pyrosetta_help.residue_decription package

Submodules

pyrosetta_help.residue_decription.betaturn module

pyrosetta_help.residue_decription.betaturn.get_betaturns(pose: Pose) → Dict[int, str][source]: There is a wee problem in that alpha-helices get classified as beta-turns And I am not sure all are beta-turns…

pyrosetta_help.residue_decription.cis module

pyrosetta_help.residue_decription.cis.get_cis_residues(pose: Pose) → List[int][source]: Returns the pose indices of residues in cis (omega of zero)

pyrosetta_help.residue_decription.hbonds module

class pyrosetta_help.residue_decription.hbonds.BondDataType(*args, **kwargs)

Bases: dict

acc_atm_name: str

acc_resi: int

acc_resn: str

distance: float

don_atm_name: str

don_resi: int

don_resn: str

energy: float

pyrosetta_help.residue_decription.hbonds.get_hbond_dicts(pose: Pose) → Dict[int, List[BondDataType]][source]

pyrosetta_help.residue_decription.hbonds.hbond2dict(pose: Pose, bond: HBond) → BondDataType[source]

pyrosetta_help.residue_decription.ss module

pyrosetta_help.residue_decription.ss.get_ss(pose: Pose) → str[source]: returns a string of the SS of types H, S, L This is not the ALBEGO classifier

pyrosetta_help.residue_decription.xlinks module

pyrosetta_help.residue_decription.xlinks.get_xlink_details(residue_i: int, pose: Pose) → dict[source]

cross-link (SSBOND, LINK etc.) => conn3 By conn3 I mean a connection that is not lower (own N) or upper (own C). So if a residue has no connection on one or both of these, technically it will be conn2 or conn1, but that’s being pedantic.

NB. Does not check for incomplete connections (which are a product of fancy meddling)

return :param residue_i: :param pose: :return: dict of keys other_idx, other_name3, other_is_protein own_atom_name other_atom_name

pyrosetta_help.residue_decription.xlinks.get_xlink_idx(residue: Residue, raise_on_bond: bool = True) → int[source]

pyrosetta_help.residue_decription.xlinks.is_xlinked(residue: Residue) → bool[source]