1.51.0",
     "requests>=2.32.3",
-    "streamlit>=1.44.0",
     "watchdog>=6.0.0",
     "ty==0.0.1a26",
 ]

src/grodecoder/databases/api.py

@@ -49,7 +49,7 @@ def assert_database_exists(path: Path):
 assert_database_exists(CSML_DB_PATH)
 
 
-ModelType = TypeVar("ModelType", Ion, Solvent, Nucleotide, AminoAcid)
+ModelType = TypeVar("ModelType", Ion, Solvent, Nucleotide, AminoAcid, mad.Residue, csml.Residue)
 
 
 def _read_database(path: Path, model: type[ModelType]) -> list[ModelType]:

src/grodecoder/identifier.py

@@ -1,5 +1,5 @@
 import time
-from typing import Iterable, Iterator
+from typing import Iterable, Iterator, Sequence
 
 from loguru import logger
 from MDAnalysis import AtomGroup
@@ -72,7 +72,8 @@ def _select_protein(universe: UniverseLike) -> AtomGroup:
     logger.debug("excluding possible methanol residues (MET) from protein")
     methanol = _find_methanol(universe)
     if methanol:
-        selection_str += f" and not index {' '.join(map(str, methanol))}"
+        indexes = " ".join(str(i) for i in methanol)  # ty complains when using map
+        selection_str += f" and not index {indexes}"
 
     logger.debug("selecting protein")
     protein = universe.select_atoms(selection_str)
@@ -135,7 +136,7 @@ def _unique_definitions(definitions: Iterable[DB.ResidueDefinition]) -> dict[str
     return unique_items
 
 
-def _remove_identified_atoms(universe: AtomGroup, molecules: list[HasAtoms]) -> AtomGroup:
+def _remove_identified_atoms(universe: AtomGroup, molecules: Sequence[HasAtoms]) -> AtomGroup:
     """Removes the atoms of the identified molecules from the universe."""
     for molecule in molecules:
         universe -= molecule.atoms