def _get_box_from_ag_coe(self, ag: prody.AtomGroup):
coords = ag.getCoords()
cmax, cmin = coords.max(0), coords.min(0)
coe = (cmax + cmin) / 2
size = self._get_box_size_from_ag_and_center(ag, coe)
origin = coe - size * self.cell / 2
return origin.astype(float), size.astype(int) + 1
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_com(self, ag: prody.AtomGroup):
return ag.getCoords().mean(axis=0)
def _get_coe(self, ag: prody.AtomGroup):
coords = ag.getCoords()
cmax, cmin = coords.max(0), coords.min(0)
coe = (cmax + cmin) / 2
return coe
def _get_box_from_ag_com(self, ag: prody.AtomGroup):
coords = ag.getCoords()
com = coords.mean(axis=0)
size = self._get_box_size_from_ag_and_center(ag, com)
origin = com - size * self.cell / 2
return origin.astype(float), size.astype(int) + 1