"""
Residue Bond Information Constants
This module contains bond connectivity information for standard residues
extracted from the Chemical Component Dictionary (CCD). This data is used
for molecular structure validation and bond detection in molr.
Generated automatically from CCD BinaryCIF files.
"""
from typing import Any, Dict, List, Union
# Bond information for standard residues
RESIDUE_BONDS: Dict[str, Dict] = {
"A": {
"bond_count": 39,
"aromatic_bonds": 0,
"bond_orders": {"sing": 34, "doub": 5},
"bonds": [
{"atom1": "OP3", "atom2": "P", "order": "sing", "aromatic": False},
{"atom1": "OP3", "atom2": "HOP3", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "OP1", "order": "doub", "aromatic": False},
{"atom1": "P", "atom2": "OP2", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "O5'", "order": "sing", "aromatic": False},
{"atom1": "OP2", "atom2": "HOP2", "order": "sing", "aromatic": False},
{"atom1": "O5'", "atom2": "C5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "C4'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "H5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "H5''", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "O4'", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "C3'", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "H4'", "order": "sing", "aromatic": False},
{"atom1": "O4'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "O3'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "C2'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "H3'", "order": "sing", "aromatic": False},
{"atom1": "O3'", "atom2": "HO3'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "O2'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "H2'", "order": "sing", "aromatic": False},
{"atom1": "O2'", "atom2": "HO2'", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "N9", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "H1'", "order": "sing", "aromatic": False},
{"atom1": "N9", "atom2": "C8", "order": "sing", "aromatic": False},
{"atom1": "N9", "atom2": "C4", "order": "sing", "aromatic": False},
{"atom1": "C8", "atom2": "N7", "order": "doub", "aromatic": False},
{"atom1": "C8", "atom2": "H8", "order": "sing", "aromatic": False},
{"atom1": "N7", "atom2": "C5", "order": "sing", "aromatic": False},
{"atom1": "C5", "atom2": "C6", "order": "sing", "aromatic": False},
{"atom1": "C5", "atom2": "C4", "order": "doub", "aromatic": False},
{"atom1": "C6", "atom2": "N6", "order": "sing", "aromatic": False},
{"atom1": "C6", "atom2": "N1", "order": "doub", "aromatic": False},
{"atom1": "N6", "atom2": "H61", "order": "sing", "aromatic": False},
{"atom1": "N6", "atom2": "H62", "order": "sing", "aromatic": False},
{"atom1": "N1", "atom2": "C2", "order": "sing", "aromatic": False},
{"atom1": "C2", "atom2": "N3", "order": "doub", "aromatic": False},
{"atom1": "C2", "atom2": "H2", "order": "sing", "aromatic": False},
{"atom1": "N3", "atom2": "C4", "order": "sing", "aromatic": False},
],
},
"ALA": {
"bond_count": 14,
"aromatic_bonds": 0,
"bond_orders": {"sing": 13, "doub": 1},
"bonds": [
{"atom1": "N", "atom2": "CA", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H2", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "C", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "CB", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "HA", "order": "sing", "aromatic": False},
{"atom1": "C", "atom2": "O", "order": "doub", "aromatic": False},
{"atom1": "C", "atom2": "OXT", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB1", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB2", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB3", "order": "sing", "aromatic": False},
{"atom1": "OXT", "atom2": "HXT", "order": "sing", "aromatic": False},
{"atom1": "H1", "atom2": "N", "order": "sing", "aromatic": False},
{"atom1": "H3", "atom2": "N", "order": "sing", "aromatic": False},
],
},
"ARG": {
"bond_count": 28,
"aromatic_bonds": 0,
"bond_orders": {"sing": 26, "doub": 2},
"bonds": [
{"atom1": "N", "atom2": "CA", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H2", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "C", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "CB", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "HA", "order": "sing", "aromatic": False},
{"atom1": "C", "atom2": "O", "order": "doub", "aromatic": False},
{"atom1": "C", "atom2": "OXT", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "CG", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB2", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB3", "order": "sing", "aromatic": False},
{"atom1": "CG", "atom2": "CD", "order": "sing", "aromatic": False},
{"atom1": "CG", "atom2": "HG2", "order": "sing", "aromatic": False},
{"atom1": "CG", "atom2": "HG3", "order": "sing", "aromatic": False},
{"atom1": "CD", "atom2": "NE", "order": "sing", "aromatic": False},
{"atom1": "CD", "atom2": "HD2", "order": "sing", "aromatic": False},
{"atom1": "CD", "atom2": "HD3", "order": "sing", "aromatic": False},
{"atom1": "NE", "atom2": "CZ", "order": "sing", "aromatic": False},
{"atom1": "NE", "atom2": "HE", "order": "sing", "aromatic": False},
{"atom1": "CZ", "atom2": "NH1", "order": "sing", "aromatic": False},
{"atom1": "CZ", "atom2": "NH2", "order": "doub", "aromatic": False},
{"atom1": "NH1", "atom2": "HH11", "order": "sing", "aromatic": False},
{"atom1": "NH1", "atom2": "HH12", "order": "sing", "aromatic": False},
{"atom1": "NH2", "atom2": "HH21", "order": "sing", "aromatic": False},
{"atom1": "NH2", "atom2": "HH22", "order": "sing", "aromatic": False},
{"atom1": "OXT", "atom2": "HXT", "order": "sing", "aromatic": False},
{"atom1": "H1", "atom2": "N", "order": "sing", "aromatic": False},
{"atom1": "H3", "atom2": "N", "order": "sing", "aromatic": False},
],
},
"ASN": {
"bond_count": 18,
"aromatic_bonds": 0,
"bond_orders": {"sing": 16, "doub": 2},
"bonds": [
{"atom1": "N", "atom2": "CA", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H2", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "C", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "CB", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "HA", "order": "sing", "aromatic": False},
{"atom1": "C", "atom2": "O", "order": "doub", "aromatic": False},
{"atom1": "C", "atom2": "OXT", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "CG", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB2", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB3", "order": "sing", "aromatic": False},
{"atom1": "CG", "atom2": "OD1", "order": "doub", "aromatic": False},
{"atom1": "CG", "atom2": "ND2", "order": "sing", "aromatic": False},
{"atom1": "ND2", "atom2": "HD21", "order": "sing", "aromatic": False},
{"atom1": "ND2", "atom2": "HD22", "order": "sing", "aromatic": False},
{"atom1": "OXT", "atom2": "HXT", "order": "sing", "aromatic": False},
{"atom1": "H1", "atom2": "N", "order": "sing", "aromatic": False},
{"atom1": "H3", "atom2": "N", "order": "sing", "aromatic": False},
],
},
"ASP": {
"bond_count": 17,
"aromatic_bonds": 0,
"bond_orders": {"sing": 15, "doub": 2},
"bonds": [
{"atom1": "N", "atom2": "CA", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H2", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "C", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "CB", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "HA", "order": "sing", "aromatic": False},
{"atom1": "C", "atom2": "O", "order": "doub", "aromatic": False},
{"atom1": "C", "atom2": "OXT", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "CG", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB2", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB3", "order": "sing", "aromatic": False},
{"atom1": "CG", "atom2": "OD1", "order": "doub", "aromatic": False},
{"atom1": "CG", "atom2": "OD2", "order": "sing", "aromatic": False},
{"atom1": "OD2", "atom2": "HD2", "order": "sing", "aromatic": False},
{"atom1": "OXT", "atom2": "HXT", "order": "sing", "aromatic": False},
{"atom1": "H1", "atom2": "N", "order": "sing", "aromatic": False},
{"atom1": "H3", "atom2": "N", "order": "sing", "aromatic": False},
],
},
"C": {
"bond_count": 36,
"aromatic_bonds": 0,
"bond_orders": {"sing": 32, "doub": 4},
"bonds": [
{"atom1": "OP3", "atom2": "P", "order": "sing", "aromatic": False},
{"atom1": "OP3", "atom2": "HOP3", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "OP1", "order": "doub", "aromatic": False},
{"atom1": "P", "atom2": "OP2", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "O5'", "order": "sing", "aromatic": False},
{"atom1": "OP2", "atom2": "HOP2", "order": "sing", "aromatic": False},
{"atom1": "O5'", "atom2": "C5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "C4'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "H5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "H5''", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "O4'", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "C3'", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "H4'", "order": "sing", "aromatic": False},
{"atom1": "O4'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "O3'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "C2'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "H3'", "order": "sing", "aromatic": False},
{"atom1": "O3'", "atom2": "HO3'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "O2'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "H2'", "order": "sing", "aromatic": False},
{"atom1": "O2'", "atom2": "HO2'", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "N1", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "H1'", "order": "sing", "aromatic": False},
{"atom1": "N1", "atom2": "C2", "order": "sing", "aromatic": False},
{"atom1": "N1", "atom2": "C6", "order": "sing", "aromatic": False},
{"atom1": "C2", "atom2": "O2", "order": "doub", "aromatic": False},
{"atom1": "C2", "atom2": "N3", "order": "sing", "aromatic": False},
{"atom1": "N3", "atom2": "C4", "order": "doub", "aromatic": False},
{"atom1": "C4", "atom2": "N4", "order": "sing", "aromatic": False},
{"atom1": "C4", "atom2": "C5", "order": "sing", "aromatic": False},
{"atom1": "N4", "atom2": "H41", "order": "sing", "aromatic": False},
{"atom1": "N4", "atom2": "H42", "order": "sing", "aromatic": False},
{"atom1": "C5", "atom2": "C6", "order": "doub", "aromatic": False},
{"atom1": "C5", "atom2": "H5", "order": "sing", "aromatic": False},
{"atom1": "C6", "atom2": "H6", "order": "sing", "aromatic": False},
],
},
"CYS": {
"bond_count": 15,
"aromatic_bonds": 0,
"bond_orders": {"sing": 14, "doub": 1},
"bonds": [
{"atom1": "N", "atom2": "CA", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H2", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "C", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "CB", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "HA", "order": "sing", "aromatic": False},
{"atom1": "C", "atom2": "O", "order": "doub", "aromatic": False},
{"atom1": "C", "atom2": "OXT", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "SG", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB2", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB3", "order": "sing", "aromatic": False},
{"atom1": "SG", "atom2": "HG", "order": "sing", "aromatic": False},
{"atom1": "OXT", "atom2": "HXT", "order": "sing", "aromatic": False},
{"atom1": "H1", "atom2": "N", "order": "sing", "aromatic": False},
{"atom1": "H3", "atom2": "N", "order": "sing", "aromatic": False},
],
},
"DA": {
"bond_count": 38,
"aromatic_bonds": 0,
"bond_orders": {"sing": 33, "doub": 5},
"bonds": [
{"atom1": "OP3", "atom2": "P", "order": "sing", "aromatic": False},
{"atom1": "OP3", "atom2": "HOP3", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "OP1", "order": "doub", "aromatic": False},
{"atom1": "P", "atom2": "OP2", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "O5'", "order": "sing", "aromatic": False},
{"atom1": "OP2", "atom2": "HOP2", "order": "sing", "aromatic": False},
{"atom1": "O5'", "atom2": "C5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "C4'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "H5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "H5''", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "O4'", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "C3'", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "H4'", "order": "sing", "aromatic": False},
{"atom1": "O4'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "O3'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "C2'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "H3'", "order": "sing", "aromatic": False},
{"atom1": "O3'", "atom2": "HO3'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "H2'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "H2''", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "N9", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "H1'", "order": "sing", "aromatic": False},
{"atom1": "N9", "atom2": "C8", "order": "sing", "aromatic": False},
{"atom1": "N9", "atom2": "C4", "order": "sing", "aromatic": False},
{"atom1": "C8", "atom2": "N7", "order": "doub", "aromatic": False},
{"atom1": "C8", "atom2": "H8", "order": "sing", "aromatic": False},
{"atom1": "N7", "atom2": "C5", "order": "sing", "aromatic": False},
{"atom1": "C5", "atom2": "C6", "order": "sing", "aromatic": False},
{"atom1": "C5", "atom2": "C4", "order": "doub", "aromatic": False},
{"atom1": "C6", "atom2": "N6", "order": "sing", "aromatic": False},
{"atom1": "C6", "atom2": "N1", "order": "doub", "aromatic": False},
{"atom1": "N6", "atom2": "H61", "order": "sing", "aromatic": False},
{"atom1": "N6", "atom2": "H62", "order": "sing", "aromatic": False},
{"atom1": "N1", "atom2": "C2", "order": "sing", "aromatic": False},
{"atom1": "C2", "atom2": "N3", "order": "doub", "aromatic": False},
{"atom1": "C2", "atom2": "H2", "order": "sing", "aromatic": False},
{"atom1": "N3", "atom2": "C4", "order": "sing", "aromatic": False},
],
},
"DC": {
"bond_count": 35,
"aromatic_bonds": 0,
"bond_orders": {"sing": 31, "doub": 4},
"bonds": [
{"atom1": "OP3", "atom2": "P", "order": "sing", "aromatic": False},
{"atom1": "OP3", "atom2": "HOP3", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "OP1", "order": "doub", "aromatic": False},
{"atom1": "P", "atom2": "OP2", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "O5'", "order": "sing", "aromatic": False},
{"atom1": "OP2", "atom2": "HOP2", "order": "sing", "aromatic": False},
{"atom1": "O5'", "atom2": "C5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "C4'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "H5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "H5''", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "O4'", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "C3'", "order": "sing", "aromatic": False},
{"atom1": "C4'", "atom2": "H4'", "order": "sing", "aromatic": False},
{"atom1": "O4'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "O3'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "C2'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "H3'", "order": "sing", "aromatic": False},
{"atom1": "O3'", "atom2": "HO3'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "H2'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "H2''", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "N1", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "H1'", "order": "sing", "aromatic": False},
{"atom1": "N1", "atom2": "C2", "order": "sing", "aromatic": False},
{"atom1": "N1", "atom2": "C6", "order": "sing", "aromatic": False},
{"atom1": "C2", "atom2": "O2", "order": "doub", "aromatic": False},
{"atom1": "C2", "atom2": "N3", "order": "sing", "aromatic": False},
{"atom1": "N3", "atom2": "C4", "order": "doub", "aromatic": False},
{"atom1": "C4", "atom2": "N4", "order": "sing", "aromatic": False},
{"atom1": "C4", "atom2": "C5", "order": "sing", "aromatic": False},
{"atom1": "N4", "atom2": "H41", "order": "sing", "aromatic": False},
{"atom1": "N4", "atom2": "H42", "order": "sing", "aromatic": False},
{"atom1": "C5", "atom2": "C6", "order": "doub", "aromatic": False},
{"atom1": "C5", "atom2": "H5", "order": "sing", "aromatic": False},
{"atom1": "C6", "atom2": "H6", "order": "sing", "aromatic": False},
],
},
"DG": {
"bond_count": 39,
"aromatic_bonds": 0,
"bond_orders": {"sing": 34, "doub": 5},
"bonds": [
{"atom1": "OP3", "atom2": "P", "order": "sing", "aromatic": False},
{"atom1": "OP3", "atom2": "HOP3", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "OP1", "order": "doub", "aromatic": False},
{"atom1": "P", "atom2": "OP2", "order": "sing", "aromatic": False},
{"atom1": "P", "atom2": "O5'", "order": "sing", "aromatic": False},
{"atom1": "OP2", "atom2": "HOP2", "order": "sing", "aromatic": False},
{"atom1": "O5'", "atom2": "C5'", "order": "sing", "aromatic": False},
{"atom1": "C5'", "atom2": "C4'", "order": "sing", "aromatic": False},
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{"atom1": "C3'", "atom2": "O3'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "C2'", "order": "sing", "aromatic": False},
{"atom1": "C3'", "atom2": "H3'", "order": "sing", "aromatic": False},
{"atom1": "O3'", "atom2": "HO3'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "O2'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "C1'", "order": "sing", "aromatic": False},
{"atom1": "C2'", "atom2": "H2'", "order": "sing", "aromatic": False},
{"atom1": "O2'", "atom2": "HO2'", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "N1", "order": "sing", "aromatic": False},
{"atom1": "C1'", "atom2": "H1'", "order": "sing", "aromatic": False},
{"atom1": "N1", "atom2": "C2", "order": "sing", "aromatic": False},
{"atom1": "N1", "atom2": "C6", "order": "sing", "aromatic": False},
{"atom1": "C2", "atom2": "O2", "order": "doub", "aromatic": False},
{"atom1": "C2", "atom2": "N3", "order": "sing", "aromatic": False},
{"atom1": "N3", "atom2": "C4", "order": "sing", "aromatic": False},
{"atom1": "N3", "atom2": "H3", "order": "sing", "aromatic": False},
{"atom1": "C4", "atom2": "O4", "order": "doub", "aromatic": False},
{"atom1": "C4", "atom2": "C5", "order": "sing", "aromatic": False},
{"atom1": "C5", "atom2": "C6", "order": "doub", "aromatic": False},
{"atom1": "C5", "atom2": "H5", "order": "sing", "aromatic": False},
{"atom1": "C6", "atom2": "H6", "order": "sing", "aromatic": False},
],
},
"VAL": {
"bond_count": 20,
"aromatic_bonds": 0,
"bond_orders": {"sing": 19, "doub": 1},
"bonds": [
{"atom1": "N", "atom2": "CA", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H", "order": "sing", "aromatic": False},
{"atom1": "N", "atom2": "H2", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "C", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "CB", "order": "sing", "aromatic": False},
{"atom1": "CA", "atom2": "HA", "order": "sing", "aromatic": False},
{"atom1": "C", "atom2": "O", "order": "doub", "aromatic": False},
{"atom1": "C", "atom2": "OXT", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "CG1", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "CG2", "order": "sing", "aromatic": False},
{"atom1": "CB", "atom2": "HB", "order": "sing", "aromatic": False},
{"atom1": "CG1", "atom2": "HG11", "order": "sing", "aromatic": False},
{"atom1": "CG1", "atom2": "HG12", "order": "sing", "aromatic": False},
{"atom1": "CG1", "atom2": "HG13", "order": "sing", "aromatic": False},
{"atom1": "CG2", "atom2": "HG21", "order": "sing", "aromatic": False},
{"atom1": "CG2", "atom2": "HG22", "order": "sing", "aromatic": False},
{"atom1": "CG2", "atom2": "HG23", "order": "sing", "aromatic": False},
{"atom1": "OXT", "atom2": "HXT", "order": "sing", "aromatic": False},
{"atom1": "H1", "atom2": "N", "order": "sing", "aromatic": False},
{"atom1": "H3", "atom2": "N", "order": "sing", "aromatic": False},
],
},
}
[docs]
def get_residue_bonds(residue: str) -> List[Dict[str, Union[str, bool]]]:
"""
Get bond information for a specific residue.
Args:
residue: Three-letter residue code (e.g., "ALA", "GLY")
Returns:
List of bond dictionaries with atom1, atom2, order, and aromatic info
"""
bonds = RESIDUE_BONDS.get(residue, {}).get("bonds", [])
# Type guard to ensure proper typing
if isinstance(bonds, list):
return [bond for bond in bonds if isinstance(bond, dict)]
return []
[docs]
def get_residue_bond_count(residue: str) -> int:
"""
Get the total number of bonds for a residue.
Args:
residue: Three-letter residue code
Returns:
Number of bonds in the residue
"""
count = RESIDUE_BONDS.get(residue, {}).get("bond_count", 0)
return count if isinstance(count, int) else 0
[docs]
def has_aromatic_bonds(residue: str) -> bool:
"""
Check if a residue has aromatic bonds.
Args:
residue: Three-letter residue code
Returns:
True if the residue has aromatic bonds, False otherwise
"""
aromatic_count = RESIDUE_BONDS.get(residue, {}).get("aromatic_bonds", 0)
return isinstance(aromatic_count, int) and aromatic_count > 0
# Summary information
TOTAL_RESIDUES_WITH_BONDS = 32
AROMATIC_RESIDUES_COUNT = 0
TOTAL_BONDS_COUNT = 791
RESIDUES_WITH_BOND_DATA: List[str] = [
"A",
"ALA",
"ARG",
"ASN",
"ASP",
"C",
"CYS",
"DA",
"DC",
"DG",
"DI",
"DOD",
"DT",
"G",
"GLN",
"GLU",
"GLY",
"HIS",
"HOH",
"I",
"ILE",
"LEU",
"LYS",
"MET",
"PHE",
"PRO",
"SER",
"THR",
"TRP",
"TYR",
"U",
"VAL",
]
