def from_prody_atomgroup(
cls,
name: ProteinKey,
protein: pd.AtomGroup,
split_type: SplitType = SplitType.KMER,
split_size: int = 16,
selection: str = "calpha",
upsample_rate: int = 50,
moment_types: List[MomentType] = (
MomentType.O_3,
MomentType.O_4,
MomentType.O_5,
MomentType.F,
),
):
"""
Construct MomentInvariants instance from a ProDy AtomGroup object.
Selects according to `selection` string, (default = alpha carbons)
`moment_types` determines which moments are calculated.
Example
--------
>>> invariants = MomentInvariants.from_prody_atomgroup(atom_group, split_type=SplitType.RADIUS, moment_types=[MomentType.O_3, MomentType.F, MomentType.phi_7, MomentType.phi_12])
"""
protein: pd.AtomGroup = protein.select("protein").select(selection)
coordinates: np.ndarray = protein.getCoords()
residue_splits = group_indices(protein.getResindices())
shape = cls(
name,
len(residue_splits),
coordinates,
residue_splits,
protein.getIndices(),
sequence=protein.getSequence(),
split_type=split_type,
split_size=split_size,
upsample_rate=upsample_rate,
moment_types=moment_types,
)
shape._split(split_type)
return shape
def get_beta_indices(protein: pd.AtomGroup) -> List[int]:
"""
Get indices of beta carbons of pd AtomGroup object
(If beta carbon doesn't exist, alpha carbon index is returned)
"""
residue_splits = group_indices(protein.getResindices())
i = 0
indices = []
for split in residue_splits:
ca = None
cb = None
for _ in split:
if protein[i].getName() == "CB":
cb = protein[i].getIndex()
if protein[i].getName() == "CA":
ca = protein[i].getIndex()
i += 1
if cb is not None:
indices.append(cb)
else:
assert ca is not None
indices.append(ca)
return indices