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