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test_make_bonds.py
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# Copyright 2019 University of Groningen
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Test the MakeBonds processor.
"""
import pytest
from vermouth.forcefield import get_native_force_field
from vermouth.molecule import Molecule
from vermouth.system import System
from vermouth.processors import MakeBonds
@pytest.mark.parametrize('nodes, edges, expected_edges', (
[
# No molecules
[],
[],
[]
],
[
# Single molecule with single node
[[{'element': 'H', 'position': [0, 0, 0]}], ],
[[], ],
[{}, ],
],
[
# Single molecule with two nodes that should be connected
[[{'element': 'H', 'position': [0, 0, 0]},
{'element': 'H', 'position': [0, 0, 0.12]}], ],
[[], ],
[{(0, 1): {'distance': 0.12}}, ],
],
[
# Two molecule with one node each that should be connected
[[{'element': 'H', 'position': [0, 0, 0]}, ],
[{'element': 'H', 'position': [0, 0, 0.12]}], ],
[[], []],
[{(0, 1): {'distance': 0.12}}],
],
[
# Single molecule with two nodes that should not be connected
[[{'element': 'H', 'position': [0, 0, 0]},
{'element': 'H', 'position': [0, 0, 0.2]}], ],
[[], ],
[{}],
],
[
# Two molecule with one node each that should not be connected
[[{'element': 'H', 'position': [0, 0, 0]}, ],
[{'element': 'H', 'position': [0, 0, 0.2]}], ],
[[], []],
[{}, {}],
],
[
# Two molecule with one node each that should not be connected because
# the element is not known
[[{'element': 'H', 'position': [0, 0, 0]}, ],
[{'element': 'X', 'position': [0, 0, 0]}], ],
[[], []],
[{}, {}],
],
[
# Single molecule with two nodes that should remain connected
[[{'element': 'H', 'position': [0, 0, 0]},
{'element': 'H', 'position': [0, 0, 0.2]}], ],
[[(0, 1, {'attr': True})], ],
[{(0, 1): {'attr': True}}],
],
[
# Single molecule with two nodes that should remain connected
[[{'element': 'H', 'position': [0, 0, 0]},
{'element': 'H', 'position': [0, 0, 0.2]}], ],
[[(0, 1, {})], ],
[{(0, 1): {}}],
],
[
# Single molecule with four nodes that should be connected
[[
{'element': 'H', 'position': [0, 0, 0]},
{'element': 'C', 'position': [0, 0, 0.145]},
{'element': 'C', 'position': [0, 0, 0.315]},
{'element': 'H', 'position': [0, 0, 0.460]},
], ],
[[], ],
[{(0, 1): {'distance': pytest.approx(0.145)},
(1, 2): {'distance': pytest.approx(0.170)},
(2, 3): {'distance': pytest.approx(0.145)}}],
],
[
# Single molecule with four nodes that should be connected
[[
{'element': 'H', 'position': [0, 0, 0]},
{'element': 'C', 'position': [0, 0, 0.145]},
{'element': 'C', 'position': [0, 0, 0.315]},
{'element': 'H', 'position': [0, 0, 0.460]},
], ],
[[(1, 2, {})], ],
[{(0, 1): {'distance': pytest.approx(0.145)},
(1, 2): {},
(2, 3): {'distance': pytest.approx(0.145)}}],
],
[
# Single molecule with four nodes that should not be connected despite
# being close enough because they're not connected in the block
[[
{'atomname': 'H1', 'element': 'H', 'resname': 'GLY', 'position': [0, 0, 0]},
{'atomname': 'C', 'element': 'C', 'resname': 'GLY', 'position': [0, 0, 0.145]},
{'atomname': 'N', 'element': 'N', 'resname': 'GLY', 'position': [0, 0, 0.315]},
{'atomname': 'H2', 'element': 'H', 'resname': 'GLY', 'position': [0, 0, 0.460]},
], ],
[[(0, 1, {}), (2, 3, {})], ],
[{(0, 1): {},
(2, 3): {}}],
],
[
# Single molecule with four nodes that should be connected despite
# being far away because they're connected in the block
[[
{'atomname': 'H1', 'element': 'H', 'resname': 'GLY', 'position': [0, 0, 0]},
{'atomname': 'C', 'element': 'C', 'resname': 'GLY', 'position': [0, 0, 0.145]},
{'atomname': 'CA', 'element': 'C', 'resname': 'GLY', 'position': [0, 0, 1.315]},
{'atomname': 'H2', 'element': 'H', 'resname': 'GLY', 'position': [0, 0, 0.460]},
], ],
[[(0, 1, {}), (2, 3, {})], ],
[{(0, 1): {},
(1, 2): {'distance': pytest.approx(1.17)},
(2, 3): {}}],
],
[
# Single molecule with four nodes that have a resname, but not atomnames
[[
{'element': 'H', 'resname': 'GLY', 'position': [0, 0, 0]},
{'element': 'C', 'resname': 'GLY', 'position': [0, 0, 0.145]},
{'element': 'N', 'resname': 'GLY', 'position': [0, 0, 0.315]},
{'element': 'H', 'resname': 'GLY', 'position': [0, 0, 0.460]},
], ],
[[(0, 1, {}), (2, 3, {})], ],
[{(0, 1): {},
(2, 3): {}}],
],
[
# Single molecule with four nodes that have a resname and duplicate
# atomnames
[[
{'atomname': 'H', 'element': 'H', 'resname': 'GLY', 'position': [0, 0, 0]},
{'atomname': 'C', 'element': 'C', 'resname': 'GLY', 'position': [0, 0, 0.145]},
{'atomname': 'N', 'element': 'N', 'resname': 'GLY', 'position': [0, 0, 0.315]},
{'atomname': 'H', 'element': 'H', 'resname': 'GLY', 'position': [0, 0, 0.460]},
], ],
[[(0, 1, {}), (2, 3, {})], ],
[{(0, 1): {},
(2, 3): {}}],
],
))
def test_make_bonds(nodes, edges, expected_edges):
"""
Test to make sure that make_bonds makes the bonds it is expected to, and not
too many.
nodes is a List[List[Dict]], allowing for multiple molecules
edges is a List[List[Tuple[Int, Int, Dict]]], allowing for
multiple molecules
expected_edges is a List[Dict[Tuple[Int, Int], Dict]], allowing for
multiple molecules
"""
system = System(force_field=get_native_force_field('universal'))
for node_set, edge_set in zip(nodes, edges):
mol = Molecule()
mol.add_nodes_from(enumerate(node_set))
mol.add_edges_from(edge_set)
system.add_molecule(mol)
system_mp = system.copy()
MakeBonds().run_system(system)
# Make sure number of connected components is the same
assert len(system.molecules) == len(expected_edges)
# Make sure that for every molecule found, the edges are correct
for found_mol, ref_edges in zip(system.molecules, expected_edges):
assert dict(found_mol.edges) == ref_edges
# Also test making bonds with multiprocessing
mb = MakeBonds()
mb.nproc = 2
mb.run_system(system)
# Make sure number of connected components is the same
assert len(system.molecules) == len(expected_edges)
# Make sure that for every molecule found, the edges are correct
for found_mol, ref_edges in zip(system.molecules, expected_edges):
assert dict(found_mol.edges) == ref_edges