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Test and fix Molecule.remove_van_der_waals_bonds #1799

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merged 4 commits into from
Nov 14, 2019
Merged

Test and fix Molecule.remove_van_der_waals_bonds #1799

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2d3b5cd
Added unit test for Molecule.remove_van_der_waals_bonds
rwest Oct 29, 2019
b349f0d
Don't modify bond dict while iterating over it.
rwest Oct 29, 2019
81593f0
Don't cython.declare unused variable.
rwest Nov 13, 2019
df170e4
Remove redundant "or" statement.
rwest Nov 13, 2019
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2 changes: 1 addition & 1 deletion rmgpy/molecule/group.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1130,7 +1130,7 @@ def remove_van_der_waals_bonds(self):
"""
Remove all bonds that are definitely only van der Waals bonds.
"""
cython.declare(atom=GroupAtom, bond=GroupBond)
cython.declare(bond=GroupBond)
for bond in self.get_all_edges():
if bond.is_van_der_waals(wildcards=False):
self.remove_bond(bond)
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11 changes: 5 additions & 6 deletions rmgpy/molecule/molecule.py
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Expand Up @@ -718,7 +718,7 @@ def is_van_der_waals(self):
Return ``True`` if the bond represents a van der Waals bond or
``False`` if not.
"""
return self.is_order(0) or self.order == 'vdW' # todo: remove 'vdW'
return self.is_order(0)

def is_order(self, other_order):
"""
Expand Down Expand Up @@ -1092,11 +1092,10 @@ def remove_van_der_waals_bonds(self):
"""
Remove all van der Waals bonds.
"""
cython.declare(atom=Atom, bond=Bond)
for atom in self.atoms:
for bond in atom.edges.values():
if bond.is_van_der_waals():
self.remove_bond(bond)
cython.declare(bond=Bond)
for bond in self.get_all_edges():
if bond.is_van_der_waals():
self.remove_bond(bond)

def sort_atoms(self):
"""
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12 changes: 12 additions & 0 deletions rmgpy/molecule/moleculeTest.py
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Expand Up @@ -2687,6 +2687,18 @@ def test_count_aromatic_rings(self):

self.assertEqual(result, [2, 1, 0])

def test_remove_van_der_waals_bonds(self):
"""Test we can remove a van-der-Waals bond"""
adjlist = """
1 X u0 p0 c0 {2,vdW}
2 H u0 p0 c0 {1,vdW}, {3,S}
3 H u0 p0 c0 {2,S}
"""
mol = Molecule().from_adjacency_list(adjlist)
self.assertEqual(len(mol.get_all_edges()), 2)
mol.remove_van_der_waals_bonds()
self.assertEqual(len(mol.get_all_edges()), 1)

################################################################################

if __name__ == '__main__':
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