diff --git a/pyproject.toml b/pyproject.toml index d3133f7..a72a52f 100644 --- a/pyproject.toml +++ b/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", ] diff --git a/src/grodecoder/databases/api.py b/src/grodecoder/databases/api.py index 5a4df93..f4a4b08 100644 --- a/src/grodecoder/databases/api.py +++ b/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]: diff --git a/src/grodecoder/identifier.py b/src/grodecoder/identifier.py index 024a308..a9a3d2e 100644 --- a/src/grodecoder/identifier.py +++ b/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 diff --git a/uv.lock b/uv.lock index 626bc4a..8775b48 100644 --- a/uv.lock +++ b/uv.lock @@ -382,7 +382,6 @@ dev = [ { name = "pytest" }, { name = "requests" }, { name = "ruff" }, - { name = "streamlit" }, { name = "ty" }, { name = "types-requests" }, { name = "watchdog" }, @@ -407,7 +406,6 @@ dev = [ { name = "pytest", specifier = ">=8.3.5" }, { name = "requests", specifier = ">=2.32.3" }, { name = "ruff", specifier = ">=0.11.2" }, - 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