bonds.py

#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 ), ]], }

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