pyrosetta_help.chain_ops package

Submodules

pyrosetta_help.chain_ops.chain_ops module

class pyrosetta_help.chain_ops.chain_ops.ChainOps(chains: List[dict])

Bases: object

Works on the list of dict (metadata.json) with among others keys

• number (pose number)

• chain (chain letter)

• gene_name (gene name)

__init__(chains: List[dict])

dump(json_filename: str = 'metadata.json')

get_entry(value)

guess key…

Parameters:

value –

Returns:

get_entry_of_key(value, key)

get_pose_of_chain(pose, value)

load(json_filename: str = 'metadata.json')

pyrosetta_help.chain_ops.transmogrifier module

class pyrosetta_help.chain_ops.transmogrifier.Murinizer(chains: List[dict])

Bases: Transmogrifier

Human –> Mouse

__init__(chains: List[dict])

class pyrosetta_help.chain_ops.transmogrifier.Transmogrifier(chains: List[dict], wanted_label: str, owned_label: str)

Bases: ChainOps

This is to convert a mutation from one species (owned_label) to another (wanted_label) based on provided sequences in the chains list of dict

__init__(chains: List[dict], wanted_label: str, owned_label: str)

align_seqs(chain_selection) → Tuple[str, str]

Align the human seq to the mouse and store it the chain dict

covert_A2B(seqA: str, seqB: str, resiA: int) → int

Given seqA and seqB as two gap aligned sequences, and an off-by-one residue number of seqA without counting gaps, return an off-by-one residue number of seqB without counting gaps.

classmethod from_chain_ops(chain_ops: ChainOps, wanted_label: str, owned_label: str)

transmogrify(mutation: str, chain_selection: str | int | dict) → str

Module contents

They were copied over from another project. They are not complete. These classes/functions do not use PyRosetta. To change a sequence to another use threading.