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"""PDB parser
Test dealing with files that are not fully
compliant with the specification.
"""
import numpy as np
import pytest
from ase import io
# Some things tested:
# Giant cell that would fail for split()
# No element field
# positions with no spaces
test_pdb = """REMARK Not a real pdb file
CRYST1 30.00015000.00015000.000 90.00 90.00 90.00 P1
ATOM 1 C 1 X 1 1.000 8.000 12.000 0.00 0.00 C
ATOM 1 C 1 X 1 2.000 6.000 4.000 0.00 0.00
ATOM 1 SI1 SIO 1 2.153 14.096 3.635 1.00 0.00 SIO
ATOM 1 O 1 1 3.846 5.672 1.323 0.40 38.51 0
ATOM 1 C1' T A 1 -2.481 5.354 0.000
ATOM 1 SIO SIO 1 -11.713-201.677 9.060************ SIO2Si
"""
@pytest.mark.filterwarnings('ignore:Length of occupancy array')
def test_pdb_read():
"""Read information from pdb file."""
with open('pdb_test.pdb', 'w') as pdb_file:
pdb_file.write(test_pdb)
expected_cell = [[30.0, 0.0, 0.0],
[0.0, 15000.0, 0.0],
[0.0, 0.0, 15000.0]]
expected_positions = [[1.000, 8.000, 12.000],
[2.000, 6.000, 4.000],
[2.153, 14.096, 3.635],
[3.846, 5.672, 1.323],
[-2.481, 5.354, 0.000],
[-11.713, -201.677, 9.060]]
expected_species = ['C', 'C', 'Si', 'O', 'C', 'Si']
pdb_atoms = io.read('pdb_test.pdb')
assert len(pdb_atoms) == 6
assert np.allclose(pdb_atoms.cell, expected_cell)
assert np.allclose(pdb_atoms.positions, expected_positions)
assert pdb_atoms.get_chemical_symbols() == expected_species
assert 'occupancy' not in pdb_atoms.arrays
def test_pdb_read_with_arrays():
"""Read information from pdb file. Includes occupancy."""
with open('pdb_test_2.pdb', 'w') as pdb_file:
# only write lines with occupancy and bfactor
pdb_file.write('\n'.join(test_pdb.splitlines()[:6]))
expected_occupancy = [0.0, 0.0, 1.0, 0.4]
expected_bfactor = [0.0, 0.0, 0.0, 38.51]
pdb_atoms = io.read('pdb_test_2.pdb')
assert len(pdb_atoms) == 4
assert np.allclose(pdb_atoms.arrays['occupancy'], expected_occupancy)
assert np.allclose(pdb_atoms.arrays['bfactor'], expected_bfactor)
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