mooonpy.molspace.topology module

..note:: the keys usef for all of these classes use the ordering rules below,

so only 1 permutation is saved or searched for, and the original order is saved in the ‘ordered’ attribute,

• Bonds: key = (id1, id2) # id1 < id2

• Angles: key = (id1, id2, id3) # id1 < id3

• Dihedrals: key = (id1, id2, id3, id4) # id1 < id4

• Impropers: key = (id1, id2, id3, id4) # id1 < id3 < id4 # center atom is always id2, sort others

..TODO:: methods for safe lookup and __set__ with autocorrected order - 7-Jul-25

class mooonpy.molspace.topology.Angles(**kwargs)

Bases: dict

angle_factory()

copy(deepcopy=False)

Return a fully independent copy of this topology container (independence verified in tests/test_molspace_copy.py).

The factory class and defaults are frozen, so the copy references the SAME factory instance by design; value objects are rebuilt fresh.

Parameters:

deepcopy – if True, use the copy.deepcopy fallback (same result, ~7-8x slower; for cross-checking only).

id_get(id1, id2, id3)

id_set(value, id1, id2, id3)

key_rule(id1, id2, id3)

class mooonpy.molspace.topology.Bonds(**kwargs)

Bases: dict

bond_factory()

copy(deepcopy=False)

Return a fully independent copy of this topology container (independence verified in tests/test_molspace_copy.py).

The factory class and defaults are frozen, so the copy references the SAME factory instance by design; value objects are rebuilt fresh.

Parameters:

deepcopy – if True, use the copy.deepcopy fallback (same result, ~7-8x slower; for cross-checking only).

id_get(id1, id2)

id_set(value, id1, id2)

key_rule(id1, id2)

new(id1, id2, **kwargs)

class mooonpy.molspace.topology.Dihedrals(**kwargs)

Bases: dict

copy(deepcopy=False)

Return a fully independent copy of this topology container (independence verified in tests/test_molspace_copy.py).

The factory class and defaults are frozen, so the copy references the SAME factory instance by design; value objects are rebuilt fresh.

Parameters:

deepcopy – if True, use the copy.deepcopy fallback (same result, ~7-8x slower; for cross-checking only).

dihedral_factory()

id_get(id1, id2, id3, id4)

id_set(value, id1, id2, id3, id4)

key_rule(id1, id2, id3, id4)

class mooonpy.molspace.topology.Impropers(**kwargs)

Bases: dict

copy(deepcopy=False)

Return a fully independent copy of this topology container (independence verified in tests/test_molspace_copy.py).

The factory class and defaults are frozen, so the copy references the SAME factory instance by design; value objects are rebuilt fresh.

Parameters:

deepcopy – if True, use the copy.deepcopy fallback (same result, ~7-8x slower; for cross-checking only).

id_get(id1, id2, id3, id4)

id_set(value, id1, id2, id3, id4)

improper_factory()

key_rule(id1, id2, id3, id4)