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import unittest
import warnings
from Bio.PDB.mmtf import MMTFParser
from Bio.PDB.MMCIFParser import MMCIFParser
from Bio.PDB.PDBExceptions import PDBConstructionWarning
class ParseMMTF(unittest.TestCase):
"""Testing with real mmtf file(s)."""
def check_atoms(self):
"""Check all atoms in self.mmtf_atoms and self.mmcif_atoms are equivalent"""
self.assertEqual(len(self.mmcif_atoms), len(self.mmtf_atoms))
for i, e in enumerate(self.mmcif_atoms):
mmtf_atom = self.mmtf_atoms[i]
mmcif_atom = self.mmcif_atoms[i]
self.assertEqual(mmtf_atom.name, mmcif_atom.name) # eg. CA, spaces are removed from atom name
self.assertEqual(mmtf_atom.fullname, mmcif_atom.fullname) # e.g. " CA ", spaces included
self.assertAlmostEqual(mmtf_atom.coord[0], mmcif_atom.coord[0], places=3)
self.assertAlmostEqual(mmtf_atom.coord[1], mmcif_atom.coord[1], places=3)
self.assertAlmostEqual(mmtf_atom.coord[2], mmcif_atom.coord[2], places=3)
self.assertEqual(mmtf_atom.bfactor, mmcif_atom.bfactor)
self.assertEqual(mmtf_atom.occupancy, mmcif_atom.occupancy)
self.assertEqual(mmtf_atom.altloc, mmcif_atom.altloc)
self.assertEqual(mmtf_atom.full_id,
mmcif_atom.full_id) # (structure id, model id, chain id, residue id, atom id)
self.assertEqual(mmtf_atom.id, mmcif_atom.name) # id of atom is the atom name (e.g. "CA")
# self.assertEqual(mmtf_atom.serial_number,mmcif_atom.serial_number) # mmCIF serial number is none
def check_residues(self):
"""Check all residues in self.mmcif_res and self.mmtf_res are equivalent"""
self.assertEqual(len(self.mmcif_res), len(self.mmtf_res))
for i, e in enumerate(self.mmcif_res):
mmcif_r = self.mmcif_res[i]
mmtf_r = self.mmtf_res[i]
self.assertEqual(mmtf_r.level, mmcif_r.level)
self.assertEqual(mmtf_r.disordered, mmcif_r.disordered)
self.assertEqual(mmtf_r.resname, mmcif_r.resname)
self.assertEqual(mmtf_r.segid, mmcif_r.segid)
self.mmcif_atoms = [x for x in mmcif_r.get_atom()]
self.mmtf_atoms = [x for x in mmtf_r.get_atom()]
self.check_atoms()
def check_mmtf_vs_cif(self, mmtf_filename, cif_filename):
"""Compare parsed structures for MMTF and CIF files."""
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
mmtf_struct = MMTFParser.get_structure(mmtf_filename)
mmcif_parser = MMCIFParser()
mmcif_struct = mmcif_parser.get_structure("example", cif_filename)
self.mmcif_atoms = [x for x in mmcif_struct.get_atoms()]
self.mmtf_atoms = [x for x in mmtf_struct.get_atoms()]
self.check_atoms()
mmcif_chains = [x for x in mmcif_struct.get_chains()]
mmtf_chains = [x for x in mmtf_struct.get_chains()]
self.assertEqual(len(mmcif_chains), len(mmtf_chains))
for i, e in enumerate(mmcif_chains):
self.mmcif_res = [x for x in mmcif_chains[i].get_residues()]
self.mmtf_res = [x for x in mmtf_chains[i].get_residues()]
self.check_residues()
self.mmcif_res = [x for x in mmcif_struct.get_residues()]
self.mmtf_res = [x for x in mmtf_struct.get_residues()]
self.check_residues()
self.assertEqual(len([x for x in mmcif_struct.get_models()]), len([x for x in mmtf_struct.get_models()]))
def test_4CUP(self):
"""Compare parsing 4CUP.mmtf and 4CUP.cif"""
self.check_mmtf_vs_cif("PDB/4CUP.mmtf", "PDB/4CUP.cif")
# TODO:
# def test_1A8O(self):
# """Compare parsing 1A8O.mmtf and 1A8O.cif"""
# self.check_mmtf_vs_cif("PDB/1A8O.mmtf", "PDB/1A8O.cif")
# TODO:
# def test_4ZHL(self):
# """Compare parsing 4ZHL.mmtf and 4ZHL.cif"""
# self.check_mmtf_vs_cif("PDB/4ZHL.mmtf", "PDB/4ZHL.cif")
class SimpleParseMMTF(unittest.TestCase):
"""Just parse some real mmtf files."""
def test_4ZHL(self):
"""Parse 4ZHL.mmtf"""
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
structure = MMTFParser.get_structure("PDB/4ZHL.mmtf")
def test_1A80(self):
"""Parse 1A8O.mmtf"""
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
structure = MMTFParser.get_structure("PDB/1A8O.mmtf")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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