M-CSA

class enzymm.mcsa_info.HomologousPDB(mcsa_id: int, reference_pdbchain: str, is_reference: bool, pdb_id: str, chain_id: str, assembly_chain_id: str, assembly: int, residues: Dict[int, HomologousResidue])

Class for a PDB Entry homologous to or identical to the structure from which a template was generated.

mcsa_id

int : M-CSA ID

Type:: int

reference_pdbchain

str : PDB identifier of the M-CSA reference PDB structure

Type:: str

is_reference

bool : If this structure is an M-CSA reference

Type:: bool

pdb_id

str : PDB identifier of the PDB structure

Type:: str

chain_id

str : Chain identifier in the PDB

Type:: str

assembly_chain_id

str : Author assigned assembly chain identifier

Type:: str

assembly

int : Assembly number (usually but not always the biological assembly)

Type:: int

residues

dict of [int , HomologousResidue] : Dictionary mapping residue indices to residues. If “is_reference” then values are ReferenceCatalyticResidue else they are NonReferenceCatalyticResidue

Type:: Dict[int, enzymm.mcsa_info.HomologousResidue]

__init__(mcsa_id: int, reference_pdbchain: str, is_reference: bool, pdb_id: str, chain_id: str, assembly_chain_id: str, assembly: int, residues: Dict[int, HomologousResidue]) → None

class enzymm.mcsa_info.HomologousResidue(name: str, number: int, auth_number: int)

Base class for a PDB residue identical or homologous to a template residue.

name

str Three letter amino-acid code

Type:: str

number

int residue id in the PDB

Type:: int

auth_number

int Author assigned residue id

Type:: int

__init__(name: str, number: int, auth_number: int) → None

class enzymm.mcsa_info.NonReferenceCatalyticResidue(name: str, number: int, auth_number: int, reference: Tuple[int, str, int])

Child Class of HomologousResidue for a non-reference PDB residue for a template residue.

reference

tuple of (int , str , int) : Tuple of mcsa_id, pdb_id, residue_index to find the reference

Type:: Tuple[int, str, int]

__init__(name: str, number: int, auth_number: int, reference: Tuple[int, str, int]) → None

class enzymm.mcsa_info.ReferenceCatalyticResidue(name: str, number: int, auth_number: int, function_location_abv: str | None, ptm: str | None, roles: List[str], roles_summary: List[str])

Child Class of HomologousResidue for a reference PDB residue for a template residue.

function_location_abv

str Functional part of the residue. Empty string means side chain. Else “main”, “main-C”, “main-N” or “ptm”

Type:: str | None

ptm

str Empty string or for post translationally modified residues, the 3-letter code of the ptm in the PDB

Type:: str | None

roles

list of str of EMO codes describing functional roles

Type:: List[str]

roles_summary

list of str discriptions of functional roles

Type:: List[str]

__init__(name: str, number: int, auth_number: int, function_location_abv: str | None, ptm: str | None, roles: List[str], roles_summary: List[str]) → None