def test_apply_link_to_residue(example_meta_molecule, link_defs,
link_to_resids, inter_types, link_inters,
link_non_edges, link_patterns, expected_nodes,
expected_inters):
links = []
processor = ApplyLinks()
for link_nodes, link_to_resid, interactions, non_edges, patterns, inter_type in zip(
link_defs, link_to_resids, link_inters, link_non_edges,
link_patterns, inter_types):
link = Link()
link.add_nodes_from(link_nodes)
link.interactions[inter_type] = interactions
link.non_edges = non_edges
link.patterns = patterns
link.make_edges_from_interaction_type(inter_type)
processor.apply_link_between_residues(example_meta_molecule, link,
link_to_resid)
for nodes, inter_idxs, inter_type in zip(expected_nodes, expected_inters,
inter_types):
for inter_nodes, inter_idx in zip(nodes, inter_idxs):
interaction = link_inters[inter_idx[0]][inter_idx[1]]
new_interactions = processor.applied_links[inter_type][
inter_nodes][0]
assert new_interactions.atoms == tuple(inter_nodes[:-1])
assert new_interactions.parameters == interaction.parameters
assert new_interactions.meta == interaction.meta
def test_parse_patterns(tokens, expected):
"""
Test that _parse_patterns works as expected.
"""
existing = [[['X', {}], ['Y', {}]]]
full_expected = copy.copy(existing)
full_expected.append(expected)
tokens = collections.deque(tokens)
context = Link()
context.patterns = existing
ffinput._parse_patterns(tokens, context, 'link')
assert context.patterns == full_expected
def test_apply_link_fail(example_meta_molecule, link_defs, link_to_resids,
inter_types, link_inters, link_non_edges,
link_patterns):
links = []
with pytest.raises(polyply.src.apply_links.MatchError):
processor = ApplyLinks()
for link_nodes, link_to_resid, interactions, non_edges, patterns, inter_type in zip(
link_defs, link_to_resids, link_inters, link_non_edges,
link_patterns, inter_types):
link = Link()
link.add_nodes_from(link_nodes)
link.interactions[inter_type] = interactions
link.non_edges = non_edges
link.patterns = patterns
link.make_edges_from_interaction_type(inter_type)
processor.apply_link_between_residues(example_meta_molecule, link,
link_to_resid)