# A* ------------------------------------------------------------------- # B* This file contains source code for the PyMOL computer program # C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. # D* ------------------------------------------------------------------- # E* It is unlawful to modify or remove this copyright notice. # F* ------------------------------------------------------------------- # G* Please see the accompanying LICENSE file for further information. # H* ------------------------------------------------------------------- # I* Additional authors of this source file include: # -* # -* # -* # Z* ------------------------------------------------------------------- bonds = { 'ACE': [ { # names ### '1HH3': 0, '3HA': 0, 'HH31': 0, '1HA': 1, '2HH3': 1, 'HH32': 1, '2HA': 2, '3HH3': 2, 'HH33': 2, 'C': 3, 'CA': 4, 'CH3': 4, 'O': 5, }, [ # bonds ### (0, 4, 1), (1, 4, 1), (2, 4, 1), (3, 4, 1), (3, 5, 2), ]], 'ALA': [ { # names ### '1HB': 0, 'HB1': 0, '1H': 1, '1HT': 1, 'H1': 1, 'HT1': 1, '2HB': 2, 'HB2': 2, '2H': 3, '2HT': 3, 'H2': 3, 'HT2': 3, '3HB': 4, 'HB3': 4, '3H': 5, '3HT': 5, 'H3': 5, 'HT3': 5, 'C': 6, 'CA': 7, 'CB': 8, 'H': 9, 'HN': 9, 'HA': 10, 'HA2': 10, 'N': 11, 'O': 12, 'O1': 12, 'OT1': 12, 'O2': 13, 'OT': 13, 'OT2': 13, 'OXT': 13, }, [ # bonds ### (0, 8, 1), (1, 11, 1), (2, 8, 1), (3, 11, 1), (4, 8, 1), (5, 11, 1), (6, 7, 1), (6, 12, 2), (7, 8, 1), (7, 10, 1), (7, 11, 1), (9, 11, 1), ]], 'ARG': [ { # names ### '1HH1': 0, 'HH11': 0, '1HH2': 1, 'HH21': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HB': 3, 'HB2': 3, '2HD': 4, 'HD2': 4, '2HG': 5, 'HG2': 5, '2HH1': 6, 'HH12': 6, '2HH2': 7, 'HH22': 7, '2H': 8, '2HT': 8, 'H2': 8, 'HT2': 8, '1HB': 9, '3HB': 9, 'HB1': 9, 'HB3': 9, '1HD': 10, '3HD': 10, 'HD1': 10, 'HD3': 10, '1HG': 11, '3HG': 11, 'HG1': 11, 'HG3': 11, '3H': 12, '3HT': 12, 'H3': 12, 'HT3': 12, 'C': 13, 'CA': 14, 'CB': 15, 'CD': 16, 'CG': 17, 'CZ': 18, 'H': 19, 'HN': 19, 'HA': 20, 'HA2': 20, 'HE': 21, 'N': 22, 'NE': 23, 'NH1': 24, 'NH2': 25, 'O': 26, 'O1': 26, 'OT1': 26, 'O2': 27, 'OT': 27, 'OT2': 27, 'OXT': 27, }, [ # bonds ### (0, 24, 1), (1, 25, 1), (2, 22, 1), (3, 15, 1), (4, 16, 1), (5, 17, 1), (6, 24, 1), (7, 25, 1), (8, 22, 1), (9, 15, 1), (10, 16, 1), (11, 17, 1), (12, 22, 1), (13, 14, 1), (13, 26, 2), (14, 15, 1), (14, 20, 1), (14, 22, 1), (15, 17, 1), (16, 17, 1), (16, 23, 1), (18, 23, 1), (18, 24, 2), (18, 25, 1), (19, 22, 1), (21, 23, 1), ]], 'ASH': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '2HB': 1, 'HB2': 1, '2H': 2, '2HT': 2, 'H2': 2, 'HT2': 2, '1HB': 3, '3HB': 3, 'HB1': 3, 'HB3': 3, '3H': 4, '3HT': 4, 'H3': 4, 'HT3': 4, 'C': 5, 'CA': 6, 'CB': 7, 'CG': 8, 'H': 9, 'HN': 9, 'HA': 10, 'HA2': 10, 'HD2': 11, 'N': 12, 'O': 13, 'O1': 13, 'OT1': 13, 'OD1': 14, 'OD2': 15, 'O2': 16, 'OT': 16, 'OT2': 16, 'OXT': 16, }, [ # bonds ### (0, 12, 1), (1, 7, 1), (2, 12, 1), (3, 7, 1), (4, 12, 1), (5, 6, 1), (5, 13, 2), (6, 7, 1), (6, 10, 1), (6, 12, 1), (7, 8, 1), (8, 14, 2), (8, 15, 1), (9, 12, 1), (11, 15, 1), ]], 'ASN': [ { # names ### '1HD2': 0, 'HD21': 0, '1H': 1, '1HT': 1, 'H1': 1, 'HT1': 1, '2HB': 2, 'HB2': 2, '2HD2': 3, 'HD22': 3, '2H': 4, '2HT': 4, 'H2': 4, 'HT2': 4, '1HB': 5, '3HB': 5, 'HB1': 5, 'HB3': 5, '3H': 6, '3HT': 6, 'H3': 6, 'HT3': 6, 'C': 7, 'CA': 8, 'CB': 9, 'CG': 10, 'H': 11, 'HN': 11, 'HA': 12, 'HA2': 12, 'N': 13, 'ND2': 14, 'O': 15, 'O1': 15, 'OT1': 15, 'OD1': 16, 'O2': 17, 'OT': 17, 'OT2': 17, 'OXT': 17, }, [ # bonds ### (0, 14, 1), (1, 13, 1), (2, 9, 1), (3, 14, 1), (4, 13, 1), (5, 9, 1), (6, 13, 1), (7, 8, 1), (7, 15, 2), (8, 9, 1), (8, 12, 1), (8, 13, 1), (9, 10, 1), (10, 14, 1), (10, 16, 2), (11, 13, 1), ]], 'ASP': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '2HB': 1, 'HB2': 1, '2H': 2, '2HT': 2, 'H2': 2, 'HT2': 2, '1HB': 3, '3HB': 3, 'HB1': 3, 'HB3': 3, '3H': 4, '3HT': 4, 'H3': 4, 'HT3': 4, 'C': 5, 'CA': 6, 'CB': 7, 'CG': 8, 'H': 9, 'HN': 9, 'HA': 10, 'HA2': 10, 'N': 11, 'O': 12, 'O1': 12, 'OT1': 12, 'OD1': 13, 'OD2': 14, 'O2': 15, 'OT': 15, 'OT2': 15, 'OXT': 15, }, [ # bonds ### (0, 11, 1), (1, 7, 1), (2, 11, 1), (3, 7, 1), (4, 11, 1), (5, 6, 1), (5, 12, 2), (6, 7, 1), (6, 10, 1), (6, 11, 1), (7, 8, 1), (8, 13, 2), (8, 14, 1), (9, 11, 1), ]], 'CYM': [ { # names ### '2HB': 0, 'HB2': 0, '3HB': 1, 'HB3': 1, 'C': 2, 'CA': 3, 'CB': 4, 'H': 5, 'HN': 5, 'HA': 6, 'HA2': 6, 'N': 7, 'O': 8, 'SG': 9, }, [ # bonds ### (0, 4, 1), (1, 4, 1), (2, 3, 1), (2, 8, 2), (3, 4, 1), (3, 6, 1), (3, 7, 1), (4, 9, 1), (5, 7, 1), ]], 'CYS': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '2HB': 1, 'HB2': 1, '2H': 2, '2HT': 2, 'H2': 2, 'HT2': 2, '1HB': 3, '3HB': 3, 'HB1': 3, 'HB3': 3, '3H': 4, '3HT': 4, 'H3': 4, 'HT3': 4, 'C': 5, 'CA': 6, 'CB': 7, 'H': 8, 'HN': 8, 'HA': 9, 'HA2': 9, 'HG': 10, 'HG1': 10, 'N': 11, 'O': 12, 'O1': 12, 'OT1': 12, 'O2': 13, 'OT': 13, 'OT2': 13, 'OXT': 13, 'SG': 14, }, [ # bonds ### (0, 11, 1), (1, 7, 1), (2, 11, 1), (3, 7, 1), (4, 11, 1), (5, 6, 1), (5, 12, 2), (6, 7, 1), (6, 9, 1), (6, 11, 1), (7, 14, 1), (8, 11, 1), (10, 14, 1), ]], 'CYX': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '2HB': 1, 'HB2': 1, '2H': 2, '2HT': 2, 'H2': 2, 'HT2': 2, '1HB': 3, '3HB': 3, 'HB1': 3, 'HB3': 3, '3H': 4, '3HT': 4, 'H3': 4, 'HT3': 4, 'C': 5, 'CA': 6, 'CB': 7, 'H': 8, 'HN': 8, 'HA': 9, 'HA2': 9, 'N': 10, 'O': 11, 'O1': 11, 'OT1': 11, 'O2': 12, 'OT': 12, 'OT2': 12, 'OXT': 12, 'SG': 13, }, [ # bonds ### (0, 10, 1), (1, 7, 1), (2, 10, 1), (3, 7, 1), (4, 10, 1), (5, 6, 1), (5, 11, 2), (6, 7, 1), (6, 9, 1), (6, 10, 1), (7, 13, 1), (8, 10, 1), ]], 'GLN': [ { # names ### '1HE2': 0, 'HE21': 0, '1H': 1, '1HT': 1, 'H1': 1, 'HT1': 1, '2HB': 2, 'HB2': 2, '2HE2': 3, 'HE22': 3, '2HG': 4, 'HG2': 4, '2H': 5, '2HT': 5, 'H2': 5, 'HT2': 5, '1HB': 6, '3HB': 6, 'HB1': 6, 'HB3': 6, '1HG': 7, '3HG': 7, 'HG1': 7, 'HG3': 7, '3H': 8, '3HT': 8, 'H3': 8, 'HT3': 8, 'C': 9, 'CA': 10, 'CB': 11, 'CD': 12, 'CG': 13, 'H': 14, 'HN': 14, 'HA': 15, 'HA2': 15, 'N': 16, 'NE2': 17, 'O': 18, 'O1': 18, 'OT1': 18, 'OE1': 19, 'O2': 20, 'OT': 20, 'OT2': 20, 'OXT': 20, }, [ # bonds ### (0, 17, 1), (1, 16, 1), (2, 11, 1), (3, 17, 1), (4, 13, 1), (5, 16, 1), (6, 11, 1), (7, 13, 1), (8, 16, 1), (9, 10, 1), (9, 18, 2), (10, 11, 1), (10, 15, 1), (10, 16, 1), (11, 13, 1), (12, 13, 1), (12, 17, 1), (12, 19, 2), (14, 16, 1), ]], 'GLP': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '2HB': 1, 'HB2': 1, '2HG': 2, 'HG2': 2, '2H': 3, '2HT': 3, 'H2': 3, 'HT2': 3, '1HB': 4, '3HB': 4, 'HB1': 4, 'HB3': 4, '1HG': 5, '3HG': 5, 'HG1': 5, 'HG3': 5, '3H': 6, '3HT': 6, 'H3': 6, 'HT3': 6, 'C': 7, 'CA': 8, 'CB': 9, 'CD': 10, 'CG': 11, 'H': 12, 'HN': 12, 'HA': 13, 'HA2': 13, 'HE2': 14, 'N': 15, 'O': 16, 'O1': 16, 'OT1': 16, 'OE1': 17, 'OE2': 18, 'O2': 19, 'OT': 19, 'OT2': 19, 'OXT': 19, }, [ # bonds ### (0, 15, 1), (1, 9, 1), (2, 11, 1), (3, 15, 1), (4, 9, 1), (5, 11, 1), (6, 15, 1), (7, 8, 1), (7, 16, 2), (8, 9, 1), (8, 13, 1), (8, 15, 1), (9, 11, 1), (10, 11, 1), (10, 17, 2), (10, 18, 1), (12, 15, 1), (14, 18, 1), ]], 'GLU': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '2HB': 1, 'HB2': 1, '2HG': 2, 'HG2': 2, '2H': 3, '2HT': 3, 'H2': 3, 'HT2': 3, '1HB': 4, '3HB': 4, 'HB1': 4, 'HB3': 4, '1HG': 5, '3HG': 5, 'HG1': 5, 'HG3': 5, '3H': 6, '3HT': 6, 'H3': 6, 'HT3': 6, 'C': 7, 'CA': 8, 'CB': 9, 'CD': 10, 'CG': 11, 'H': 12, 'HN': 12, 'HA': 13, 'HA2': 13, 'N': 14, 'O': 15, 'O1': 15, 'OT1': 15, 'OE1': 16, 'OE2': 17, 'O2': 18, 'OT': 18, 'OT2': 18, 'OXT': 18, }, [ # bonds ### (0, 14, 1), (1, 9, 1), (2, 11, 1), (3, 14, 1), (4, 9, 1), (5, 11, 1), (6, 14, 1), (7, 8, 1), (7, 15, 2), (8, 9, 1), (8, 13, 1), (8, 14, 1), (9, 11, 1), (10, 11, 1), (10, 16, 2), (10, 17, 1), (12, 14, 1), ]], 'GLY': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '2H': 1, '2HT': 1, 'H2': 1, 'HT2': 1, '1HA': 2, '3HA': 2, 'HA1': 2, 'HA3': 2, '3H': 3, '3HT': 3, 'H3': 3, 'HT3': 3, 'C': 4, 'CA': 5, 'H': 6, 'HN': 6, '2HA': 7, 'HA': 7, 'HA2': 7, 'N': 8, 'O': 9, 'O1': 9, 'OT1': 9, 'O2': 10, 'OT': 10, 'OT2': 10, 'OXT': 10, }, [ # bonds ### (0, 8, 1), (1, 8, 1), (2, 5, 1), (3, 8, 1), (4, 5, 1), (4, 9, 2), (5, 7, 1), (5, 8, 1), (6, 8, 1), ]], 'HID': [ { # names ### '1HD': 0, 'HD1': 0, '1HE': 1, 'HE1': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HB': 3, 'HB2': 3, '2HD': 4, 'HD2': 4, '2H': 5, '2HT': 5, 'H2': 5, 'HT2': 5, '1HB': 6, '3HB': 6, 'HB1': 6, 'HB3': 6, '3H': 7, '3HT': 7, 'H3': 7, 'HT3': 7, 'C': 8, 'CA': 9, 'CB': 10, 'CD2': 11, 'CE1': 12, 'CG': 13, 'H': 14, 'HN': 14, 'HA': 15, 'HA2': 15, 'N': 16, 'ND1': 17, 'NE2': 18, 'O': 19, 'O1': 19, 'OT1': 19, 'O2': 20, 'OT': 20, 'OT2': 20, 'OXT': 20, }, [ # bonds ### (0, 17, 1), (1, 12, 1), (2, 16, 1), (3, 10, 1), (4, 11, 1), (5, 16, 1), (6, 10, 1), (7, 16, 1), (8, 9, 1), (8, 19, 2), (9, 10, 1), (9, 15, 1), (9, 16, 1), (10, 13, 1), (11, 13, 2), (11, 18, 1), (12, 17, 1), (12, 18, 2), (13, 17, 1), (14, 16, 1), ]], 'HIE': [ { # names ### '1HE': 0, 'HE1': 0, '1H': 1, '1HT': 1, 'H1': 1, 'HT1': 1, '2HB': 2, 'HB2': 2, '2HD': 3, 'HD1': 3, 'HD2': 3, '2HE': 4, 'HE2': 4, '2H': 5, '2HT': 5, 'H2': 5, 'HT2': 5, '1HB': 6, '3HB': 6, 'HB1': 6, 'HB3': 6, '3H': 7, '3HT': 7, 'H3': 7, 'HT3': 7, 'C': 8, 'CA': 9, 'CB': 10, 'CD2': 11, 'CE1': 12, 'CG': 13, 'H': 14, 'HN': 14, 'HA': 15, 'HA2': 15, 'N': 16, 'ND1': 17, 'NE2': 18, 'O': 19, 'O1': 19, 'OT1': 19, 'O2': 20, 'OT': 20, 'OT2': 20, 'OXT': 20, }, [ # bonds ### (0, 12, 1), (1, 16, 1), (2, 10, 1), (3, 11, 1), (4, 18, 1), (5, 16, 1), (6, 10, 1), (7, 16, 1), (8, 9, 1), (8, 19, 2), (9, 10, 1), (9, 15, 1), (9, 16, 1), (10, 13, 1), (11, 13, 2), (11, 18, 1), (12, 17, 2), (12, 18, 1), (13, 17, 1), (14, 16, 1), ]], 'HIP': [ { # names ### '1HD': 0, 'HD1': 0, '1HE': 1, 'HE1': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HB': 3, 'HB2': 3, '2HD': 4, 'HD2': 4, '2HE': 5, 'HE2': 5, '2H': 6, '2HT': 6, 'H2': 6, 'HT2': 6, '1HB': 7, '3HB': 7, 'HB1': 7, 'HB3': 7, '3H': 8, '3HT': 8, 'H3': 8, 'HT3': 8, 'C': 9, 'CA': 10, 'CB': 11, 'CD2': 12, 'CE1': 13, 'CG': 14, 'H': 15, 'HN': 15, 'HA': 16, 'HA2': 16, 'N': 17, 'ND1': 18, 'NE2': 19, 'O': 20, 'O1': 20, 'OT1': 20, 'O2': 21, 'OT': 21, 'OT2': 21, 'OXT': 21, }, [ # bonds ### (0, 18, 1), (1, 13, 1), (2, 17, 1), (3, 11, 1), (4, 12, 1), (5, 19, 1), (6, 17, 1), (7, 11, 1), (8, 17, 1), (9, 10, 1), (9, 20, 2), (10, 11, 1), (10, 16, 1), (10, 17, 1), (11, 14, 1), (12, 14, 2), (12, 19, 1), (13, 18, 2), (13, 19, 1), (14, 18, 1), (15, 17, 1), ]], 'ILE': [ { # names ### '1HD1': 0, 'HD1': 0, 'HD11': 0, '1HG2': 1, 'HG21': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HD1': 3, 'HD12': 3, 'HD2': 3, '2HG1': 4, 'HG12': 4, '2HG2': 5, 'HG22': 5, '2H': 6, '2HT': 6, 'H2': 6, 'HT2': 6, '3HD1': 7, 'HD13': 7, 'HD3': 7, '1HG1': 8, '3HG1': 8, 'HG11': 8, 'HG13': 8, '3HG2': 9, 'HG23': 9, '3H': 10, '3HT': 10, 'H3': 10, 'HT3': 10, 'C': 11, 'CA': 12, 'CB': 13, 'CD': 14, 'CD1': 14, 'CG1': 15, 'CG2': 16, 'H': 17, 'HN': 17, 'HA': 18, 'HA2': 18, 'HB': 19, 'N': 20, 'O': 21, 'O1': 21, 'OT1': 21, 'O2': 22, 'OT': 22, 'OT2': 22, 'OXT': 22, }, [ # bonds ### (0, 14, 1), (1, 16, 1), (2, 20, 1), (3, 14, 1), (4, 15, 1), (5, 16, 1), (6, 20, 1), (7, 14, 1), (8, 15, 1), (9, 16, 1), (10, 20, 1), (11, 12, 1), (11, 21, 2), (12, 13, 1), (12, 18, 1), (12, 20, 1), (13, 15, 1), (13, 16, 1), (13, 19, 1), (14, 15, 1), (17, 20, 1), ]], 'LEU': [ { # names ### '1HD1': 0, 'HD11': 0, '1HD2': 1, 'HD21': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HB': 3, 'HB2': 3, '2HD1': 4, 'HD12': 4, '2HD2': 5, 'HD22': 5, '2H': 6, '2HT': 6, 'H2': 6, 'HT2': 6, '1HB': 7, '3HB': 7, 'HB1': 7, 'HB3': 7, '3HD1': 8, 'HD13': 8, '3HD2': 9, 'HD23': 9, '3H': 10, '3HT': 10, 'H3': 10, 'HT3': 10, 'C': 11, 'CA': 12, 'CB': 13, 'CD1': 14, 'CD2': 15, 'CG': 16, 'H': 17, 'HN': 17, 'HA': 18, 'HA2': 18, 'HG': 19, 'N': 20, 'O': 21, 'O1': 21, 'OT1': 21, 'O2': 22, 'OT': 22, 'OT2': 22, 'OXT': 22, }, [ # bonds ### (0, 14, 1), (1, 15, 1), (2, 20, 1), (3, 13, 1), (4, 14, 1), (5, 15, 1), (6, 20, 1), (7, 13, 1), (8, 14, 1), (9, 15, 1), (10, 20, 1), (11, 12, 1), (11, 21, 2), (12, 13, 1), (12, 18, 1), (12, 20, 1), (13, 16, 1), (14, 16, 1), (15, 16, 1), (16, 19, 1), (17, 20, 1), ]], 'LYS': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '1HZ': 1, 'HZ1': 1, '2HB': 2, 'HB2': 2, '2HD': 3, 'HD2': 3, '2HE': 4, 'HE2': 4, '2HG': 5, 'HG2': 5, '2H': 6, '2HT': 6, 'H2': 6, 'HT2': 6, '2HZ': 7, 'HZ2': 7, '1HB': 8, '3HB': 8, 'HB1': 8, 'HB3': 8, '1HD': 9, '3HD': 9, 'HD1': 9, 'HD3': 9, '1HE': 10, '3HE': 10, 'HE1': 10, 'HE3': 10, '1HG': 11, '3HG': 11, 'HG1': 11, 'HG3': 11, '3H': 12, '3HT': 12, 'H3': 12, 'HT3': 12, '3HZ': 13, 'HZ3': 13, 'C': 14, 'CA': 15, 'CB': 16, 'CD': 17, 'CE': 18, 'CG': 19, 'H': 20, 'HN': 20, 'HA': 21, 'HA2': 21, 'N': 22, 'NZ': 23, 'O': 24, 'O1': 24, 'OT1': 24, 'O2': 25, 'OT': 25, 'OT2': 25, 'OXT': 25, }, [ # bonds ### (0, 22, 1), (1, 23, 1), (2, 16, 1), (3, 17, 1), (4, 18, 1), (5, 19, 1), (6, 22, 1), (7, 23, 1), (8, 16, 1), (9, 17, 1), (10, 18, 1), (11, 19, 1), (12, 22, 1), (13, 23, 1), (14, 15, 1), (14, 24, 2), (15, 16, 1), (15, 21, 1), (15, 22, 1), (16, 19, 1), (17, 18, 1), (17, 19, 1), (18, 23, 1), (20, 22, 1), ]], 'MET': [ { # names ### '1HE': 0, 'HE1': 0, '1H': 1, '1HT': 1, 'H1': 1, 'HT1': 1, '2HB': 2, 'HB2': 2, '2HE': 3, 'HE2': 3, '2HG': 4, 'HG2': 4, '2H': 5, '2HT': 5, 'H2': 5, 'HT2': 5, '1HB': 6, '3HB': 6, 'HB1': 6, 'HB3': 6, '3HE': 7, 'HE3': 7, '1HG': 8, '3HG': 8, 'HG1': 8, 'HG3': 8, '3H': 9, '3HT': 9, 'H3': 9, 'HT3': 9, 'C': 10, 'CA': 11, 'CB': 12, 'CE': 13, 'CG': 14, 'H': 15, 'HN': 15, 'HA': 16, 'HA2': 16, 'N': 17, 'O': 18, 'O1': 18, 'OT1': 18, 'O2': 19, 'OT': 19, 'OT2': 19, 'OXT': 19, 'SD': 20, }, [ # bonds ### (0, 13, 1), (1, 17, 1), (2, 12, 1), (3, 13, 1), (4, 14, 1), (5, 17, 1), (6, 12, 1), (7, 13, 1), (8, 14, 1), (9, 17, 1), (10, 11, 1), (10, 18, 2), (11, 12, 1), (11, 16, 1), (11, 17, 1), (12, 14, 1), (13, 20, 1), (14, 20, 1), (15, 17, 1), ]], 'NME': [ { # names ### '1HA': 0, '1HH3': 0, 'H02': 0, 'HH31': 0, '2HA': 1, '2HH3': 1, 'H03': 1, 'HH32': 1, '3HA': 2, '3HH3': 2, 'H04': 2, 'HH33': 2, 'C01': 3, 'CA': 3, 'CH3': 3, 'H': 4, 'H01': 4, 'HN': 4, 'N': 5, 'N01': 5, }, [ # bonds ### (0, 3, 1), (1, 3, 1), (2, 3, 1), (3, 5, 1), (4, 5, 1), ]], 'PHE': [ { # names ### '1HD': 0, 'HD1': 0, '1HE': 1, 'HE1': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HB': 3, 'HB2': 3, '2HD': 4, 'HD2': 4, '2HE': 5, 'HE2': 5, '2H': 6, '2HT': 6, 'H2': 6, 'HT2': 6, '1HB': 7, '3HB': 7, 'HB1': 7, 'HB3': 7, '3H': 8, '3HT': 8, 'H3': 8, 'HT3': 8, 'C': 9, 'CA': 10, 'CB': 11, 'CD1': 12, 'CD2': 13, 'CE1': 14, 'CE2': 15, 'CG': 16, 'CZ': 17, 'H': 18, 'HN': 18, 'HA': 19, 'HA2': 19, 'HZ': 20, 'N': 21, 'O': 22, 'O1': 22, 'OT1': 22, 'O2': 23, 'OT': 23, 'OT2': 23, 'OXT': 23, }, [ # bonds ### (0, 12, 1), (1, 14, 1), (2, 21, 1), (3, 11, 1), (4, 13, 1), (5, 15, 1), (6, 21, 1), (7, 11, 1), (8, 21, 1), (9, 10, 1), (9, 22, 2), (10, 11, 1), (10, 19, 1), (10, 21, 1), (11, 16, 1), (12, 14, 1), (12, 16, 2), (13, 15, 2), (13, 16, 1), (14, 17, 2), (15, 17, 1), (17, 20, 1), (18, 21, 1), ]], 'PRO': [ { # names ### '2H': 0, 'H2': 0, '2HB': 1, 'HB2': 1, '2HD': 2, 'HD2': 2, '2HG': 3, 'HG2': 3, '1H': 4, '3H': 4, 'H3': 4, '1HB': 5, '3HB': 5, 'HB1': 5, 'HB3': 5, '1HD': 6, '3HD': 6, 'HD1': 6, 'HD3': 6, '1HG': 7, '3HG': 7, 'HG1': 7, 'HG3': 7, 'C': 8, 'CA': 9, 'CB': 10, 'CD': 11, 'CG': 12, 'HA': 13, 'N': 14, 'O': 15, 'O1': 15, 'OT1': 15, 'O2': 16, 'OT': 16, 'OT2': 16, 'OXT': 16, }, [ # bonds ### (0, 14, 1), (1, 10, 1), (2, 11, 1), (3, 12, 1), (4, 14, 1), (5, 10, 1), (6, 11, 1), (7, 12, 1), (8, 9, 1), (8, 15, 2), (9, 10, 1), (9, 13, 1), (9, 14, 1), (10, 12, 1), (11, 12, 1), (11, 14, 1), ]], 'SER': [ { # names ### '1H': 0, '1HT': 0, 'H1': 0, 'HT1': 0, '2HB': 1, 'HB2': 1, '2H': 2, '2HT': 2, 'H2': 2, 'HT2': 2, '1HB': 3, '3HB': 3, 'HB1': 3, 'HB3': 3, '3H': 4, '3HT': 4, 'H3': 4, 'HT3': 4, 'C': 5, 'CA': 6, 'CB': 7, 'H': 8, 'HN': 8, 'HA': 9, 'HA2': 9, 'HG': 10, 'HG1': 10, 'N': 11, 'O': 12, 'O1': 12, 'OT1': 12, 'OG': 13, 'O2': 14, 'OT': 14, 'OT2': 14, 'OXT': 14, }, [ # bonds ### (0, 11, 1), (1, 7, 1), (2, 11, 1), (3, 7, 1), (4, 11, 1), (5, 6, 1), (5, 12, 2), (6, 7, 1), (6, 9, 1), (6, 11, 1), (7, 13, 1), (8, 11, 1), (10, 13, 1), ]], 'THR': [ { # names ### '1HG': 0, 'HG1': 0, '1HG2': 1, 'HG21': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HG2': 3, 'HG22': 3, '2H': 4, '2HT': 4, 'H2': 4, 'HT2': 4, '3HG2': 5, 'HG23': 5, '3H': 6, '3HT': 6, 'H3': 6, 'HT3': 6, 'C': 7, 'CA': 8, 'CB': 9, 'CG2': 10, 'H': 11, 'HN': 11, 'HA': 12, 'HA2': 12, 'HB': 13, 'N': 14, 'O': 15, 'O1': 15, 'OT1': 15, 'OG1': 16, 'O2': 17, 'OT': 17, 'OT2': 17, 'OXT': 17, }, [ # bonds ### (0, 16, 1), (1, 10, 1), (2, 14, 1), (3, 10, 1), (4, 14, 1), (5, 10, 1), (6, 14, 1), (7, 8, 1), (7, 15, 2), (8, 9, 1), (8, 12, 1), (8, 14, 1), (9, 10, 1), (9, 13, 1), (9, 16, 1), (11, 14, 1), ]], 'TRP': [ { # names ### '1HD': 0, 'HD1': 0, '1HE': 1, 'HE1': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HB': 3, 'HB2': 3, '2HH': 4, 'HH2': 4, '2H': 5, '2HT': 5, 'H2': 5, 'HT2': 5, '2HZ': 6, 'HZ2': 6, '1HB': 7, '3HB': 7, 'HB1': 7, 'HB3': 7, '3HE': 8, 'HE3': 8, '3H': 9, '3HT': 9, 'H3': 9, 'HT3': 9, '1HZ': 10, '3HZ': 10, 'HZ3': 10, 'C': 11, 'CA': 12, 'CB': 13, 'CD1': 14, 'CD2': 15, 'CE2': 16, 'CE3': 17, 'CG': 18, 'CH2': 19, 'CZ2': 20, 'CZ3': 21, 'H': 22, 'HN': 22, 'HA': 23, 'HA2': 23, 'N': 24, 'NE1': 25, 'O': 26, 'O1': 26, 'OT1': 26, 'O2': 27, 'OT': 27, 'OT2': 27, 'OXT': 27, }, [ # bonds ### (0, 14, 1), (1, 25, 1), (2, 24, 1), (3, 13, 1), (4, 19, 1), (5, 24, 1), (6, 20, 1), (7, 13, 1), (8, 17, 1), (9, 24, 1), (10, 21, 1), (11, 12, 1), (11, 26, 2), (12, 13, 1), (12, 23, 1), (12, 24, 1), (13, 18, 1), (14, 18, 2), (14, 25, 1), (15, 16, 2), (15, 17, 1), (15, 18, 1), (16, 20, 1), (16, 25, 1), (17, 21, 2), (19, 20, 2), (19, 21, 1), (22, 24, 1), ]], 'TYR': [ { # names ### '1HD': 0, 'HD1': 0, '1HE': 1, 'HE1': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HB': 3, 'HB2': 3, '2HD': 4, 'HD2': 4, '2HE': 5, 'HE2': 5, '2H': 6, '2HT': 6, 'H2': 6, 'HT2': 6, '1HB': 7, '3HB': 7, 'HB1': 7, 'HB3': 7, '3H': 8, '3HT': 8, 'H3': 8, 'HT3': 8, 'C': 9, 'CA': 10, 'CB': 11, 'CD1': 12, 'CD2': 13, 'CE1': 14, 'CE2': 15, 'CG': 16, 'CZ': 17, 'H': 18, 'HN': 18, 'HA': 19, 'HA2': 19, 'HH': 20, 'N': 21, 'O': 22, 'O1': 22, 'OT1': 22, 'OH': 23, 'O2': 24, 'OT': 24, 'OT2': 24, 'OXT': 24, }, [ # bonds ### (0, 12, 1), (1, 14, 1), (2, 21, 1), (3, 11, 1), (4, 13, 1), (5, 15, 1), (6, 21, 1), (7, 11, 1), (8, 21, 1), (9, 10, 1), (9, 22, 2), (10, 11, 1), (10, 19, 1), (10, 21, 1), (11, 16, 1), (12, 14, 1), (12, 16, 2), (13, 15, 2), (13, 16, 1), (14, 17, 2), (15, 17, 1), (17, 23, 1), (18, 21, 1), (20, 23, 1), ]], 'VAL': [ { # names ### '1HG1': 0, 'HG11': 0, '1HG2': 1, 'HG21': 1, '1H': 2, '1HT': 2, 'H1': 2, 'HT1': 2, '2HG1': 3, 'HG12': 3, '2HG2': 4, 'HG22': 4, '2H': 5, '2HT': 5, 'H2': 5, 'HT2': 5, '3HG1': 6, 'HG13': 6, '3HG2': 7, 'HG23': 7, '3H': 8, '3HT': 8, 'H3': 8, 'HT3': 8, 'C': 9, 'CA': 10, 'CB': 11, 'CG1': 12, 'CG2': 13, 'H': 14, 'HN': 14, 'HA': 15, 'HA2': 15, 'HB': 16, 'N': 17, 'O': 18, 'O1': 18, 'OT1': 18, 'O2': 19, 'OT': 19, 'OT2': 19, 'OXT': 19, }, [ # bonds ### (0, 12, 1), (1, 13, 1), (2, 17, 1), (3, 12, 1), (4, 13, 1), (5, 17, 1), (6, 12, 1), (7, 13, 1), (8, 17, 1), (9, 10, 1), (9, 18, 2), (10, 11, 1), (10, 15, 1), (10, 17, 1), (11, 12, 1), (11, 13, 1), (11, 16, 1), (14, 17, 1), ]], }