Module protkit.properties.bond_lengths
Implements class BondLengths to calculate the bond lengths in a residue,
chain or protein.
Expand source code
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors: Fred Senekal (FS)
# Contact: fred@silicogenesis.com
# License: GPLv3
"""
Implements class `BondLengths` to calculate the bond lengths in a residue,
chain or protein.
"""
from typing import Dict, List, Tuple, Optional
from protkit.structure.atom import Atom
from protkit.structure.residue import Residue
from protkit.structure.chain import Chain
from protkit.structure.protein import Protein
from protkit.geometry.math import Math
class BondLengths:
HEAVY_ATOM_BONDS = {
"ALA": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB")
],
"ASN": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "OD1"),
("CG", "ND2")
],
"ASP": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "OD1"),
("CG", "OD2")
],
"ARG": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD"),
("CD", "NE"),
("NE", "CZ"),
("CZ", "NH1"),
("CZ", "NH2")
],
"CYS": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "SG")
],
"GLN": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD"),
("CD", "OE1"),
("CD", "NE2")
],
"GLY": [
("N", "CA"),
("CA", "C"),
("C", "O")
],
"GLU": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD"),
("CD", "OE1"),
("CD", "OE2")
],
"HIS": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "ND1"),
("CG", "CD2"),
("ND1", "CE1"),
("CD2", "NE2"),
("CE1", "NE2")
],
"ILE": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG1"),
("CB", "CG2"),
("CG1", "CD1")
],
"LEU": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD1"),
("CG", "CD2")
],
"LYS": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD"),
("CD", "CE"),
("CE", "NZ")
],
"MET": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "SD"),
("SD", "CE")
],
"PHE": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD1"),
("CG", "CD2"),
("CD1", "CE1"),
("CD2", "CE2"),
("CE1", "CZ"),
("CE2", "CZ")
],
"PRO": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD"),
("N", "CD"),
],
"SER": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "OG")
],
"THR": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "OG1"),
("CB", "CG2")
],
"TRP": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD1"),
("CG", "CD2"),
("CD1", "NE1"),
("CD2", "CE2"),
("CD2", "CE3"),
("NE1", "CE2"),
("CE2", "CZ2"),
("CE3", "CZ3"),
("CZ2", "CH2"),
("CZ3", "CH2"),
],
"TYR": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG"),
("CG", "CD1"),
("CG", "CD2"),
("CD1", "CE1"),
("CD2", "CE2"),
("CE1", "CZ"),
("CE2", "CZ"),
("CZ", "OH")
],
"VAL": [
("N", "CA"),
("CA", "C"),
("C", "O"),
("CA", "CB"),
("CB", "CG1"),
("CB", "CG2")
]
}
@staticmethod
def atom_distance(atom1: Atom, atom2: Atom) -> float:
"""
Calculates the Euclidean distance between two atoms.
Args:
atom1 (Atom): The first atom.
atom2 (Atom): The second atom.
Returns:
float: The distance between the two atoms.
Raises:
None
"""
return Math.euclidean_distance(atom1.x, atom1.y, atom1.z, atom2.x, atom2.y, atom2.z)
@staticmethod
def bond_lengths_of_residue(residue: Residue,
assign_attribute: bool = False,
key: str = "bond_lengths") -> Dict[Tuple[str, str], float]:
"""
Returns the bond lengths of the residue.
Args:
residue (Residue): The residue for which to return the bond lengths.
assign_attribute (bool): Whether to assign the bond lengths to the residue.
key (str): The key to use for the attribute.
Returns:
Dict[Tuple[str, str], float]: A dictionary containing the bond lengths of the residue.
"""
bonds = {}
defined_bonds = BondLengths.HEAVY_ATOM_BONDS.get(residue.residue_type, [])
for (atom1, atom2) in defined_bonds:
a1 = residue.get_atom(atom1)
a2 = residue.get_atom(atom2)
if a1 and a2:
bonds[(atom1, atom2)] = BondLengths.atom_distance(a1, a2)
else:
bonds[(atom1, atom2)] = None
if assign_attribute:
residue.set_attribute(key, bonds)
return bonds
@staticmethod
def bond_lengths_of_chain(chain: Chain,
assign_attribute: bool = False,
key: str = "bond_lengths") -> Dict[str, Dict]:
"""
Returns the bond lengths of the chain.
Args:
chain (Chain): The chain for which to return the bond lengths.
assign_attribute (bool): Whether to assign the bond lengths to the chain.
key (str): The key to use for the attribute.
Returns:
Dict[str, Dict]: A dictionary containing the bond lengths of the chain.
"""
bonds = {}
for residue in chain.residues:
bonds[residue.residue_code] = BondLengths.bond_lengths_of_residue(residue, assign_attribute=assign_attribute, key=key)
return bonds
@staticmethod
def bond_lengths_of_protein(protein: Protein,
assign_attribute: bool = False,
key: str = "bond_lengths") -> Dict[str, Dict]:
"""
Returns the bond lengths of the protein.
Args:
protein (Protein): The protein for which to return the bond lengths.
assign_attribute (bool): Whether to assign the bond lengths to the protein.
key (str): The key to use for the attribute.
Returns:
Dict[str, Dict]: A dictionary containing the bond lengths of the protein.
"""
bonds = {}
for chain in protein.chains:
bonds[chain.chain_id] = BondLengths.bond_lengths_of_chain(chain, assign_attribute=assign_attribute, key=key)
return bonds
@staticmethod
def peptide_bond_length(residue1: Residue, residue2: Residue) -> Optional[float]:
"""
Returns the peptide bond length between two residues. Specifically, the bond length
between the C atom of the first residue and the N atom of the second residue.
Args:
residue1 (Residue): The first residue.
residue2 (Residue): The second residue.
Returns:
float: The bond length between the two residues. If the atoms are not found, None is returned.
"""
a1 = residue1.get_atom("C")
a2 = residue2.get_atom("N")
if a1 and a2:
return BondLengths.atom_distance(a1, a2)
else:
return None
@staticmethod
def peptide_bond_lengths_of_chain(chain: Chain,
assign_attribute: bool = False,
key: str = "peptide_bond_lengths") -> List[float]:
"""
Returns the peptide bond lengths of the chain.
Args:
chain (Chain): The chain for which to return the peptide bond lengths.
assign_attribute (bool): Whether to assign the peptide bond lengths to the chain.
key (str): The key to use for the attribute.
Returns:
dict: A dictionary containing the peptide bond lengths of the chain.
"""
bonds = []
for i in range(chain.num_residues - 1):
bonds.append(BondLengths.peptide_bond_length(chain.get_residue(i), chain.get_residue(i + 1)))
if assign_attribute:
chain.set_attribute(key, bonds)
return bonds
@staticmethod
def peptide_bond_lengths_of_protein(protein: Protein,
assign_attribute: bool = False,
key: str = "peptide_bond_lengths") -> Dict[str, List[float]]:
"""
Returns the peptide bond lengths of the protein.
Args:
protein (Protein): The protein for which to return the peptide bond lengths.
assign_attribute (bool): Whether to assign the peptide bond lengths to the protein.
key (str): The key to use for the attribute.
Returns:
dict: A dictionary containing the peptide bond lengths of the protein.
"""
bonds = {}
for chain in protein.chains:
bonds[chain.chain_id] = BondLengths.peptide_bond_lengths_of_chain(chain, assign_attribute=assign_attribute, key=key)
return bondsClasses
class BondLengths-
Expand source code
class BondLengths: HEAVY_ATOM_BONDS = { "ALA": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB") ], "ASN": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "OD1"), ("CG", "ND2") ], "ASP": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "OD1"), ("CG", "OD2") ], "ARG": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD"), ("CD", "NE"), ("NE", "CZ"), ("CZ", "NH1"), ("CZ", "NH2") ], "CYS": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "SG") ], "GLN": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD"), ("CD", "OE1"), ("CD", "NE2") ], "GLY": [ ("N", "CA"), ("CA", "C"), ("C", "O") ], "GLU": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD"), ("CD", "OE1"), ("CD", "OE2") ], "HIS": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "ND1"), ("CG", "CD2"), ("ND1", "CE1"), ("CD2", "NE2"), ("CE1", "NE2") ], "ILE": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG1"), ("CB", "CG2"), ("CG1", "CD1") ], "LEU": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD1"), ("CG", "CD2") ], "LYS": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD"), ("CD", "CE"), ("CE", "NZ") ], "MET": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "SD"), ("SD", "CE") ], "PHE": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD1"), ("CG", "CD2"), ("CD1", "CE1"), ("CD2", "CE2"), ("CE1", "CZ"), ("CE2", "CZ") ], "PRO": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD"), ("N", "CD"), ], "SER": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "OG") ], "THR": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "OG1"), ("CB", "CG2") ], "TRP": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD1"), ("CG", "CD2"), ("CD1", "NE1"), ("CD2", "CE2"), ("CD2", "CE3"), ("NE1", "CE2"), ("CE2", "CZ2"), ("CE3", "CZ3"), ("CZ2", "CH2"), ("CZ3", "CH2"), ], "TYR": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG"), ("CG", "CD1"), ("CG", "CD2"), ("CD1", "CE1"), ("CD2", "CE2"), ("CE1", "CZ"), ("CE2", "CZ"), ("CZ", "OH") ], "VAL": [ ("N", "CA"), ("CA", "C"), ("C", "O"), ("CA", "CB"), ("CB", "CG1"), ("CB", "CG2") ] } @staticmethod def atom_distance(atom1: Atom, atom2: Atom) -> float: """ Calculates the Euclidean distance between two atoms. Args: atom1 (Atom): The first atom. atom2 (Atom): The second atom. Returns: float: The distance between the two atoms. Raises: None """ return Math.euclidean_distance(atom1.x, atom1.y, atom1.z, atom2.x, atom2.y, atom2.z) @staticmethod def bond_lengths_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "bond_lengths") -> Dict[Tuple[str, str], float]: """ Returns the bond lengths of the residue. Args: residue (Residue): The residue for which to return the bond lengths. assign_attribute (bool): Whether to assign the bond lengths to the residue. key (str): The key to use for the attribute. Returns: Dict[Tuple[str, str], float]: A dictionary containing the bond lengths of the residue. """ bonds = {} defined_bonds = BondLengths.HEAVY_ATOM_BONDS.get(residue.residue_type, []) for (atom1, atom2) in defined_bonds: a1 = residue.get_atom(atom1) a2 = residue.get_atom(atom2) if a1 and a2: bonds[(atom1, atom2)] = BondLengths.atom_distance(a1, a2) else: bonds[(atom1, atom2)] = None if assign_attribute: residue.set_attribute(key, bonds) return bonds @staticmethod def bond_lengths_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "bond_lengths") -> Dict[str, Dict]: """ Returns the bond lengths of the chain. Args: chain (Chain): The chain for which to return the bond lengths. assign_attribute (bool): Whether to assign the bond lengths to the chain. key (str): The key to use for the attribute. Returns: Dict[str, Dict]: A dictionary containing the bond lengths of the chain. """ bonds = {} for residue in chain.residues: bonds[residue.residue_code] = BondLengths.bond_lengths_of_residue(residue, assign_attribute=assign_attribute, key=key) return bonds @staticmethod def bond_lengths_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "bond_lengths") -> Dict[str, Dict]: """ Returns the bond lengths of the protein. Args: protein (Protein): The protein for which to return the bond lengths. assign_attribute (bool): Whether to assign the bond lengths to the protein. key (str): The key to use for the attribute. Returns: Dict[str, Dict]: A dictionary containing the bond lengths of the protein. """ bonds = {} for chain in protein.chains: bonds[chain.chain_id] = BondLengths.bond_lengths_of_chain(chain, assign_attribute=assign_attribute, key=key) return bonds @staticmethod def peptide_bond_length(residue1: Residue, residue2: Residue) -> Optional[float]: """ Returns the peptide bond length between two residues. Specifically, the bond length between the C atom of the first residue and the N atom of the second residue. Args: residue1 (Residue): The first residue. residue2 (Residue): The second residue. Returns: float: The bond length between the two residues. If the atoms are not found, None is returned. """ a1 = residue1.get_atom("C") a2 = residue2.get_atom("N") if a1 and a2: return BondLengths.atom_distance(a1, a2) else: return None @staticmethod def peptide_bond_lengths_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "peptide_bond_lengths") -> List[float]: """ Returns the peptide bond lengths of the chain. Args: chain (Chain): The chain for which to return the peptide bond lengths. assign_attribute (bool): Whether to assign the peptide bond lengths to the chain. key (str): The key to use for the attribute. Returns: dict: A dictionary containing the peptide bond lengths of the chain. """ bonds = [] for i in range(chain.num_residues - 1): bonds.append(BondLengths.peptide_bond_length(chain.get_residue(i), chain.get_residue(i + 1))) if assign_attribute: chain.set_attribute(key, bonds) return bonds @staticmethod def peptide_bond_lengths_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "peptide_bond_lengths") -> Dict[str, List[float]]: """ Returns the peptide bond lengths of the protein. Args: protein (Protein): The protein for which to return the peptide bond lengths. assign_attribute (bool): Whether to assign the peptide bond lengths to the protein. key (str): The key to use for the attribute. Returns: dict: A dictionary containing the peptide bond lengths of the protein. """ bonds = {} for chain in protein.chains: bonds[chain.chain_id] = BondLengths.peptide_bond_lengths_of_chain(chain, assign_attribute=assign_attribute, key=key) return bondsClass variables
var HEAVY_ATOM_BONDS
Static methods
def atom_distance(atom1: Atom, atom2: Atom) ‑> float-
Calculates the Euclidean distance between two atoms.
Args
atom1:Atom- The first atom.
atom2:Atom- The second atom.
Returns
float- The distance between the two atoms.
Raises
None
Expand source code
@staticmethod def atom_distance(atom1: Atom, atom2: Atom) -> float: """ Calculates the Euclidean distance between two atoms. Args: atom1 (Atom): The first atom. atom2 (Atom): The second atom. Returns: float: The distance between the two atoms. Raises: None """ return Math.euclidean_distance(atom1.x, atom1.y, atom1.z, atom2.x, atom2.y, atom2.z) def bond_lengths_of_chain(chain: Chain, assign_attribute: bool = False, key: str = 'bond_lengths') ‑> Dict[str, Dict]-
Returns the bond lengths of the chain.
Args
chain:Chain- The chain for which to return the bond lengths.
assign_attribute:bool- Whether to assign the bond lengths to the chain.
key:str- The key to use for the attribute.
Returns
Dict[str, Dict]- A dictionary containing the bond lengths of the chain.
Expand source code
@staticmethod def bond_lengths_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "bond_lengths") -> Dict[str, Dict]: """ Returns the bond lengths of the chain. Args: chain (Chain): The chain for which to return the bond lengths. assign_attribute (bool): Whether to assign the bond lengths to the chain. key (str): The key to use for the attribute. Returns: Dict[str, Dict]: A dictionary containing the bond lengths of the chain. """ bonds = {} for residue in chain.residues: bonds[residue.residue_code] = BondLengths.bond_lengths_of_residue(residue, assign_attribute=assign_attribute, key=key) return bonds def bond_lengths_of_protein(protein: Protein, assign_attribute: bool = False, key: str = 'bond_lengths') ‑> Dict[str, Dict]-
Returns the bond lengths of the protein.
Args
protein:Protein- The protein for which to return the bond lengths.
assign_attribute:bool- Whether to assign the bond lengths to the protein.
key:str- The key to use for the attribute.
Returns
Dict[str, Dict]- A dictionary containing the bond lengths of the protein.
Expand source code
@staticmethod def bond_lengths_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "bond_lengths") -> Dict[str, Dict]: """ Returns the bond lengths of the protein. Args: protein (Protein): The protein for which to return the bond lengths. assign_attribute (bool): Whether to assign the bond lengths to the protein. key (str): The key to use for the attribute. Returns: Dict[str, Dict]: A dictionary containing the bond lengths of the protein. """ bonds = {} for chain in protein.chains: bonds[chain.chain_id] = BondLengths.bond_lengths_of_chain(chain, assign_attribute=assign_attribute, key=key) return bonds def bond_lengths_of_residue(residue: Residue, assign_attribute: bool = False, key: str = 'bond_lengths') ‑> Dict[Tuple[str, str], float]-
Returns the bond lengths of the residue.
Args
residue:Residue- The residue for which to return the bond lengths.
assign_attribute:bool- Whether to assign the bond lengths to the residue.
key:str- The key to use for the attribute.
Returns
Dict[Tuple[str, str], float]- A dictionary containing the bond lengths of the residue.
Expand source code
@staticmethod def bond_lengths_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "bond_lengths") -> Dict[Tuple[str, str], float]: """ Returns the bond lengths of the residue. Args: residue (Residue): The residue for which to return the bond lengths. assign_attribute (bool): Whether to assign the bond lengths to the residue. key (str): The key to use for the attribute. Returns: Dict[Tuple[str, str], float]: A dictionary containing the bond lengths of the residue. """ bonds = {} defined_bonds = BondLengths.HEAVY_ATOM_BONDS.get(residue.residue_type, []) for (atom1, atom2) in defined_bonds: a1 = residue.get_atom(atom1) a2 = residue.get_atom(atom2) if a1 and a2: bonds[(atom1, atom2)] = BondLengths.atom_distance(a1, a2) else: bonds[(atom1, atom2)] = None if assign_attribute: residue.set_attribute(key, bonds) return bonds def peptide_bond_length(residue1: Residue, residue2: Residue) ‑> Optional[float]-
Returns the peptide bond length between two residues. Specifically, the bond length between the C atom of the first residue and the N atom of the second residue.
Args
residue1:Residue- The first residue.
residue2:Residue- The second residue.
Returns
float- The bond length between the two residues. If the atoms are not found, None is returned.
Expand source code
@staticmethod def peptide_bond_length(residue1: Residue, residue2: Residue) -> Optional[float]: """ Returns the peptide bond length between two residues. Specifically, the bond length between the C atom of the first residue and the N atom of the second residue. Args: residue1 (Residue): The first residue. residue2 (Residue): The second residue. Returns: float: The bond length between the two residues. If the atoms are not found, None is returned. """ a1 = residue1.get_atom("C") a2 = residue2.get_atom("N") if a1 and a2: return BondLengths.atom_distance(a1, a2) else: return None def peptide_bond_lengths_of_chain(chain: Chain, assign_attribute: bool = False, key: str = 'peptide_bond_lengths') ‑> List[float]-
Returns the peptide bond lengths of the chain.
Args
chain:Chain- The chain for which to return the peptide bond lengths.
assign_attribute:bool- Whether to assign the peptide bond lengths to the chain.
key:str- The key to use for the attribute.
Returns
dict- A dictionary containing the peptide bond lengths of the chain.
Expand source code
@staticmethod def peptide_bond_lengths_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "peptide_bond_lengths") -> List[float]: """ Returns the peptide bond lengths of the chain. Args: chain (Chain): The chain for which to return the peptide bond lengths. assign_attribute (bool): Whether to assign the peptide bond lengths to the chain. key (str): The key to use for the attribute. Returns: dict: A dictionary containing the peptide bond lengths of the chain. """ bonds = [] for i in range(chain.num_residues - 1): bonds.append(BondLengths.peptide_bond_length(chain.get_residue(i), chain.get_residue(i + 1))) if assign_attribute: chain.set_attribute(key, bonds) return bonds def peptide_bond_lengths_of_protein(protein: Protein, assign_attribute: bool = False, key: str = 'peptide_bond_lengths') ‑> Dict[str, List[float]]-
Returns the peptide bond lengths of the protein.
Args
protein:Protein- The protein for which to return the peptide bond lengths.
assign_attribute:bool- Whether to assign the peptide bond lengths to the protein.
key:str- The key to use for the attribute.
Returns
dict- A dictionary containing the peptide bond lengths of the protein.
Expand source code
@staticmethod def peptide_bond_lengths_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "peptide_bond_lengths") -> Dict[str, List[float]]: """ Returns the peptide bond lengths of the protein. Args: protein (Protein): The protein for which to return the peptide bond lengths. assign_attribute (bool): Whether to assign the peptide bond lengths to the protein. key (str): The key to use for the attribute. Returns: dict: A dictionary containing the peptide bond lengths of the protein. """ bonds = {} for chain in protein.chains: bonds[chain.chain_id] = BondLengths.peptide_bond_lengths_of_chain(chain, assign_attribute=assign_attribute, key=key) return bonds