def test_build_geometric_constraint_string():
"""
Test build_geometric_constraint_string() function
Notes
-----
Atom indices in constraits_string is 1-indexed
Atom indices in dihedral_idxs is 0-indexed
"""
constraints_dict = {
'freeze': [{
'type': 'xyz',
'indices': [0, 1, 2, 5, 6],
}, {
'type': 'distance',
'indices': [0, 4],
}],
'set': [
{
'type': 'distance',
'indices': [0, 3],
'value': 1.0,
},
{
'type': 'angle',
'indices': [1, 0, 3],
'value': 30.0,
},
{
'type': 'dihedral',
'indices': [0, 1, 2, 3],
'value': 60.0,
},
]
}
constraints_string = build_geometric_constraint_string(constraints_dict)
# validate the constraints string
assert constraints_string.strip() == '\n'.join([
'$freeze', 'xyz 1-3,6-7', 'distance 1 5', '$set', 'distance 1 4 1.0',
'angle 2 1 4 30.0', 'dihedral 1 2 3 4 60.0'
])
# test with dihedral_idx_values
dihedral_idx_values = [(1, 2, 3, 4, 90.0), (2, 3, 4, 5, 120.0)]
constraints_string2 = build_geometric_constraint_string(
constraints_dict, dihedral_idx_values=dihedral_idx_values)
assert constraints_string2.strip() == '\n'.join([
'$freeze', 'xyz 1-3,6-7', 'distance 1 5', '$set', 'distance 1 4 1.0',
'angle 2 1 4 30.0', 'dihedral 1 2 3 4 60.0', 'dihedral 2 3 4 5 90.0',
'dihedral 3 4 5 6 120.0'
])
def write_constraints_txt(self):
""" write a constraints.txt file for geomeTRIC """
if self.extra_constraints is None:
constraints_string = "$set\n"
for d1, d2, d3, d4, v in self.dihedral_idx_values:
# geomeTRIC use atomic index starting from 1
constraints_string += f"dihedral {d1 + 1} {d2 + 1} {d3 + 1} {d4 + 1} {float(v)}\n"
else:
constraints_string = build_geometric_constraint_string(
self.extra_constraints, self.dihedral_idx_values)
with open('constraints.txt', 'w') as outfile:
outfile.write(constraints_string)