Module protkit.properties.bond_angles
Implements class to calculate bond angles BondAngles to calculate bond angles
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 to calculate bond angles `BondAngles` to calculate bond angles
in a residue, chain or protein.
"""
from typing import List, Dict, Tuple
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 BondAngles:
HEAVY_ATOM_BOND_ANGLES = {
"ALA": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB")
},
"ARG": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD"),
("CG", "CD", "NE"),
("CD", "NE", "CZ"),
("NE", "CZ", "NH1"),
("NE", "CZ", "NH2"),
("NH1", "CZ", "NH2")
},
"ASN": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "OD1"),
("CB", "CG", "ND2"),
("ND2", "CG", "OD1")
},
"ASP": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "OD1"),
("CB", "CG", "OD2"),
("OD1", "CG", "OD2")
},
"CYS": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "SG")
},
"GLU": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD"),
("CG", "CD", "OE1"),
("CG", "CD", "OE2"),
("OE1", "CD", "OE2")
},
"GLN": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD"),
("CG", "CD", "OE1"),
("CG", "CD", "NE2"),
("OE1", "CD", "NE2")
},
"GLY": {
("N", "CA", "C"),
("CA", "C", "O")
},
"HIS": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "ND1"),
("CB", "CG", "CD2"),
("CG", "ND1", "CE1"),
("ND1", "CE1", "NE2"),
("CE1", "NE2", "CD2"),
("NE2", "CD2", "CG"),
("CD2", "CG", "ND1")
},
"ILE": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG1"),
("CB", "CG1", "CD1"),
("CA", "CB", "CG2"),
("CG1", "CB", "CG2")
},
"LEU": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD1"),
("CB", "CG", "CD2"),
("CD1", "CG", "CD2")
},
"LYS": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD"),
("CG", "CD", "CE"),
("CD", "CE", "NZ")
},
"MET": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "SD"),
("CG", "SD", "CE")
},
"PHE": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD1"),
("CB", "CG", "CD2"),
("CD1", "CG", "CD2"),
("CG", "CD1", "CE1"),
("CD1", "CE1", "CZ"),
("CE1", "CZ", "CE2"),
("CZ", "CE2", "CD2"),
("CE2", "CD2", "CG")
},
"PRO": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD"),
("CG", "CD", "N"),
("CA", "N", "CD")
},
"SER": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "OG")
},
"THR": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "OG1"),
("CA", "CB", "CG2"),
("OG1", "CB", "CG2")
},
"TRP": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD1"),
("CB", "CG", "CD2"),
("CD1", "CG", "CD2"),
("CG", "CD1", "NE1"),
("CD1", "NE1", "CE2"),
("NE1", "CE2", "CD2"),
("CE2", "CD2", "CG"),
("CG", "CD2", "CE3"),
("NE1", "CE2", "CZ2"),
("CE3", "CD2", "CE2"),
("CD2", "CE2", "CZ2"),
("CE2", "CZ2", "CH2"),
("CZ2", "CH2", "CZ3"),
("CH2", "CZ3", "CE3"),
("CZ3", "CE3", "CD2")
},
"TYR": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG"),
("CB", "CG", "CD1"),
("CB", "CG", "CD2"),
("CD1", "CG", "CD2"),
("CG", "CD1", "CE1"),
("CG", "CD2", "CE2"),
("CD1", "CE1", "CZ"),
("CD2", "CE2", "CZ"),
("CE1", "CZ", "CE2"),
("CE1", "CZ", "OH"),
("CE2", "CZ", "OH")
},
"VAL": {
("N", "CA", "C"),
("CA", "C", "O"),
("N", "CA", "CB"),
("C", "CA", "CB"),
("CA", "CB", "CG1"),
("CA", "CB", "CG2"),
("CG1", "CB", "CG2")
}
}
@staticmethod
def angle(a1: Atom, a2: Atom, a3: Atom) -> float:
"""
Calculates the angle between three atoms.
Args:
a1 (Atom): The first atom.
a2 (Atom): The second atom.
a3 (Atom): The third atom.
Returns:
float: The angle between the three atoms.
"""
return Math.angle(a1.x, a1.y, a1.z, a2.x, a2.y, a2.z, a3.x, a3.y, a3.z)
@staticmethod
def bond_angles_of_residue(residue: Residue,
assign_attribute: bool = False,
key: str = "bond_angles") -> Dict[Tuple[str, str, str], float]:
"""
Returns the bond angles of a residue
Args:
residue (Residue): The residue for which to return the bond angles
assign_attribute (bool): Whether to assign the bond angles to the residue
key (str): The key to use to access the bond angles
Returns:
Dict[Tuple[str, str, str], float]: A dictionary of bond angles
"""
angles = {}
defined_angles = BondAngles.HEAVY_ATOM_BOND_ANGLES.get(residue.residue_type, set())
for (atom1, atom2, atom3) in defined_angles:
a1 = residue.get_atom(atom1)
a2 = residue.get_atom(atom2)
a3 = residue.get_atom(atom3)
if a1 and a2 and a3:
angles[(atom1, atom2, atom3)] = BondAngles.angle(a1, a2, a3)
else:
angles[(atom1, atom2, atom3)] = None
if assign_attribute:
residue.set_attribute(key, angles)
return angles
@staticmethod
def bond_angles_of_chain(chain: Chain,
assign_attribute: bool = False,
key: str = "bond_angles") -> Dict[str, Dict]:
"""
Returns the bond angles of a chain
Args:
chain (Chain): The chain for which to return the bond angles
assign_attribute (bool): Whether to assign the bond angles to the chain
key (str): The key to use to access the bond angles
Returns:
Dict[str, Dict]: A dictionary of bond angles.
"""
angles = {}
for residue in chain.residues:
angles[residue.residue_code] = BondAngles.bond_angles_of_residue(residue, assign_attribute=assign_attribute, key=key)
return angles
@staticmethod
def bond_angles_of_protein(protein: Protein,
assign_attribute: bool = False,
key: str = "bond_angles") -> Dict[str, Dict]:
"""
Returns the bond angles of a protein
Args:
protein (Protein): The protein for which to return the bond angles
assign_attribute (bool): Whether to assign the bond angles to the protein
key (str): The key to use to access the bond angles
Returns:
Dict[str, Dict]: A dictionary of bond angles.
"""
angles = {}
for chain in protein.chains:
angles[chain.chain_id] = BondAngles.bond_angles_of_chain(chain, assign_attribute=assign_attribute, key=key)
return anglesClasses
class BondAngles-
Expand source code
class BondAngles: HEAVY_ATOM_BOND_ANGLES = { "ALA": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB") }, "ARG": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD"), ("CG", "CD", "NE"), ("CD", "NE", "CZ"), ("NE", "CZ", "NH1"), ("NE", "CZ", "NH2"), ("NH1", "CZ", "NH2") }, "ASN": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "OD1"), ("CB", "CG", "ND2"), ("ND2", "CG", "OD1") }, "ASP": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "OD1"), ("CB", "CG", "OD2"), ("OD1", "CG", "OD2") }, "CYS": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "SG") }, "GLU": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD"), ("CG", "CD", "OE1"), ("CG", "CD", "OE2"), ("OE1", "CD", "OE2") }, "GLN": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD"), ("CG", "CD", "OE1"), ("CG", "CD", "NE2"), ("OE1", "CD", "NE2") }, "GLY": { ("N", "CA", "C"), ("CA", "C", "O") }, "HIS": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "ND1"), ("CB", "CG", "CD2"), ("CG", "ND1", "CE1"), ("ND1", "CE1", "NE2"), ("CE1", "NE2", "CD2"), ("NE2", "CD2", "CG"), ("CD2", "CG", "ND1") }, "ILE": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG1"), ("CB", "CG1", "CD1"), ("CA", "CB", "CG2"), ("CG1", "CB", "CG2") }, "LEU": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD1"), ("CB", "CG", "CD2"), ("CD1", "CG", "CD2") }, "LYS": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD"), ("CG", "CD", "CE"), ("CD", "CE", "NZ") }, "MET": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "SD"), ("CG", "SD", "CE") }, "PHE": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD1"), ("CB", "CG", "CD2"), ("CD1", "CG", "CD2"), ("CG", "CD1", "CE1"), ("CD1", "CE1", "CZ"), ("CE1", "CZ", "CE2"), ("CZ", "CE2", "CD2"), ("CE2", "CD2", "CG") }, "PRO": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD"), ("CG", "CD", "N"), ("CA", "N", "CD") }, "SER": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "OG") }, "THR": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "OG1"), ("CA", "CB", "CG2"), ("OG1", "CB", "CG2") }, "TRP": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD1"), ("CB", "CG", "CD2"), ("CD1", "CG", "CD2"), ("CG", "CD1", "NE1"), ("CD1", "NE1", "CE2"), ("NE1", "CE2", "CD2"), ("CE2", "CD2", "CG"), ("CG", "CD2", "CE3"), ("NE1", "CE2", "CZ2"), ("CE3", "CD2", "CE2"), ("CD2", "CE2", "CZ2"), ("CE2", "CZ2", "CH2"), ("CZ2", "CH2", "CZ3"), ("CH2", "CZ3", "CE3"), ("CZ3", "CE3", "CD2") }, "TYR": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG"), ("CB", "CG", "CD1"), ("CB", "CG", "CD2"), ("CD1", "CG", "CD2"), ("CG", "CD1", "CE1"), ("CG", "CD2", "CE2"), ("CD1", "CE1", "CZ"), ("CD2", "CE2", "CZ"), ("CE1", "CZ", "CE2"), ("CE1", "CZ", "OH"), ("CE2", "CZ", "OH") }, "VAL": { ("N", "CA", "C"), ("CA", "C", "O"), ("N", "CA", "CB"), ("C", "CA", "CB"), ("CA", "CB", "CG1"), ("CA", "CB", "CG2"), ("CG1", "CB", "CG2") } } @staticmethod def angle(a1: Atom, a2: Atom, a3: Atom) -> float: """ Calculates the angle between three atoms. Args: a1 (Atom): The first atom. a2 (Atom): The second atom. a3 (Atom): The third atom. Returns: float: The angle between the three atoms. """ return Math.angle(a1.x, a1.y, a1.z, a2.x, a2.y, a2.z, a3.x, a3.y, a3.z) @staticmethod def bond_angles_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "bond_angles") -> Dict[Tuple[str, str, str], float]: """ Returns the bond angles of a residue Args: residue (Residue): The residue for which to return the bond angles assign_attribute (bool): Whether to assign the bond angles to the residue key (str): The key to use to access the bond angles Returns: Dict[Tuple[str, str, str], float]: A dictionary of bond angles """ angles = {} defined_angles = BondAngles.HEAVY_ATOM_BOND_ANGLES.get(residue.residue_type, set()) for (atom1, atom2, atom3) in defined_angles: a1 = residue.get_atom(atom1) a2 = residue.get_atom(atom2) a3 = residue.get_atom(atom3) if a1 and a2 and a3: angles[(atom1, atom2, atom3)] = BondAngles.angle(a1, a2, a3) else: angles[(atom1, atom2, atom3)] = None if assign_attribute: residue.set_attribute(key, angles) return angles @staticmethod def bond_angles_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "bond_angles") -> Dict[str, Dict]: """ Returns the bond angles of a chain Args: chain (Chain): The chain for which to return the bond angles assign_attribute (bool): Whether to assign the bond angles to the chain key (str): The key to use to access the bond angles Returns: Dict[str, Dict]: A dictionary of bond angles. """ angles = {} for residue in chain.residues: angles[residue.residue_code] = BondAngles.bond_angles_of_residue(residue, assign_attribute=assign_attribute, key=key) return angles @staticmethod def bond_angles_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "bond_angles") -> Dict[str, Dict]: """ Returns the bond angles of a protein Args: protein (Protein): The protein for which to return the bond angles assign_attribute (bool): Whether to assign the bond angles to the protein key (str): The key to use to access the bond angles Returns: Dict[str, Dict]: A dictionary of bond angles. """ angles = {} for chain in protein.chains: angles[chain.chain_id] = BondAngles.bond_angles_of_chain(chain, assign_attribute=assign_attribute, key=key) return anglesClass variables
var HEAVY_ATOM_BOND_ANGLES
Static methods
def angle(a1: Atom, a2: Atom, a3: Atom) ‑> float-
Calculates the angle between three atoms.
Args
a1:Atom- The first atom.
a2:Atom- The second atom.
a3:Atom- The third atom.
Returns
float- The angle between the three atoms.
Expand source code
@staticmethod def angle(a1: Atom, a2: Atom, a3: Atom) -> float: """ Calculates the angle between three atoms. Args: a1 (Atom): The first atom. a2 (Atom): The second atom. a3 (Atom): The third atom. Returns: float: The angle between the three atoms. """ return Math.angle(a1.x, a1.y, a1.z, a2.x, a2.y, a2.z, a3.x, a3.y, a3.z) def bond_angles_of_chain(chain: Chain, assign_attribute: bool = False, key: str = 'bond_angles') ‑> Dict[str, Dict]-
Returns the bond angles of a chain
Args
chain:Chain- The chain for which to return the bond angles
assign_attribute:bool- Whether to assign the bond angles to the chain
key:str- The key to use to access the bond angles
Returns
Dict[str, Dict]- A dictionary of bond angles.
Expand source code
@staticmethod def bond_angles_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "bond_angles") -> Dict[str, Dict]: """ Returns the bond angles of a chain Args: chain (Chain): The chain for which to return the bond angles assign_attribute (bool): Whether to assign the bond angles to the chain key (str): The key to use to access the bond angles Returns: Dict[str, Dict]: A dictionary of bond angles. """ angles = {} for residue in chain.residues: angles[residue.residue_code] = BondAngles.bond_angles_of_residue(residue, assign_attribute=assign_attribute, key=key) return angles def bond_angles_of_protein(protein: Protein, assign_attribute: bool = False, key: str = 'bond_angles') ‑> Dict[str, Dict]-
Returns the bond angles of a protein
Args
protein:Protein- The protein for which to return the bond angles
assign_attribute:bool- Whether to assign the bond angles to the protein
key:str- The key to use to access the bond angles
Returns
Dict[str, Dict]- A dictionary of bond angles.
Expand source code
@staticmethod def bond_angles_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "bond_angles") -> Dict[str, Dict]: """ Returns the bond angles of a protein Args: protein (Protein): The protein for which to return the bond angles assign_attribute (bool): Whether to assign the bond angles to the protein key (str): The key to use to access the bond angles Returns: Dict[str, Dict]: A dictionary of bond angles. """ angles = {} for chain in protein.chains: angles[chain.chain_id] = BondAngles.bond_angles_of_chain(chain, assign_attribute=assign_attribute, key=key) return angles def bond_angles_of_residue(residue: Residue, assign_attribute: bool = False, key: str = 'bond_angles') ‑> Dict[Tuple[str, str, str], float]-
Returns the bond angles of a residue
Args
residue:Residue- The residue for which to return the bond angles
assign_attribute:bool- Whether to assign the bond angles to the residue
key:str- The key to use to access the bond angles
Returns
Dict[Tuple[str, str, str], float]- A dictionary of bond angles
Expand source code
@staticmethod def bond_angles_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "bond_angles") -> Dict[Tuple[str, str, str], float]: """ Returns the bond angles of a residue Args: residue (Residue): The residue for which to return the bond angles assign_attribute (bool): Whether to assign the bond angles to the residue key (str): The key to use to access the bond angles Returns: Dict[Tuple[str, str, str], float]: A dictionary of bond angles """ angles = {} defined_angles = BondAngles.HEAVY_ATOM_BOND_ANGLES.get(residue.residue_type, set()) for (atom1, atom2, atom3) in defined_angles: a1 = residue.get_atom(atom1) a2 = residue.get_atom(atom2) a3 = residue.get_atom(atom3) if a1 and a2 and a3: angles[(atom1, atom2, atom3)] = BondAngles.angle(a1, a2, a3) else: angles[(atom1, atom2, atom3)] = None if assign_attribute: residue.set_attribute(key, angles) return angles