Skip to content

Find and fix a bug in Molecule isomorphism #1894

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mjohnson541 merged 2 commits into from
Aug 20, 2020
Merged

Find and fix a bug in Molecule isomorphism #1894

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
92aa1d9
A (failing) isomorphism test.
rwest Feb 20, 2020
bcd515c
When checking isomorphism of Molecules, also check the initial map
rwest Feb 20, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
46 changes: 46 additions & 0 deletions rmgpy/molecule/isomorphismTest.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -485,3 +485,49 @@ def test_isotope_subgraph_isomorphism_molecule_and_group():
assert_true(methanei.is_subgraph_isomorphic(group_methane))
assert_true(methane.is_subgraph_isomorphic(group_methane))
assert_false(methanei.is_isomorphic(methane))

def test_isomorphism_wrong_mapping():
"""
Checks isomorphism finds things not isomorphic if given a wrong mapping.
"""
# These molecules are not isomorphic
n1butane = Molecule().from_adjacency_list("""
1 *1 X u0 p0 c0 {2,S}
2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} {6,S}
3 *3 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S}
4 *4 H u0 p0 c0 {3,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {3,S}
8 C u0 p0 c0 {3,S} {9,S} {10,S} {11,S}
9 H u0 p0 c0 {8,S}
10 H u0 p0 c0 {8,S}
11 C u0 p0 c0 {8,S} {12,S} {13,S} {14,S}
12 H u0 p0 c0 {11,S}
13 H u0 p0 c0 {11,S}
14 H u0 p0 c0 {11,S}
""")

n2butane = Molecule().from_adjacency_list("""
1 *1 X u0 p0 c0 {3,S}
2 *2 C u0 p0 c0 {3,S} {5,S} {6,S} {4,S}
3 *3 C u0 p0 c0 {2,S} {1,S} {7,S} {8,S}
4 *4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {3,S}
8 C u0 p0 c0 {3,S} {9,S} {10,S} {11,S}
9 H u0 p0 c0 {8,S}
10 H u0 p0 c0 {8,S}
11 C u0 p0 c0 {8,S} {12,S} {13,S} {14,S}
12 H u0 p0 c0 {11,S}
13 H u0 p0 c0 {11,S}
14 H u0 p0 c0 {11,S}
""")
assert_false(n1butane.is_isomorphic(n2butane))
assert_false(n1butane.is_isomorphic(n2butane, generate_initial_map=True))

mapping = {}
for label in ['*1', '*2', '*3', '*4']:
mapping[n1butane.get_labeled_atoms(label)[0]] = n2butane.get_labeled_atoms(label)[0]
assert_false(n1butane.is_isomorphic(n2butane, initial_map=mapping))
5 changes: 5 additions & 0 deletions rmgpy/molecule/molecule.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1452,6 +1452,11 @@ def is_isomorphic(self, other, initial_map=None, generate_initial_map=False, sav
# check multiplicity
if self.multiplicity != other.multiplicity:
return False

# if given an initial map, ensure that it's valid.
if initial_map:
if not self.is_mapping_valid(other, initial_map, equivalent=True):
return False

if generate_initial_map:
initial_map = dict()
Expand Down