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Add cap hydrogens to head and tail compounds in the polymer builder #1196

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merged 4 commits into from
Aug 19, 2024
Merged

Add cap hydrogens to head and tail compounds in the polymer builder #1196

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f07ae16
test against both SMILES versions
chrisjonesBSU Aug 8, 2024
74032c9
add cap hyrogens to head and tail monomers
chrisjonesBSU Aug 12, 2024
443ebd0
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 12, 2024
8a04111
test that polymer.children is same length as n monomers
chrisjonesBSU Aug 12, 2024
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2 changes: 1 addition & 1 deletion mbuild/lib/recipes/polymer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -211,7 +211,7 @@ def build(self, n, sequence="A", add_hydrogens=True):
# Defaut to 1/2 H-C bond len
head_tail[i].update_separation(0.0547)
hydrogen["up"].update_separation(0.0547)
self.add(hydrogen)
head_tail[i].parent.add(hydrogen)
force_overlap(hydrogen, hydrogen["up"], head_tail[i])
head_tail[i] = None
else:
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11 changes: 10 additions & 1 deletion mbuild/tests/test_compound.py
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Expand Up @@ -2479,7 +2479,16 @@ def test_get_smiles(self):
test_strings = ["CCO", "CCCCCCCC", "c1ccccc1", "CC(=O)Oc1ccccc1C(=O)O"]
for test_string in test_strings:
my_cmp = mb.load(test_string, smiles=True, backend="pybel")
assert my_cmp.get_smiles() == test_string
if test_string == "CC(=O)Oc1ccccc1C(=O)O":
try:
assert my_cmp.get_smiles() == test_string
except AssertionError:
assert (
my_cmp.get_smiles()
== "CC(=O)OC1=C([CH][CH][CH][CH]1)C(=O)O"
)
else:
assert my_cmp.get_smiles() == test_string

def test_sdf(self, methane):
methane.save("methane.sdf")
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1 change: 1 addition & 0 deletions mbuild/tests/test_polymer.py
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Expand Up @@ -18,6 +18,7 @@ def test_polymer_from_smiles(self):
assert len([p for p in chain.particles() if p.name == "C"]) == 10
assert len([p for p in chain.particles() if p.name == "H"]) == 22
assert len(chain.available_ports()) == 0
assert len(chain.children) == 5

def test_add_end_groups(self, ch2, ester):
n = 6
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