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chemical.py
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import torch
from icecream import ic
import numpy as np
num2aa=[
'ALA','ARG','ASN','ASP','CYS',
'GLN','GLU','GLY','HIS','ILE',
'LEU','LYS','MET','PHE','PRO',
'SER','THR','TRP','TYR','VAL',
'UNK','MAS',
]
# Mapping 3 letter AA to 1 letter AA (e.g. ALA to A)
one_letter = ["A", "R", "N", "D", "C", \
"Q", "E", "G", "H", "I", \
"L", "K", "M", "F", "P", \
"S", "T", "W", "Y", "V", "?", "-"]
aa2num= {x:i for i,x in enumerate(num2aa)}
aa2num['MEN'] = 20
aa_321 = {a:b for a,b in zip(num2aa,one_letter)}
aa_123 = {val:key for key,val in aa_321.items()}
# create single letter code string from parsed integer sequence
def seq2chars(seq):
out = ''.join([aa_321[num2aa[a]] for a in seq])
return out
# full sc atom representation (Nx14)
aa2long=[
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), # ala
(" N "," CA "," C "," O "," CB "," CG "," CD "," NE "," CZ "," NH1"," NH2", None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD "," HE ","1HH1","2HH1","1HH2","2HH2"), # arg
(" N "," CA "," C "," O "," CB "," CG "," OD1"," ND2", None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD2","2HD2", None, None, None, None, None, None, None), # asn
(" N "," CA "," C "," O "," CB "," CG "," OD1"," OD2", None, None, None, None, None, None," H "," HA ","1HB ","2HB ", None, None, None, None, None, None, None, None, None), # asp
(" N "," CA "," C "," O "," CB "," SG ", None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB "," HG ", None, None, None, None, None, None, None, None), # cys
(" N "," CA "," C "," O "," CB "," CG "," CD "," OE1"," NE2", None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HE2","2HE2", None, None, None, None, None), # gln
(" N "," CA "," C "," O "," CB "," CG "," CD "," OE1"," OE2", None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ", None, None, None, None, None, None, None), # glu
(" N "," CA "," C "," O ", None, None, None, None, None, None, None, None, None, None," H ","1HA ","2HA ", None, None, None, None, None, None, None, None, None, None), # gly
(" N "," CA "," C "," O "," CB "," CG "," ND1"," CD2"," CE1"," NE2", None, None, None, None," H "," HA ","1HB ","2HB "," HD2"," HE1"," HE2", None, None, None, None, None, None), # his
(" N "," CA "," C "," O "," CB "," CG1"," CG2"," CD1", None, None, None, None, None, None," H "," HA "," HB ","1HG2","2HG2","3HG2","1HG1","2HG1","1HD1","2HD1","3HD1", None, None), # ile
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2", None, None, None, None, None, None," H "," HA ","1HB ","2HB "," HG ","1HD1","2HD1","3HD1","1HD2","2HD2","3HD2", None, None), # leu
(" N "," CA "," C "," O "," CB "," CG "," CD "," CE "," NZ ", None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD ","1HE ","2HE ","1HZ ","2HZ ","3HZ "), # lys
(" N "," CA "," C "," O "," CB "," CG "," SD "," CE ", None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HE ","2HE ","3HE ", None, None, None, None), # met
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," CE1"," CE2"," CZ ", None, None, None," H "," HA ","1HB ","2HB "," HD1"," HD2"," HE1"," HE2"," HZ ", None, None, None, None), # phe
(" N "," CA "," C "," O "," CB "," CG "," CD ", None, None, None, None, None, None, None," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD ", None, None, None, None, None, None), # pro
(" N "," CA "," C "," O "," CB "," OG ", None, None, None, None, None, None, None, None," H "," HG "," HA ","1HB ","2HB ", None, None, None, None, None, None, None, None), # ser
(" N "," CA "," C "," O "," CB "," OG1"," CG2", None, None, None, None, None, None, None," H "," HG1"," HA "," HB ","1HG2","2HG2","3HG2", None, None, None, None, None, None), # thr
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," NE1"," CE2"," CE3"," CZ2"," CZ3"," CH2"," H "," HA ","1HB ","2HB "," HD1"," HE1"," HZ2"," HH2"," HZ3"," HE3", None, None, None), # trp
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," CE1"," CE2"," CZ "," OH ", None, None," H "," HA ","1HB ","2HB "," HD1"," HE1"," HE2"," HD2"," HH ", None, None, None, None), # tyr
(" N "," CA "," C "," O "," CB "," CG1"," CG2", None, None, None, None, None, None, None," H "," HA "," HB ","1HG1","2HG1","3HG1","1HG2","2HG2","3HG2", None, None, None, None), # val
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), # unk
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), # mask
]
# build the "alternate" sc mapping
aa2longalt=[
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), # ala
(" N "," CA "," C "," O "," CB "," CG "," CD "," NE "," CZ "," NH1"," NH2", None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD "," HE ","1HH1","2HH1","1HH2","2HH2"), # arg
(" N "," CA "," C "," O "," CB "," CG "," OD1"," ND2", None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD2","2HD2", None, None, None, None, None, None, None), # asn
(" N "," CA "," C "," O "," CB "," CG "," OD2"," OD1", None, None, None, None, None, None," H "," HA ","1HB ","2HB ", None, None, None, None, None, None, None, None, None), # asp
(" N "," CA "," C "," O "," CB "," SG ", None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB "," HG ", None, None, None, None, None, None, None, None), # cys
(" N "," CA "," C "," O "," CB "," CG "," CD "," OE1"," NE2", None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HE2","2HE2", None, None, None, None, None), # gln
(" N "," CA "," C "," O "," CB "," CG "," CD "," OE2"," OE1", None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ", None, None, None, None, None, None, None), # glu
(" N "," CA "," C "," O ", None, None, None, None, None, None, None, None, None, None," H ","1HA ","2HA ", None, None, None, None, None, None, None, None, None, None), # gly
(" N "," CA "," C "," O "," CB "," CG "," NE2"," CD2"," CE1"," ND1", None, None, None, None," H "," HA ","1HB ","2HB "," HD2"," HE1"," HE2", None, None, None, None, None, None), # his
(" N "," CA "," C "," O "," CB "," CG1"," CG2"," CD1", None, None, None, None, None, None," H "," HA "," HB ","1HG2","2HG2","3HG2","1HG1","2HG1","1HD1","2HD1","3HD1", None, None), # ile
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2", None, None, None, None, None, None," H "," HA ","1HB ","2HB "," HG ","1HD1","2HD1","3HD1","1HD2","2HD2","3HD2", None, None), # leu
(" N "," CA "," C "," O "," CB "," CG "," CD "," CE "," NZ ", None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD ","1HE ","2HE ","1HZ ","2HZ ","3HZ "), # lys
(" N "," CA "," C "," O "," CB "," CG "," SD "," CE ", None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HE ","2HE ","3HE ", None, None, None, None), # met
(" N "," CA "," C "," O "," CB "," CG "," CD2"," CD1"," CE2"," CE1"," CZ ", None, None, None," H "," HD2"," HE2"," HZ "," HE1"," HD1"," HA ","1HB ","2HB ", None, None, None, None), # phe
(" N "," CA "," C "," O "," CB "," CG "," CD ", None, None, None, None, None, None, None," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD ", None, None, None, None, None, None), # pro
(" N "," CA "," C "," O "," CB "," OG ", None, None, None, None, None, None, None, None," H "," HG "," HA ","1HB ","2HB ", None, None, None, None, None, None, None, None), # ser
(" N "," CA "," C "," O "," CB "," OG1"," CG2", None, None, None, None, None, None, None," H "," HG1"," HA "," HB ","1HG2","2HG2","3HG2", None, None, None, None, None, None), # thr
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," NE1"," CE2"," CE3"," CZ2"," CZ3"," CH2"," H "," HA ","1HB ","2HB "," HD1"," HE1"," HZ2"," HH2"," HZ3"," HE3", None, None, None), # trp
(" N "," CA "," C "," O "," CB "," CG "," CD2"," CD1"," CE2"," CE1"," CZ "," OH ", None, None," H "," HA ","1HB ","2HB "," HD2"," HE2"," HE1"," HD1"," HH ", None, None, None, None), # tyr
(" N "," CA "," C "," O "," CB "," CG1"," CG2", None, None, None, None, None, None, None," H "," HA "," HB ","1HG1","2HG1","3HG1","1HG2","2HG2","3HG2", None, None, None, None), # val
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), # unk
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), # mask
]
aabonds=[
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB ","1HB "),(" CB ","2HB "),(" CB ","3HB ")) , # ala
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD "),(" CG ","1HG "),(" CG ","2HG "),(" CD "," NE "),(" CD ","1HD "),(" CD ","2HD "),(" NE "," CZ "),(" NE "," HE "),(" CZ "," NH1"),(" CZ "," NH2"),(" NH1","1HH1"),(" NH1","2HH1"),(" NH2","1HH2"),(" NH2","2HH2")) , # arg
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," OD1"),(" CG "," ND2"),(" ND2","1HD2"),(" ND2","2HD2")) , # asn
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," OD1"),(" CG "," OD2")) , # asp
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," SG "),(" CB ","1HB "),(" CB ","2HB "),(" SG "," HG ")) , # cys
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD "),(" CG ","1HG "),(" CG ","2HG "),(" CD "," OE1"),(" CD "," NE2"),(" NE2","1HE2"),(" NE2","2HE2")) , # gln
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD "),(" CG ","1HG "),(" CG ","2HG "),(" CD "," OE1"),(" CD "," OE2")) , # glu
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA ","1HA "),(" CA ","2HA "),(" C "," O ")) , # gly
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," ND1"),(" CG "," CD2"),(" ND1"," CE1"),(" CD2"," NE2"),(" CD2"," HD2"),(" CE1"," NE2"),(" CE1"," HE1"),(" NE2"," HE2")) , # his
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG1"),(" CB "," CG2"),(" CB "," HB "),(" CG1"," CD1"),(" CG1","1HG1"),(" CG1","2HG1"),(" CG2","1HG2"),(" CG2","2HG2"),(" CG2","3HG2"),(" CD1","1HD1"),(" CD1","2HD1"),(" CD1","3HD1")) , # ile
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD1"),(" CG "," CD2"),(" CG "," HG "),(" CD1","1HD1"),(" CD1","2HD1"),(" CD1","3HD1"),(" CD2","1HD2"),(" CD2","2HD2"),(" CD2","3HD2")) , # leu
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD "),(" CG ","1HG "),(" CG ","2HG "),(" CD "," CE "),(" CD ","1HD "),(" CD ","2HD "),(" CE "," NZ "),(" CE ","1HE "),(" CE ","2HE "),(" NZ ","1HZ "),(" NZ ","2HZ "),(" NZ ","3HZ ")) , # lys
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," SD "),(" CG ","1HG "),(" CG ","2HG "),(" SD "," CE "),(" CE ","1HE "),(" CE ","2HE "),(" CE ","3HE ")) , # met
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD1"),(" CG "," CD2"),(" CD1"," CE1"),(" CD1"," HD1"),(" CD2"," CE2"),(" CD2"," HD2"),(" CE1"," CZ "),(" CE1"," HE1"),(" CE2"," CZ "),(" CE2"," HE2"),(" CZ "," HZ ")) , # phe
((" N "," CA "),(" N "," CD "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD "),(" CG ","1HG "),(" CG ","2HG "),(" CD ","1HD "),(" CD ","2HD ")) , # pro
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," OG "),(" CB ","1HB "),(" CB ","2HB "),(" OG "," HG ")) , # ser
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," OG1"),(" CB "," CG2"),(" CB "," HB "),(" OG1"," HG1"),(" CG2","1HG2"),(" CG2","2HG2"),(" CG2","3HG2")) , # thr
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD1"),(" CG "," CD2"),(" CD1"," NE1"),(" CD1"," HD1"),(" CD2"," CE2"),(" CD2"," CE3"),(" NE1"," CE2"),(" NE1"," HE1"),(" CE2"," CZ2"),(" CE3"," CZ3"),(" CE3"," HE3"),(" CZ2"," CH2"),(" CZ2"," HZ2"),(" CZ3"," CH2"),(" CZ3"," HZ3"),(" CH2"," HH2")) , # trp
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG "),(" CB ","1HB "),(" CB ","2HB "),(" CG "," CD1"),(" CG "," CD2"),(" CD1"," CE1"),(" CD1"," HD1"),(" CD2"," CE2"),(" CD2"," HD2"),(" CE1"," CZ "),(" CE1"," HE1"),(" CE2"," CZ "),(" CE2"," HE2"),(" CZ "," OH "),(" OH "," HH ")) , # tyr
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB "," CG1"),(" CB "," CG2"),(" CB "," HB "),(" CG1","1HG1"),(" CG1","2HG1"),(" CG1","3HG1"),(" CG2","1HG2"),(" CG2","2HG2"),(" CG2","3HG2")), # val
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB ","1HB "),(" CB ","2HB "),(" CB ","3HB ")) , # unk
((" N "," CA "),(" N "," H "),(" CA "," C "),(" CA "," CB "),(" CA "," HA "),(" C "," O "),(" CB ","1HB "),(" CB ","2HB "),(" CB ","3HB ")) , # mask
]
aa2type = [
("Nbb", "CAbb","CObb","OCbb","CH3", None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None, None, None), # ala
("Nbb", "CAbb","CObb","OCbb","CH2", "CH2", "CH2", "NtrR","aroC","Narg","Narg", None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hpol","Hpol","Hpol","Hpol"), # arg
("Nbb", "CAbb","CObb","OCbb","CH2", "CNH2","ONH2","NH2O", None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hpol","Hpol", None, None, None, None, None, None, None), # asn
("Nbb", "CAbb","CObb","OCbb","CH2", "COO", "OOC", "OOC", None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo", None, None, None, None, None, None, None, None, None), # asp
("Nbb", "CAbb","CObb","OCbb","CH2", "SH1", None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","HS", None, None, None, None, None, None, None, None), # cys
("Nbb", "CAbb","CObb","OCbb","CH2", "CH2", "CNH2","ONH2","NH2O", None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hpol", None, None, None, None, None), # gln
("Nbb", "CAbb","CObb","OCbb","CH2", "CH2", "COO", "OOC", "OOC", None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None, None), # glu
("Nbb", "CAbb","CObb","OCbb", None, None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo", None, None, None, None, None, None, None, None, None, None), # gly
("Nbb", "CAbb","CObb","OCbb","CH2", "CH0", "Nhis","aroC","aroC","Ntrp", None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hpol","Hapo","Hapo", None, None, None, None, None, None), # his
("Nbb", "CAbb","CObb","OCbb","CH1", "CH2", "CH3", "CH3", None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo", None, None), # ile
("Nbb", "CAbb","CObb","OCbb","CH2", "CH1", "CH3", "CH3", None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo", None, None), # leu
("Nbb", "CAbb","CObb","OCbb","CH2", "CH2", "CH2", "CH2", "Nlys", None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hpol","Hpol"), # lys
("Nbb", "CAbb","CObb","OCbb","CH2", "CH2", "S", "CH3", None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo", None, None, None, None), # met
("Nbb", "CAbb","CObb","OCbb","CH2", "CH0", "aroC","aroC","aroC","aroC","aroC", None, None, None,"HNbb","Hapo","Hapo","Hapo","Haro","Haro","Haro","Haro","Haro", None, None, None, None), # phe
("Npro","CAbb","CObb","OCbb","CH2", "CH2", "CH2", None, None, None, None, None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None), # pro
("Nbb", "CAbb","CObb","OCbb","CH2", "OH", None, None, None, None, None, None, None, None,"HNbb","Hpol","Hapo","Hapo","Hapo", None, None, None, None, None, None, None, None), # ser
("Nbb", "CAbb","CObb","OCbb","CH1", "OH", "CH3", None, None, None, None, None, None, None,"HNbb","Hpol","Hapo","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None), # thr
("Nbb", "CAbb","CObb","OCbb","CH2", "CH0", "aroC","CH0", "Ntrp","CH0", "aroC","aroC","aroC","aroC","HNbb","Haro","Hapo","Hapo","Hapo","Hpol","Haro","Haro","Haro","Haro", None, None, None), # trp
("Nbb", "CAbb","CObb","OCbb","CH2", "CH0", "aroC","aroC","aroC","aroC","CH0", "OHY", None, None,"HNbb","Haro","Haro","Haro","Haro","Hapo","Hapo","Hapo","Hpol", None, None, None, None), # tyr
("Nbb", "CAbb","CObb","OCbb","CH1", "CH3", "CH3", None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo", None, None, None, None), # val
("Nbb", "CAbb","CObb","OCbb","CH3", None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None, None, None), # unk
("Nbb", "CAbb","CObb","OCbb","CH3", None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None, None, None), # mask
]
# tip atom
aa2tip = [
" CB ", # ala
" CZ ", # arg
" ND2", # asn
" CG ", # asp
" SG ", # cys
" NE2", # gln
" CD ", # glu
" CA ", # gly
" NE2", # his
" CD1", # ile
" CG ", # leu
" NZ ", # lys
" SD ", # met
" CZ ", # phe
" CG ", # pro
" OG ", # ser
" OG1", # thr
" CH2", # trp
" OH ", # tyr
" CB ", # val
" CB ", # unknown (gap etc)
" CB " # masked
]
torsions=[
[ None, None, None, None ], # ala
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD "], [" CB "," CG "," CD "," NE "], [" CG "," CD "," NE "," CZ "] ], # arg
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," OD1"], None, None ], # asn
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," OD1"], None, None ], # asp
[ [" N "," CA "," CB "," SG "], [" CA "," CB "," SG "," HG "], None, None ], # cys
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD "], [" CB "," CG "," CD "," OE1"], None ], # gln
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD "], [" CB "," CG "," CD "," OE1"], None ], # glu
[ None, None, None, None ], # gly
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," ND1"], [" CD2"," CE1"," HE1"," NE2"], None ], # his (protonation handled as a pseudo-torsion)
[ [" N "," CA "," CB "," CG1"], [" CA "," CB "," CG1"," CD1"], None, None ], # ile
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD1"], None, None ], # leu
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD "], [" CB "," CG "," CD "," CE "], [" CG "," CD "," CE "," NZ "] ], # lys
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," SD "], [" CB "," CG "," SD "," CE "], None ], # met
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD1"], None, None ], # phe
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD "], [" CB "," CG "," CD ","1HD "], None ], # pro
[ [" N "," CA "," CB "," OG "], [" CA "," CB "," OG "," HG "], None, None ], # ser
[ [" N "," CA "," CB "," OG1"], [" CA "," CB "," OG1"," HG1"], None, None ], # thr
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD1"], None, None ], # trp
[ [" N "," CA "," CB "," CG "], [" CA "," CB "," CG "," CD1"], [" CE1"," CZ "," OH "," HH "], None ], # tyr
[ [" N "," CA "," CB "," CG1"], None, None, None ], # val
[ None, None, None, None ], # unk
[ None, None, None, None ], # mask
]
# ideal N, CA, C initial coordinates
init_N = torch.tensor([-0.5272, 1.3593, 0.000]).float()
init_CA = torch.zeros_like(init_N)
init_C = torch.tensor([1.5233, 0.000, 0.000]).float()
INIT_CRDS = torch.full((36, 3), np.nan)
INIT_CRDS[:3] = torch.stack((init_N, init_CA, init_C), dim=0) # (3,3)
norm_N = init_N / (torch.norm(init_N, dim=-1, keepdim=True) + 1e-5)
norm_C = init_C / (torch.norm(init_C, dim=-1, keepdim=True) + 1e-5)
cos_ideal_NCAC = torch.sum(norm_N*norm_C, dim=-1) # cosine of ideal N-CA-C bond angle
#fd Rosetta ideal coords
#fd - uses same "frame-building" as AF2
ideal_coords = [
[ # 0 ala
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3341, -0.4928, 0.9132)],
[' CB ', 8, (-0.5289,-0.7734,-1.1991)],
['1HB ', 8, (-0.1265, -1.7863, -1.1851)],
['2HB ', 8, (-1.6173, -0.8147, -1.1541)],
['3HB ', 8, (-0.2229, -0.2744, -2.1172)],
],
[ # 1 arg
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3467, -0.5055, 0.9018)],
[' CB ', 8, (-0.5042,-0.7698,-1.2118)],
['1HB ', 4, ( 0.3635, -0.5318, 0.8781)],
['2HB ', 4, ( 0.3639, -0.5323, -0.8789)],
[' CG ', 4, (0.6396,1.3794, 0.000)],
['1HG ', 5, (0.3639, -0.5139, 0.8900)],
['2HG ', 5, (0.3641, -0.5140, -0.8903)],
[' CD ', 5, (0.5492,1.3801, 0.000)],
['1HD ', 6, (0.3637, -0.5135, 0.8895)],
['2HD ', 6, (0.3636, -0.5134, -0.8893)],
[' NE ', 6, (0.5423,1.3491, 0.000)],
[' NH1', 7, (0.2012,2.2965, 0.000)],
[' NH2', 7, (2.0824,1.0030, 0.000)],
[' CZ ', 7, (0.7650,1.1090, 0.000)],
[' HE ', 7, (0.4701,-0.8955, 0.000)],
['1HH1', 7, (-0.8059,2.3776, 0.000)],
['1HH2', 7, (2.5160,0.0898, 0.000)],
['2HH1', 7, (0.7745,3.1277, 0.000)],
['2HH2', 7, (2.6554,1.8336, 0.000)],
],
[ # 2 asn
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3233, -0.4967, 0.9162)],
[' CB ', 8, (-0.5341,-0.7799,-1.1874)],
['1HB ', 4, ( 0.3641, -0.5327, 0.8795)],
['2HB ', 4, ( 0.3639, -0.5323, -0.8789)],
[' CG ', 4, (0.5778,1.3881, 0.000)],
[' ND2', 5, (0.5839,-1.1711, 0.000)],
[' OD1', 5, (0.6331,1.0620, 0.000)],
['1HD2', 5, (1.5825, -1.2322, 0.000)],
['2HD2', 5, (0.0323, -2.0046, 0.000)],
],
[ # 3 asp
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3233, -0.4967, 0.9162)],
[' CB ', 8, (-0.5162,-0.7757,-1.2144)],
['1HB ', 4, ( 0.3639, -0.5324, 0.8791)],
['2HB ', 4, ( 0.3640, -0.5325, -0.8792)],
[' CG ', 4, (0.5926,1.4028, 0.000)],
[' OD1', 5, (0.5746,1.0629, 0.000)],
[' OD2', 5, (0.5738,-1.0627, 0.000)],
],
[ # 4 cys
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3481, -0.5059, 0.9006)],
[' CB ', 8, (-0.5046,-0.7727,-1.2189)],
['1HB ', 4, ( 0.3639, -0.5324, 0.8791)],
['2HB ', 4, ( 0.3638, -0.5322, -0.8787)],
[' SG ', 4, (0.7386,1.6511, 0.000)],
[' HG ', 5, (0.1387,1.3221, 0.000)],
],
[ # 5 gln
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3363, -0.5013, 0.9074)],
[' CB ', 8, (-0.5226,-0.7776,-1.2109)],
['1HB ', 4, ( 0.3638, -0.5323, 0.8789)],
['2HB ', 4, ( 0.3638, -0.5322, -0.8788)],
[' CG ', 4, (0.6225,1.3857, 0.000)],
['1HG ', 5, ( 0.3531, -0.5156, 0.8931)],
['2HG ', 5, ( 0.3531, -0.5156, -0.8931)],
[' CD ', 5, (0.5788,1.4021, 0.000)],
[' NE2', 6, (0.5908,-1.1895, 0.000)],
[' OE1', 6, (0.6347,1.0584, 0.000)],
['1HE2', 6, (1.5825, -1.2525, 0.000)],
['2HE2', 6, (0.0380, -2.0229, 0.000)],
],
[ # 6 glu
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3363, -0.5013, 0.9074)],
[' CB ', 8, (-0.5197,-0.7737,-1.2137)],
['1HB ', 4, ( 0.3638, -0.5323, 0.8789)],
['2HB ', 4, ( 0.3638, -0.5322, -0.8788)],
[' CG ', 4, (0.6287,1.3862, 0.000)],
['1HG ', 5, ( 0.3531, -0.5156, 0.8931)],
['2HG ', 5, ( 0.3531, -0.5156, -0.8931)],
[' CD ', 5, (0.5850,1.3849, 0.000)],
[' OE1', 6, (0.5752,1.0618, 0.000)],
[' OE2', 6, (0.5741,-1.0635, 0.000)],
],
[ # 7 gly
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
['1HA ', 0, ( -0.3676, -0.5329, 0.8771)],
['2HA ', 0, ( -0.3674, -0.5325, -0.8765)],
],
[ # 8 his
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3299, -0.5180, 0.9001)],
[' CB ', 8, (-0.5163,-0.7809,-1.2129)],
['1HB ', 4, ( 0.3640, -0.5325, 0.8793)],
['2HB ', 4, ( 0.3637, -0.5321, -0.8786)],
[' CG ', 4, (0.6016,1.3710, 0.000)],
[' CD2', 5, (0.8918,-1.0184, 0.000)],
[' CE1', 5, (2.0299,0.8564, 0.000)],
[' HE1', 5, (2.8542, 1.5693, 0.000)],
[' HD2', 5, ( 0.6584, -2.0835, 0.000) ],
[' ND1', 6, (-1.8631, -1.0722, 0.000)],
[' NE2', 6, (-1.8625, 1.0707, 0.000)],
[' HE2', 6, (-1.5439, 2.0292, 0.000)],
],
[ # 9 ile
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3405, -0.5028, 0.9044)],
[' CB ', 8, (-0.5140,-0.7885,-1.2184)],
[' HB ', 4, (0.3637, -0.4714, 0.9125)],
[' CG1', 4, (0.5339,1.4348,0.000)],
[' CG2', 4, (0.5319,-0.7693,-1.1994)],
['1HG2', 4, (1.6215, -0.7588, -1.1842)],
['2HG2', 4, (0.1785, -1.7986, -1.1569)],
['3HG2', 4, (0.1773, -0.3016, -2.1180)],
[' CD1', 5, (0.6106,1.3829, 0.000)],
['1HG1', 5, (0.3637, -0.5338, 0.8774)],
['2HG1', 5, (0.3640, -0.5322, -0.8793)],
['1HD1', 5, (1.6978, 1.3006, 0.000)],
['2HD1', 5, (0.2873, 1.9236, -0.8902)],
['3HD1', 5, (0.2888, 1.9224, 0.8896)],
],
[ # 10 leu
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.525, -0.000, -0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3435, -0.5040, 0.9027)],
[' CB ', 8, (-0.5175,-0.7692,-1.2220)],
['1HB ', 4, ( 0.3473, -0.5346, 0.8827)],
['2HB ', 4, ( 0.3476, -0.5351, -0.8836)],
[' CG ', 4, (0.6652,1.3823, 0.000)],
[' CD1', 5, (0.5083,1.4353, 0.000)],
[' CD2', 5, (0.5079,-0.7600,1.2163)],
[' HG ', 5, (0.3640, -0.4825, -0.9075)],
['1HD1', 5, (1.5984, 1.4353, 0.000)],
['2HD1', 5, (0.1462, 1.9496, -0.8903)],
['3HD1', 5, (0.1459, 1.9494, 0.8895)],
['1HD2', 5, (1.5983, -0.7606, 1.2158)],
['2HD2', 5, (0.1456, -0.2774, 2.1243)],
['3HD2', 5, (0.1444, -1.7871, 1.1815)],
],
[ # 11 lys
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3335, -0.5005, 0.9097)],
['1HB ', 4, ( 0.3640, -0.5324, 0.8791)],
['2HB ', 4, ( 0.3639, -0.5324, -0.8790)],
[' CB ', 8, (-0.5259,-0.7785,-1.2069)],
['1HG ', 5, (0.3641, -0.5229, 0.8852)],
['2HG ', 5, (0.3637, -0.5227, -0.8841)],
[' CG ', 4, (0.6291,1.3869, 0.000)],
[' CD ', 5, (0.5526,1.4174, 0.000)],
['1HD ', 6, (0.3641, -0.5239, 0.8848)],
['2HD ', 6, (0.3638, -0.5219, -0.8850)],
[' CE ', 6, (0.5544,1.4170, 0.000)],
[' NZ ', 7, (0.5566,1.3801, 0.000)],
['1HE ', 7, (0.4199, -0.4638, 0.9482)],
['2HE ', 7, (0.4202, -0.4631, -0.8172)],
['1HZ ', 7, (1.6223, 1.3980, 0.0658)],
['2HZ ', 7, (0.2970, 1.9326, -0.7584)],
['3HZ ', 7, (0.2981, 1.9319, 0.8909)],
],
[ # 12 met
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3303, -0.4990, 0.9108)],
['1HB ', 4, ( 0.3635, -0.5318, 0.8781)],
['2HB ', 4, ( 0.3641, -0.5326, -0.8795)],
[' CB ', 8, (-0.5331,-0.7727,-1.2048)],
['1HG ', 5, (0.3637, -0.5256, 0.8823)],
['2HG ', 5, (0.3638, -0.5249, -0.8831)],
[' CG ', 4, (0.6298,1.3858,0.000)],
[' SD ', 5, (0.6953,1.6645,0.000)],
[' CE ', 6, (0.3383,1.7581,0.000)],
['1HE ', 6, (1.7054, 2.0532, -0.0063)],
['2HE ', 6, (0.1906, 2.3099, -0.9072)],
['3HE ', 6, (0.1917, 2.3792, 0.8720)],
],
[ # 13 phe
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3303, -0.4990, 0.9108)],
['1HB ', 4, ( 0.3635, -0.5318, 0.8781)],
['2HB ', 4, ( 0.3641, -0.5326, -0.8795)],
[' CB ', 8, (-0.5150,-0.7729,-1.2156)],
[' CG ', 4, (0.6060,1.3746, 0.000)],
[' CD1', 5, (0.7078,1.1928, 0.000)],
[' CD2', 5, (0.7084,-1.1920, 0.000)],
[' CE1', 5, (2.0900,1.1940, 0.000)],
[' CE2', 5, (2.0897,-1.1939, 0.000)],
[' CZ ', 5, (2.7809, 0.000, 0.000)],
[' HD1', 5, (0.1613, 2.1362, 0.000)],
[' HD2', 5, (0.1621, -2.1360, 0.000)],
[' HE1', 5, (2.6335, 2.1384, 0.000)],
[' HE2', 5, (2.6344, -2.1378, 0.000)],
[' HZ ', 5, (3.8700, 0.000, 0.000)],
],
[ # 14 pro
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' HA ', 0, (-0.3868, -0.5380, 0.8781)],
['1HB ', 4, ( 0.3762, -0.5355, 0.8842)],
['2HB ', 4, ( 0.3762, -0.5355, -0.8842)],
[' CB ', 8, (-0.5649,-0.5888,-1.2966)],
[' CG ', 4, (0.3657,1.4451,0.0000)],
[' CD ', 5, (0.3744,1.4582, 0.0)],
['1HG ', 5, (0.3798, -0.5348, 0.8830)],
['2HG ', 5, (0.3798, -0.5348, -0.8830)],
['1HD ', 6, (0.3798, -0.5348, 0.8830)],
['2HD ', 6, (0.3798, -0.5348, -0.8830)],
],
[ # 15 ser
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3425, -0.5041, 0.9048)],
['1HB ', 4, ( 0.3637, -0.5321, 0.8786)],
['2HB ', 4, ( 0.3636, -0.5319, -0.8782)],
[' CB ', 8, (-0.5146,-0.7595,-1.2073)],
[' OG ', 4, (0.5021,1.3081, 0.000)],
[' HG ', 5, (0.2647, 0.9230, 0.000)],
],
[ # 16 thr
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3364, -0.5015, 0.9078)],
[' HB ', 4, ( 0.3638, -0.5006, 0.8971)],
['1HG2', 4, ( 1.6231, -0.7142, -1.2097)],
['2HG2', 4, ( 0.1792, -1.7546, -1.2237)],
['3HG2', 4, ( 0.1808, -0.2222, -2.1269)],
[' CB ', 8, (-0.5172,-0.7952,-1.2130)],
[' CG2', 4, (0.5334,-0.7239,-1.2267)],
[' OG1', 4, (0.4804,1.3506,0.000)],
[' HG1', 5, (0.3194, 0.9056, 0.000)],
],
[ # 17 trp
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3436, -0.5042, 0.9031)],
['1HB ', 4, ( 0.3639, -0.5323, 0.8790)],
['2HB ', 4, ( 0.3638, -0.5322, -0.8787)],
[' CB ', 8, (-0.5136,-0.7712,-1.2173)],
[' CG ', 4, (0.5984,1.3741, 0.000)],
[' CD1', 5, (0.8151,1.0921, 0.000)],
[' CD2', 5, (0.8753,-1.1538, 0.000)],
[' CE2', 5, (2.1865,-0.6707, 0.000)],
[' CE3', 5, (0.6541,-2.5366, 0.000)],
[' NE1', 5, (2.1309,0.7003, 0.000)],
[' CH2', 5, (3.0315,-2.8930, 0.000)],
[' CZ2', 5, (3.2813,-1.5205, 0.000)],
[' CZ3', 5, (1.7521,-3.3888, 0.000)],
[' HD1', 5, (0.4722, 2.1252, 0.000)],
[' HE1', 5, ( 2.9291, 1.3191, 0.000)],
[' HE3', 5, (-0.3597, -2.9356, 0.000)],
[' HZ2', 5, (4.3053, -1.1462, 0.000)],
[' HZ3', 5, ( 1.5712, -4.4640, 0.000)],
[' HH2', 5, ( 3.8700, -3.5898, 0.000)],
],
[ # 18 tyr
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3305, -0.4992, 0.9112)],
['1HB ', 4, ( 0.3642, -0.5327, 0.8797)],
['2HB ', 4, ( 0.3637, -0.5321, -0.8785)],
[' CB ', 8, (-0.5305,-0.7799,-1.2051)],
[' CG ', 4, (0.6104,1.3840, 0.000)],
[' CD1', 5, (0.6936,1.2013, 0.000)],
[' CD2', 5, (0.6934,-1.2011, 0.000)],
[' CE1', 5, (2.0751,1.2013, 0.000)],
[' CE2', 5, (2.0748,-1.2011, 0.000)],
[' OH ', 5, (4.1408, 0.000, 0.000)],
[' CZ ', 5, (2.7648, 0.000, 0.000)],
[' HD1', 5, (0.1485, 2.1455, 0.000)],
[' HD2', 5, (0.1484, -2.1451, 0.000)],
[' HE1', 5, (2.6200, 2.1450, 0.000)],
[' HE2', 5, (2.6199, -2.1453, 0.000)],
[' HH ', 6, (0.3190, 0.9057, 0.000)],
],
[ # 19 val
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3497, -0.5068, 0.9002)],
[' CB ', 8, (-0.5105,-0.7712,-1.2317)],
[' CG1', 4, (0.5326,1.4252, 0.000)],
[' CG2', 4, (0.5177,-0.7693,1.2057)],
[' HB ', 4, (0.3541, -0.4754, -0.9148)],
['1HG1', 4, (1.6228, 1.4063, 0.000)],
['2HG1', 4, (0.1790, 1.9457, -0.8898)],
['3HG1', 4, (0.1798, 1.9453, 0.8903)],
['1HG2', 4, (1.6073, -0.7659, 1.1989)],
['2HG2', 4, (0.1586, -0.2971, 2.1203)],
['3HG2', 4, (0.1582, -1.7976, 1.1631)],
],
[ # 20 unk
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3341, -0.4928, 0.9132)],
[' CB ', 8, (-0.5289,-0.7734,-1.1991)],
['1HB ', 8, (-0.1265, -1.7863, -1.1851)],
['2HB ', 8, (-1.6173, -0.8147, -1.1541)],
['3HB ', 8, (-0.2229, -0.2744, -2.1172)],
],
[ # 21 mask
[' N ', 0, (-0.5272, 1.3593, 0.000)],
[' CA ', 0, (0.000, 0.000, 0.000)],
[' C ', 0, (1.5233, 0.000, 0.000)],
[' O ', 3, (0.6303, 1.0574, 0.000)],
[' H ', 2, (0.4920,-0.8821, 0.0000)],
[' HA ', 0, (-0.3341, -0.4928, 0.9132)],
[' CB ', 8, (-0.5289,-0.7734,-1.1991)],
['1HB ', 8, (-0.1265, -1.7863, -1.1851)],
['2HB ', 8, (-1.6173, -0.8147, -1.1541)],
['3HB ', 8, (-0.2229, -0.2744, -2.1172)],
],
]