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import openmm.app as app
import pdbfixer
import tempfile
import time
from pathlib import Path
from urllib.request import urlopen
from io import StringIO
import pytest
@pytest.fixture(scope="module")
def file_content():
return (Path(__file__).parent / "data" / "4JSV.pdb").read_text()
def remove_chains_and_verify(file_content, expected_chain_ids_remaining, **kws):
# Create a PDBFixer instance for the given pdbid
fixer = pdbfixer.PDBFixer(pdbfile=StringIO(file_content))
# Remove specified chains.
fixer.removeChains(**kws)
# Check to make sure asserted chains remain.
chain_ids_remaining = [c.id for c in fixer.topology.chains()]
assert expected_chain_ids_remaining == chain_ids_remaining
def test_removechain_ids(file_content):
remove_chains_and_verify(file_content, ['B', 'D', 'A', 'C', 'B', 'A'], chainIds=[])
remove_chains_and_verify(file_content, ['A', 'C', 'A'], chainIds=['B', 'D'])
remove_chains_and_verify(file_content, ['B', 'D', 'B'], chainIds=['A', 'C'])
remove_chains_and_verify(file_content, ['D', 'C'], chainIds=['B', 'A'])
remove_chains_and_verify(file_content, [], chainIds=['B', 'D', 'A', 'C'])
def test_removechain_indices(file_content):
remove_chains_and_verify(file_content, ['B', 'D', 'A', 'C', 'B', 'A'], chainIndices=[])
remove_chains_and_verify(file_content, ['A', 'C', 'B', 'A'], chainIndices=[0, 1])
remove_chains_and_verify(file_content, ['B', 'D', 'B', 'A'], chainIndices=[2, 3])
remove_chains_and_verify(file_content, ['D', 'C', 'B', 'A'], chainIndices=[0, 2])
remove_chains_and_verify(file_content, [], chainIndices=[0, 1, 2, 3, 4, 5])
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