"""Tests for structure analysis module."""
from unittest.mock import MagicMock, mock_open, patch
from biopython_mcp import structure
class TestFetchPDBStructure:
"""Tests for fetch_pdb_structure function."""
@patch("biopython_mcp.structure.PDBList")
def test_fetch_pdb_success(self, mock_pdblist: MagicMock) -> None:
"""Test successful PDB structure fetch."""
mock_list_instance = MagicMock()
mock_list_instance.retrieve_pdb_file.return_value = "/tmp/pdb1abc.ent"
mock_pdblist.return_value = mock_list_instance
result = structure.fetch_pdb_structure("1ABC")
assert result["success"] is True
assert result["pdb_id"] == "1ABC"
assert "file_path" in result
mock_list_instance.retrieve_pdb_file.assert_called_once()
@patch("biopython_mcp.structure.PDBList")
def test_fetch_pdb_failure(self, mock_pdblist: MagicMock) -> None:
"""Test PDB fetch failure."""
mock_list_instance = MagicMock()
mock_list_instance.retrieve_pdb_file.side_effect = Exception("Network error")
mock_pdblist.return_value = mock_list_instance
result = structure.fetch_pdb_structure("1ABC")
assert result["success"] is False
assert "error" in result
assert "Network error" in result["error"]
class TestCalculateStructureStats:
"""Tests for calculate_structure_stats function."""
@patch("biopython_mcp.structure.PDBParser")
@patch("builtins.open", mock_open(read_data="PDB DATA"))
def test_calculate_stats_success(self, mock_parser: MagicMock) -> None:
"""Test successful structure statistics calculation."""
# Mock structure
mock_structure = MagicMock()
mock_model = MagicMock()
mock_chain = MagicMock()
mock_residue = MagicMock()
mock_atom = MagicMock()
# Set up chain
mock_chain.get_id.return_value = "A"
mock_chain.__iter__.return_value = [mock_residue]
# Set up residue
mock_residue.get_id.return_value = ("H_ALA", 1, " ")
mock_residue.__iter__.return_value = [mock_atom]
# Set up model
mock_model.__iter__.return_value = [mock_chain]
# Set up structure
mock_structure.__iter__.return_value = [mock_model]
mock_parser_instance = MagicMock()
mock_parser_instance.get_structure.return_value = mock_structure
mock_parser.return_value = mock_parser_instance
result = structure.calculate_structure_stats("/tmp/test.pdb")
assert result["success"] is True
assert "num_atoms" in result
assert "num_residues" in result
assert "num_chains" in result
@patch("biopython_mcp.structure.PDBParser")
def test_calculate_stats_file_not_found(self, mock_parser: MagicMock) -> None:
"""Test statistics calculation with non-existent file."""
mock_parser_instance = MagicMock()
mock_parser_instance.get_structure.side_effect = FileNotFoundError("File not found")
mock_parser.return_value = mock_parser_instance
result = structure.calculate_structure_stats("/nonexistent/file.pdb")
assert result["success"] is False
assert "error" in result
@patch("biopython_mcp.structure.PDBParser")
def test_calculate_stats_parse_error(self, mock_parser: MagicMock) -> None:
"""Test statistics calculation with parse error."""
mock_parser_instance = MagicMock()
mock_parser_instance.get_structure.side_effect = Exception("Parse error")
mock_parser.return_value = mock_parser_instance
result = structure.calculate_structure_stats("/tmp/test.pdb")
assert result["success"] is False
assert "Parse error" in result["error"]
class TestFindActiveSite:
"""Tests for find_active_site function."""
@patch("biopython_mcp.structure.PDBParser")
@patch("builtins.open", mock_open(read_data="PDB DATA"))
def test_find_active_site_success(self, mock_parser: MagicMock) -> None:
"""Test successful active site finding."""
# Mock atoms
mock_atom1 = MagicMock()
mock_atom1.get_name.return_value = "CA"
mock_atom2 = MagicMock()
mock_atom2.get_name.return_value = "CB"
# Mock residue
mock_residue = MagicMock()
mock_residue.get_resname.return_value = "SER"
mock_residue.__iter__.return_value = [mock_atom1, mock_atom2]
# Mock chain
mock_chain = MagicMock()
mock_chain.__getitem__.return_value = mock_residue
# Mock model
mock_model = MagicMock()
mock_model.__getitem__.return_value = mock_chain
# Mock structure
mock_structure = MagicMock()
mock_structure.__getitem__.return_value = mock_model
mock_parser_instance = MagicMock()
mock_parser_instance.get_structure.return_value = mock_structure
mock_parser.return_value = mock_parser_instance
result = structure.find_active_site("/tmp/test.pdb", [100, 101], "A")
assert result["success"] is True
assert "active_site" in result
assert len(result["active_site"]) == 2
assert result["chain_id"] == "A"
assert result["num_residues_analyzed"] == 2
@patch("biopython_mcp.structure.PDBParser")
def test_find_active_site_residue_not_found(self, mock_parser: MagicMock) -> None:
"""Test active site finding with non-existent residue."""
mock_chain = MagicMock()
mock_chain.__getitem__.side_effect = KeyError("Residue not found")
mock_model = MagicMock()
mock_model.__getitem__.return_value = mock_chain
mock_structure = MagicMock()
mock_structure.__getitem__.return_value = mock_model
mock_parser_instance = MagicMock()
mock_parser_instance.get_structure.return_value = mock_structure
mock_parser.return_value = mock_parser_instance
result = structure.find_active_site("/tmp/test.pdb", [999], "A")
# Function returns success=True but includes error info for missing residues
assert result["success"] is True
assert "active_site" in result
assert len(result["active_site"]) == 1
assert "error" in result["active_site"][0]
assert "not found" in result["active_site"][0]["error"].lower()
@patch("biopython_mcp.structure.PDBParser")
def test_find_active_site_parse_error(self, mock_parser: MagicMock) -> None:
"""Test active site finding with parse error."""
mock_parser_instance = MagicMock()
mock_parser_instance.get_structure.side_effect = Exception("Parse error")
mock_parser.return_value = mock_parser_instance
result = structure.find_active_site("/tmp/test.pdb", [100], "A")
assert result["success"] is False
assert "error" in result
