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from pathlib import Path
import pytest
from Bio.PDB.MMCIFParser import MMCIFParser
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Structure import Structure
from prodigy_prot.modules.parsers import get_parser, parse_structure, validate_structure
from . import TEST_DATA
@pytest.fixture
def input_structure_cif():
yield Path(TEST_DATA, "2oob.cif")
@pytest.fixture
def input_structure_pdb() -> Path:
return Path(TEST_DATA, "2oob.pdb")
def test_get_parser_pdb(input_structure_pdb):
parser = get_parser(input_structure_pdb)
assert isinstance(parser, PDBParser)
def test_get_parser_cif(input_structure_cif):
parser = get_parser(input_structure_cif)
assert isinstance(parser, MMCIFParser)
def test_validate_structure_pdb(input_structure_pdb):
parser = PDBParser()
structure = parser.get_structure("test_structure", input_structure_pdb)
assert isinstance(structure, Structure)
result = validate_structure(structure)
assert result == structure
def test_validate_stucture_cif(input_structure_cif):
parser = MMCIFParser()
structure = parser.get_structure("test_structure", input_structure_cif)
assert isinstance(structure, Structure)
result = validate_structure(structure)
assert result == structure
def test_parse_structure_pdb(input_structure_pdb):
parser = PDBParser()
structure = parser.get_structure(input_structure_pdb.stem, input_structure_pdb)
result, num_chains, num_res = parse_structure(input_structure_pdb)
assert result == structure
assert num_chains == 2
assert num_res == 116
def test_parse_structure_cif(input_structure_cif):
parser = MMCIFParser()
structure = parser.get_structure(input_structure_cif.stem, input_structure_cif)
result, num_chains, num_res = parse_structure(input_structure_cif)
assert result == structure
assert num_chains == 2
assert num_res == 116
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