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RoseTTAFold-All-Atom/rf2aa/chemical.py
Rohith Krishna f87f5b8cdf initial commit
2024-03-04 22:38:17 -08:00

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import sys, os, gzip, json
import torch
import numpy as np
from pathlib import Path
from typing import Optional
import threading
import scipy.sparse
import scipy.sparse.csgraph
script_dir = os.path.dirname(os.path.realpath(__file__))+'/'
from rf2aa.scoring import *
# process ideal frames
def make_frame(X, Y):
Xn = X / torch.linalg.norm(X)
Y = Y - torch.dot(Y, Xn) * Xn
Yn = Y / torch.linalg.norm(Y)
Z = torch.cross(Xn,Yn)
Zn = Z / torch.linalg.norm(Z)
return torch.stack((Xn,Yn,Zn), dim=-1)
# ang between vectors
def th_ang_v(ab,bc,eps:float=1e-8):
def th_norm(x,eps:float=1e-8):
return x.square().sum(-1,keepdim=True).add(eps).sqrt()
def th_N(x,alpha:float=0):
return x/th_norm(x).add(alpha)
ab, bc = th_N(ab),th_N(bc)
cos_angle = torch.clamp( (ab*bc).sum(-1), -1, 1)
sin_angle = torch.sqrt(1-cos_angle.square() + eps)
dih = torch.stack((cos_angle,sin_angle),-1)
return dih
# dihedral between vectors
def th_dih_v(ab,bc,cd):
def th_cross(a,b):
a,b = torch.broadcast_tensors(a,b)
return torch.cross(a,b, dim=-1)
def th_norm(x,eps:float=1e-8):
return x.square().sum(-1,keepdim=True).add(eps).sqrt()
def th_N(x,alpha:float=0):
return x/th_norm(x).add(alpha)
ab, bc, cd = th_N(ab),th_N(bc),th_N(cd)
n1 = th_N( th_cross(ab,bc) )
n2 = th_N( th_cross(bc,cd) )
sin_angle = (th_cross(n1,bc)*n2).sum(-1)
cos_angle = (n1*n2).sum(-1)
dih = torch.stack((cos_angle,sin_angle),-1)
return dih
# dihedral between points
def th_dih(a,b,c,d):
return th_dih_v(a-b,b-c,c-d)
# helper function to load chemical database with specified config
def initialize_chemdata(config, worker_id=None):
ChemicalData(config)
# A singleton class that stores chemical data
class ChemicalData:
_ChemicalDataStore = None
# initialize once
def __new__(cls, *args, **kwds):
#print ('__new__', cls._ChemicalDataStore)
if not cls._ChemicalDataStore:
cls._ChemicalDataStore = super().__new__(cls)
cls._ChemicalDataStore.init(*args, **kwds)
return cls._ChemicalDataStore
@classmethod
def reset(cls):
cls._ChemicalDataStore = None
def init(self, params):
self.load_base_data(params)
self.load_derived_data(params)
self.params = params
def load_base_data(self, params):
self.NAATOKENS = 20+2+10+1+47 # 20 AAs, UNK, MASK, 8 NAs,HIS_D, 47 atoms
self.UNKINDEX = 20 # residue unknown
self.MASKINDEX = 21 # protein mask
self.NHEAVYPROT = 14
self.NHEAVY = 23
self.NTOTAL = 36
self.NNAPROTAAS = 32
self.NPROTAAS = 22 # include UNK/MAS
self.CHAIN_GAP = 200
# internal coords
self.NPROTTORS = 7
self.NPROTANGS = 3
self.NNATORS = 10
self.NTOTALTORS = self.NPROTTORS+self.NNATORS
self.NTOTALDOFS = self.NTOTALTORS+self.NPROTANGS
#bond types
self.num2btype = [0,1,2,3,4,5,6,7] # UNK, SINGLE, DOUBLE, TRIPLE, AROMATIC,
# PEPTIDE/NA BACKBONE, PROTEIN-LIGAND (PEPTIDE), OTHER
self.NBTYPES = len(self.num2btype)
self.num2aa=[
'ALA','ARG','ASN','ASP','CYS',
'GLN','GLU','GLY','HIS','ILE',
'LEU','LYS','MET','PHE','PRO',
'SER','THR','TRP','TYR','VAL',
'UNK','MAS',
' DA',' DC',' DG',' DT', ' DX',
' RA',' RC',' RG',' RU', ' RX',
'HIS_D', # only used for cart_bonded
'Al', 'As', 'Au', 'B',
'Be', 'Br', 'C', 'Ca', 'Cl',
'Co', 'Cr', 'Cu', 'F', 'Fe',
'Hg', 'I', 'Ir', 'K', 'Li', 'Mg',
'Mn', 'Mo', 'N', 'Ni', 'O',
'Os', 'P', 'Pb', 'Pd', 'Pr',
'Pt', 'Re', 'Rh', 'Ru', 'S',
'Sb', 'Se', 'Si', 'Sn', 'Tb',
'Te', 'U', 'W', 'V', 'Y', 'Zn',
'ATM'
]
self.aa2num= {x:i for i,x in enumerate(self.num2aa)}
self.aa2num['MEN'] = 20
# Mapping 3 letter AA to 1 letter AA (e.g. ALA to A)
self.one_letter = ["A", "R", "N", "D", "C", \
"Q", "E", "G", "H", "I", \
"L", "K", "M", "F", "P", \
"S", "T", "W", "Y", "V", "?", "-"]
self.n_non_protein = len(self.num2aa) - len(self.one_letter)
self.aa_321 = {a:b for a,b in zip(self.num2aa,self.one_letter+['a']*self.n_non_protein)}
self.frame_priority2atom = [
"F", "Cl", "Br", "I", "O", "S", "Se", "Te", "N", "P", "As", "Sb",
"C", "Si", "Sn", "Pb", "B", "Al", "Zn", "Hg", "Cu", "Au", "Ni", "Pd",
"Pt", "Co", "Rh", "Ir", "Pr", "Fe", "Ru", "Os", "Mn", "Re", "Cr", "Mo",
"W", "V", "U", "Tb", "Y", "Be", "Mg", "Ca", "Li", "K", "ATM"]
# these atomic numbers are incorrect, but keeping for fold&dock3 and correcting it
# in util.writepdb() during output.
self.atom_num= [
9, 17, 35, 53, 8, 16, 34, 52, 7, 15, 33, 51,
6, 14, 32, 50, 82, 5, 13, 30, 80, 29, 79, 28,
46, 78, 27, 45, 77, 26, 44, 76, 25, 75, 24, 42,
23, 74, 92, 65, 39, 4, 12, 20, 3, 19, 0] # in same order as frame priority
self.atom2frame_priority = {x:i for i,x in enumerate(self.frame_priority2atom)}
self.atomnum2atomtype = dict(zip(self.atom_num, self.frame_priority2atom))
self.atomtype2atomnum = {v:k for k,v in self.atomnum2atomtype.items()}
self.to1letter = {
"ALA":'A', "ARG":'R', "ASN":'N', "ASP":'D', "CYS":'C',
"GLN":'Q', "GLU":'E', "GLY":'G', "HIS":'H', "ILE":'I',
"LEU":'L', "LYS":'K', "MET":'M', "PHE":'F', "PRO":'P',
"SER":'S', "THR":'T', "TRP":'W', "TYR":'Y', "VAL":'V',
"DA":'a', "DC":'c', "DG":'g', "DT":'t',
"A":'b', "C":'d', "G":'h', "U":'u',
}
# this is taken from a query string for a link named "metals in PDB" on BioLiP website
# hopefully they put a lot of thought into it
self.METAL_RES_NAMES = ['LA','NI','3CO','K','CR','ZN','CD','PD','TB','YT3','OS','EU','NA','RB','W','YB','HO3',
'CE','MN','TL','LI','MN3','AU3','AU','EU3','AL','3NI','FE2','PT','FE','CA','AG','CU1',
'LU','HG','CO','SR','MG','PB','CS','GA','BA','SM','SB','CU','MO','CU2']
# full sc atom representation
if (not params.use_phospate_frames_for_NA):
# USE RIBOSE FRAME
self.aa2long=[
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), #0 ala
(" N "," CA "," C "," O "," CB "," CG "," CD "," NE "," CZ "," NH1"," NH2", None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD "," HE ","1HH1","2HH1","1HH2","2HH2"), #1 arg
(" N "," CA "," C "," O "," CB "," CG "," OD1"," ND2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD2","2HD2", None, None, None, None, None, None, None), #2 asn
(" N "," CA "," C "," O "," CB "," CG "," OD1"," OD2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ", None, None, None, None, None, None, None, None, None), #3 asp
(" N "," CA "," C "," O "," CB "," SG ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB "," HG ", None, None, None, None, None, None, None, None), #4 cys
(" N "," CA "," C "," O "," CB "," CG "," CD "," OE1"," NE2", None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HE2","2HE2", None, None, None, None, None), #5 gln
(" N "," CA "," C "," O "," CB "," CG "," CD "," OE1"," OE2", None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ", None, None, None, None, None, None, None), #6 glu
(" N "," CA "," C "," O ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H ","1HA ","2HA ", None, None, None, None, None, None, None, None, None, None), #7 gly
(" N "," CA "," C "," O "," CB "," CG "," ND1"," CD2"," CE1"," NE2", None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","2HD ","1HE ","2HE ", None, None, None, None, None, None), #8 his
(" N "," CA "," C "," O "," CB "," CG1"," CG2"," CD1", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA "," HB ","1HG2","2HG2","3HG2","1HG1","2HG1","1HD1","2HD1","3HD1", None, None), #9 ile
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB "," HG ","1HD1","2HD1","3HD1","1HD2","2HD2","3HD2", None, None), #10 leu
(" N "," CA "," C "," O "," CB "," CG "," CD "," CE "," NZ ", None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD ","1HE ","2HE ","1HZ ","2HZ ","3HZ "), #11 lys
(" N "," CA "," C "," O "," CB "," CG "," SD "," CE ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HE ","2HE ","3HE ", None, None, None, None), #12 met
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," CE1"," CE2"," CZ ", None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","2HD ","1HE ","2HE "," HZ ", None, None, None, None), #13 phe
(" N "," CA "," C "," O "," CB "," CG "," CD ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD ", None, None, None, None, None, None), #14 pro
(" N "," CA "," C "," O "," CB "," OG ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HG "," HA ","1HB ","2HB ", None, None, None, None, None, None, None, None), #15 ser
(" N "," CA "," C "," O "," CB "," OG1"," CG2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HG1"," HA "," HB ","1HG2","2HG2","3HG2", None, None, None, None, None, None), #16 thr
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," CE2"," CE3"," NE1"," CZ2"," CZ3"," CH2", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","1HE "," HZ2"," HH2"," HZ3"," HE3", None, None, None), #17 trp
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," CE1"," CE2"," CZ "," OH ", None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","1HE ","2HE ","2HD "," HH ", None, None, None, None), #18 tyr
(" N "," CA "," C "," O "," CB "," CG1"," CG2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA "," HB ","1HG1","2HG1","3HG1","1HG2","2HG2","3HG2", None, None, None, None), #19 val
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), #20 unk
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), #21 mask
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," N9 "," C4 "," N3 "," C2 "," N1 "," C6 "," C5 "," N7 "," C8 "," N6 ", None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H2 "," H61"," H62"," H8 ", None, None), #22 DA
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," N1 "," C2 "," O2 "," N3 "," C4 "," N4 "," C5 "," C6 ", None, None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H42"," H41"," H5 "," H6 ", None, None), #23 DC
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," N9 "," C4 "," N3 "," C2 "," N1 "," C6 "," C5 "," N7 "," C8 "," N2 "," O6 ", None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H1 "," H22"," H21"," H8 ", None, None), #24 DG
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," N1 "," C2 "," O2 "," N3 "," C4 "," O4 "," C5 "," C7 "," C6 ", None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H3 "," H71"," H72"," H73"," H6 ", None), #25 DT
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'", None, None, None, None, None, None, None, None, None, None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'", None, None, None, None, None, None), #26 DX (unk DNA)
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'"," N1 "," C2 "," N3 "," C4 "," C5 "," C6 "," N6 "," N7 "," C8 "," N9 ", None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H2 "," H61"," H62"," H8 ", None, None), #27 A
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'"," N1 "," C2 "," O2 "," N3 "," C4 "," N4 "," C5 "," C6 ", None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H42"," H41"," H5 "," H6 ", None, None), #28 C
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'"," N1 "," C2 "," N2 "," N3 "," C4 "," C5 "," C6 "," O6 "," N7 "," C8 "," N9 "," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H1 "," H22"," H21"," H8 ", None, None), #29 G
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'"," N1 "," C2 "," O2 "," N3 "," C4 "," O4 "," C5 "," C6 ", None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H3 "," H5 "," H6 ", None, None, None), #30 U
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'", None, None, None, None, None, None, None, None, None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'", None, None, None, None, None, None), #31 RX (unk RNA)
(" N "," CA "," C "," O "," CB "," CG "," NE2"," CD2"," CE1"," ND1", None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","2HD ","1HE ","1HD ", None, None, None, None, None, None), #-1 his_d
]
# build the "alternate" sc mapping
self.aa2longalt=[
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None, 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, None, None, None, None, None, None, 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, None, None, None, 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, None, None, None, 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, None, 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, None, None, None, None, 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, None, None, None, None, 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, 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, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","2HD ","1HE ","2HE ", None, None, None, None, None, None), # his
(" N "," CA "," C "," O "," CB "," CG1"," CG2"," CD1", None, None, None, None, None, None, None, None, None, 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, None, None, None, 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, None, None, None, None, 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, None, None, None, 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, None, None, None, None, None, None, None, None, None," H ","2HD ","2HE "," HZ ","1HE ","1HD "," HA ","1HB ","2HB ", None, None, None, None), # phe
(" N "," CA "," C "," O "," CB "," CG "," CD ", None, None, None, None, None, None, None, None, None, 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, None, 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, None, None, 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"," CE2"," CE3"," NE1"," CZ2"," CZ3"," CH2", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","1HE "," HZ2"," HH2"," HZ3"," HE3", None, None, None), # trp
(" N "," CA "," C "," O "," CB "," CG "," CD2"," CD1"," CE2"," CE1"," CZ "," OH ", None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","2HD ","2HE ","1HE ","1HD "," HH ", None, None, None, None), # tyr
(" N "," CA "," C "," O "," CB "," CG1"," CG2", None, None, None, None, None, None, None, None, None, 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, 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, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), # mask
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," N9 "," C4 "," N3 "," C2 "," N1 "," C6 "," C5 "," N7 "," C8 "," N6 ", None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H2 "," H61"," H62"," H8 ", None, None), #22 DA
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," N1 "," C2 "," O2 "," N3 "," C4 "," N4 "," C5 "," C6 ", None, None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H42"," H41"," H5 "," H6 ", None, None), #23 DC
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," N9 "," C4 "," N3 "," C2 "," N1 "," C6 "," C5 "," N7 "," C8 "," N2 "," O6 ", None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H1 "," H22"," H21"," H8 ", None, None), #24 DG
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," N1 "," C2 "," O2 "," N3 "," C4 "," O4 "," C5 "," C7 "," C6 ", None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H3 "," H71"," H72"," H73"," H6 ", None), #25 DT
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'", None, None, None, None, None, None, None, None, None, None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'", None, None, None, None, None, None), #26 DX (unk DNA)
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'"," N1 "," C2 "," N3 "," C4 "," C5 "," C6 "," N6 "," N7 "," C8 "," N9 ", None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H2 "," H61"," H62"," H8 ", None, None), #27 A
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'"," N1 "," C2 "," O2 "," N3 "," C4 "," N4 "," C5 "," C6 ", None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H42"," H41"," H5 "," H6 ", None, None), #28 C
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'"," N1 "," C2 "," N2 "," N3 "," C4 "," C5 "," C6 "," O6 "," N7 "," C8 "," N9 "," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H1 "," H22"," H21"," H8 ", None, None), #29 G
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'"," N1 "," C2 "," O2 "," N3 "," C4 "," O4 "," C5 "," C6 ", None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H3 "," H5 "," H6 ", None, None, None), #30 U
(" O4'"," C1'"," C2'"," OP1"," P "," OP2"," O5'"," C5'"," C4'"," C3'"," O3'"," O2'", None, None, None, None, None, None, None, None, None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'", None, None, None, None, None, None), #31 RX (unk RNA)
]
self.aa2type = [
("Nbb", "CAbb","CObb","OCbb","CH3", None, None, None, None, None, None, None, None, None, 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, None, None, None, None, None, None, 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, None, None, None, 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, None, None, None, 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, None, 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, None, None, None, None, 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, None, None, None, None, 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, 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, None, None, None, None, None, 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, None, None, None, 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, None, None, None, 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, None, None, None, None, 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, None, None, None, 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, None, None, None, None, None, None, 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, None, None, 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, None, 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, None, None, 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", "CH0", "aroC","Ntrp","aroC","aroC","aroC", None, None, None, None, None, None, None, None, None,"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, None, None, None, None, None, None, None, 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, None, None, 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, 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, None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None, None, None), # mask
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "Npro","aroC","Nhis","aroC","Nhis","aroC","aroC","Nhis","aroC","NH2O", None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Haro","Hpol","Hpol","Haro", None, None), # DA
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "Npro","CObb","OCbb","Nhis","aroC","NH2O","aroC","aroC", None, None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hpol","Haro","Haro", None, None), # DC
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "Npro","aroC","Nhis","aroC","Ntrp","CObb","aroC","Nhis","aroC","NH2O","OCbb", None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hpol","Hpol","Haro", None, None), # DG
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "Npro","CObb","OCbb","Ntrp","CObb","OCbb","aroC","CH3", "aroC", None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Hapo","Hapo","Haro", None), # DT
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", None, None, None, None, None, None, None, None, None, None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None), # DX (unk DNA)
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "OH", "Nhis","aroC","Nhis","aroC","aroC","aroC","NH2O","Nhis","aroC","Npro", None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Haro","Hpol","Hpol","Haro", None, None), # A
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "OH", "Npro","CObb","OCbb","Nhis","aroC","NH2O","aroC","aroC", None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Hpol","Hpol","Haro","Haro", None, None), # C
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "OH", "Ntrp","aroC","NH2O","Nhis","aroC","aroC","CObb","OCbb","Nhis","aroC","Npro","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Hpol","Hpol","Hpol","Haro", None, None), # G
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "OH", "Npro","CObb","OCbb","Ntrp","CObb","OCbb","aroC","aroC", None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Hpol","Hapo","Haro", None, None, None), # U
("Oet3", "CH1","CH2","OOC","Phos", "OOC", "Oet2","CH2", "CH1", "CH1", "Oet2", "OH", None, None, None, None, None, None, None, None, None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo", None, None, None, None, None, None), # RX (unk RNA)
("Nbb", "CAbb","CObb","OCbb","CH2", "CH0", "Nhis","aroC","aroC","Ntrp", None, None, None, None, None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hpol","Hapo","Hapo", None, None, None, None, None, None), # HIS-D NOT CORRECT!!!!!!!!!!
(None, "genAl", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Al
(None, "genAs", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # As
(None, "genAu", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Au
(None, "genB", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # B
(None, "genBe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Be
(None, "genBr", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Br
(None, "genC", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # C
(None, "genCa", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Ca
(None, "genCl", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Cl
(None, "genCo", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Co
(None, "genCr", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Cr
(None, "genCu", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Cu
(None, "genF", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # F
(None, "genFe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Fe
(None, "genHg", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Hg
(None, "genI", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # I
(None, "genIr", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Ir
(None, "genK", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # K
(None, "genLi", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Li
(None, "genMg", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Mg
(None, "genMn", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Mn
(None, "genMo", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Mo
(None, "genN", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # N
(None, "genNi", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Ni
(None, "genO", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # O
(None, "genOs", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Os
(None, "genP", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # P
(None, "genPb", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Pb
(None, "genPd", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Pd
(None, "genPr", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Pr
(None, "genPt", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Pt
(None, "genRe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Re
(None, "genRh", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Rh
(None, "genRu", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Ru
(None, "genS", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # S
(None, "genSb", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Sb
(None, "genSe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Se
(None, "genSi", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Si
(None, "genSn", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Sn
(None, "genTb", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Tb
(None, "genTe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Te
(None, "genU", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # U
(None, "genW", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # W
(None, "genV", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # V
(None, "genY", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Y
(None, "genZn", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Zn
(None, "genATM", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # ATM
]
self.aa2elt = [
("N","C","C","O","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#ala
("N","C","C","O","C","C","C","N","C","N","N",None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H","H","H"),#arg
("N","C","C","O","C","C","O","N",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H",None,None,None,None,None,None,None),#asn
("N","C","C","O","C","C","O","O",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H",None,None,None,None,None,None,None,None,None),#asp
("N","C","C","O","C","S",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#cys
("N","C","C","O","C","C","C","O","N",None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H",None,None,None,None,None),#gln
("N","C","C","O","C","C","C","O","O",None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H",None,None,None,None,None,None,None),#glu
("N","C","C","O",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H",None,None,None,None,None,None,None,None,None,None),#gly
("N","C","C","O","C","C","N","C","C","N",None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H",None,None,None,None,None,None),#his
("N","C","C","O","C","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#ile
("N","C","C","O","C","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#leu
("N","C","C","O","C","C","C","C","N",None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H","H","H"),#lys
("N","C","C","O","C","C","S","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H",None,None,None,None),#met
("N","C","C","O","C","C","C","C","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H",None,None,None,None),#phe
("N","C","C","O","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H",None,None,None,None,None,None),#pro
("N","C","C","O","C","O",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#ser
("N","C","C","O","C","O","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H",None,None,None,None,None,None),#thr
("N","C","C","O","C","C","C","C","C","C","N","C","C","C",None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H",None,None,None),#trp
("N","C","C","O","C","C","C","C","C","C","C","O",None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H",None,None,None,None),#tyr
("N","C","C","O","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H",None,None,None,None),#val
("N","C","C","O","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#unk
("N","C","C","O","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#mask
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"N" ,"C" ,"N" ,"C" ,"N" ,"C" ,"C" ,"N" ,"C" ,"N" ,None,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None),#DA
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"N" ,"C" ,"O" ,"N" ,"C" ,"N" ,"C" ,"C" ,None,None,None,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None),#DC
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"N" ,"C" ,"N" ,"C" ,"N", "C" ,"C" ,"N" ,"C" ,"N" ,"O" ,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None),#DG
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"N" ,"C" ,"O" ,"N" ,"C" ,"O" ,"C" ,"C" ,"C" ,None,None,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None),#DT
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,None,None,None,None,None,None,None,None,None,None,None,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None,None,None,None,None),#DX
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"O" ,"N" ,"C" ,"N" ,"C" ,"C" ,"C" ,"N" ,"N" ,"C" ,"N" ,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None),#A
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"O" ,"N" ,"C" ,"O" ,"N" ,"C" ,"N" ,"C" ,"C" ,None,None,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None),#C
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"O" ,"N" ,"C" ,"N" ,"N" ,"C" ,"C" ,"C" ,"O" ,"N" ,"C" ,"N" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None),#G
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"O" ,"N" ,"C" ,"O" ,"N" ,"C" ,"O" ,"C" ,"C" ,None,None,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None,None),#U
("O" ,"C" ,"C" ,"O" ,"P" ,"O" ,"O" ,"C" ,"C" ,"C" ,"O" ,"O" ,None,None,None,None,None,None,None,None,None,None,None,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,"H" ,None,None,None,None,None),#RX
]
# frames for generic FAPE
##NOTE: 1st entry must be "backbone frame"
self.frames=[
[ [" N "," CA "," C "],[" CA "," C "," O "] ], # ala
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "], [" CG "," CD "," NE "] ], # arg
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # asn
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # asp
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "] ], # cys
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "] ], # gln
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "] ], # glu
[ [" N "," CA "," C "],[" CA "," C "," O "] ], # gly
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # his
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG1"] ], # ile
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # leu
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "], [" CG "," CD "," CE "] ], # lys
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," SD "] ], # met
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # phe
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "]], # pro
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," OG "] ], # ser
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," OG1"] ], # thr
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # trp
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # tyr
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "] ], # val
[ [" N "," CA "," C "],[" CA "," C "," O "] ], # unk
[ [" N "," CA "," C "],[" CA "," C "," O "] ], # mask
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N9 "], [" C4'"," C3'"," O3'"] ], #DA
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N1 "], [" C4'"," C3'"," O3'"] ], #DC
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N9 "], [" C4'"," C3'"," O3'"] ], #DG
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N1 "], [" C4'"," C3'"," O3'"] ], #DT
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C4'"," C3'"," O3'"] ], #DX
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N9 "], [" C4'"," C3'"," O3'"] ], #A
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N1 "], [" C4'"," C3'"," O3'"] ], #C
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N9 "], [" C4'"," C3'"," O3'"] ], #G
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N1 "], [" C4'"," C3'"," O3'"] ], #U
[ [" O4'"," C1'"," C2'"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C4'"," C3'"," O3'"] ], #RX
]
#fd Rosetta ideal coords
#fd - uses same "frame-building" as AF2
# FRAMES:
# base = 0
# omega/phi/psi = 1-3 (omega unused)
# chi_1-4(prot) = 4-7
# CB_bend = 8
# NA alpha/beta/gamma/delta = 9-12 (NA epsilon/zeta no frame)
# NA nu2/nu1/nu0 = 13-15
# chi_1(NA) = 16
self.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)],
['1HE ', 5, (2.8542, 1.5693, 0.000)],
['2HD ', 5, ( 0.6584, -2.0835, 0.000) ],
[' ND1', 6, (-1.8631, -1.0722, 0.000)],
[' NE2', 6, (-1.8625, 1.0707, 0.000)],
['2HE ', 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)],
['1HD ', 5, (0.1613, 2.1362, 0.000)],
['2HD ', 5, (0.1621, -2.1360, 0.000)],
['1HE ', 5, (2.6335, 2.1384, 0.000)],
['2HE ', 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)],
['1HD ', 5, (0.4722, 2.1252, 0.000)],
['1HE ', 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)],
['1HD ', 5, (0.1485, 2.1455, 0.000)],
['2HD ', 5, (0.1484, -2.1451, 0.000)],
['1HE ', 5, (2.6200, 2.1450, 0.000)],
['2HE ', 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)],
],
[ # 22 DA
[" O4'",0, (-0.3894, 1.3649, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5186, 0.0000, 0.0000)],
[" N9 ",0, (-0.5962, -0.6345, -1.1746)],
[" H1'",0, (-0.3458, -0.5730, 0.8726)],
[" C3'",14, (0.3241, 1.4829, 0.000)],
[" H2'",14, (0.4107, -0.5097, -0.8844)],
["H2''",14, (0.4106, -0.5096, 0.8840)],
[" C4'",13, (0.3513, 1.4879, 0.000)],
[" O3'",13, (0.5035, -0.6292, 1.1839)],
[" H3'",13, (0.4310, -0.5496, -0.8502)],
[" C5'",12, (0.63111, 1.3722, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.4966, 1.3523, 0.000)],
[" H5'",11, (0.3740, -0.5366, 0.8839)],
["H5''",11, (0.3748, -0.5365, -0.8842)],
[" P ",10, (0.81940, 1.3660, 0.000)],
[" OP1", 9, (0.4669, 1.4096, 0.000)],
[" OP2", 9, (0.4615, -0.9241, 1.0676)],
[" C4 ",16, (0.8119, 1.1084, 0.0000)],
[" N3 ",16, (0.4328, 2.3976, 0.0000)],
[" C2 ",16, (1.4957, 3.1983, 0.0000)],
[" N1 ",16, (2.7960, 2.8816, 0.0000)],
[" C6 ",16, (3.1433, 1.5760, 0.0000)],
[" C5 ",16, (2.1084, 0.6255, 0.0000)],
[" N7 ",16, (2.1145, -0.7627, 0.0000)],
[" C8 ",16, (0.8438, -1.0825, 0.0000)],
[" N6 ",16, (4.4402, 1.2598, 0.0000)],
[" H2 ",16, (1.2740, 4.2755, 0.0000)],
[" H8 ",16, (0.4867, -2.1227, 0.0000)],
[" H61",16, (5.1313, 1.9828, 0.0000)],
[" H62",16, (4.7211, 0.3001, 0.0000)],
],
[ # 23 DC
[" O4'",0, (-0.3894, 1.3649, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5186, 0.0000, 0.0000)],
[" N1 ",0, (-0.5962, -0.6345, -1.1746)],
[" H1'",0, (-0.3458, -0.5730, 0.8726)],
[" C3'",14, (0.3241, 1.4829, 0.000)],
[" H2'",14, (0.4107, -0.5097, -0.8844)],
["H2''",14, (0.4106, -0.5096, 0.8840)],
[" C4'",13, (0.3513, 1.4879, 0.000)],
[" O3'",13, (0.5035, -0.6292, 1.1839)],
[" H3'",13, (0.4310, -0.5496, -0.8502)],
[" C5'",12, (0.63111, 1.3722, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.4966, 1.3523, 0.000)],
[" H5'",11, (0.3740, -0.5366, 0.8839)],
["H5''",11, (0.3748, -0.5365, -0.8842)],
[" P ",10, (0.81940, 1.3660, 0.000)],
[" OP1", 9, (0.4669, 1.4096, 0.000)],
[" OP2", 9, (0.4615, -0.9241, 1.0676)],
[" C2 ",16, (0.6758, 1.2249, 0.0000)],
[" O2 ",16, (0.0158, 2.2756, 0.0000)],
[" N3 ",16, (2.0283, 1.2334, 0.0000)],
[" C4 ",16, (2.7022, 0.0815, 0.0000)],
[" N4 ",16, (4.0356, 0.1372, 0.0000)],
[" C5 ",16, (2.0394, -1.1794, 0.0000)],
[" C6 ",16, (0.7007, -1.1745, 0.0000)],
[" H42",16, (4.5715, -0.7074, 0.0000)],
[" H41",16, (4.4992, 1.0229, 0.0000)],
[" H5 ",16, (2.6061, -2.1225, 0.0000)],
[" H6 ",16, (0.1563, -2.1302, 0.0000)],
],
[ # 24 DG
[" O4'",0, (-0.3894, 1.3649, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5186, 0.0000, 0.0000)],
[" N9 ",0, (-0.5962, -0.6345, -1.1746)],
[" H1'",0, (-0.3458, -0.5730, 0.8726)],
[" C3'",14, (0.3241, 1.4829, 0.000)],
[" H2'",14, (0.4107, -0.5097, -0.8844)],
["H2''",14, (0.4106, -0.5096, 0.8840)],
[" C4'",13, (0.3513, 1.4879, 0.000)],
[" O3'",13, (0.5035, -0.6292, 1.1839)],
[" H3'",13, (0.4310, -0.5496, -0.8502)],
[" C5'",12, (0.63111, 1.3722, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.4966, 1.3523, 0.000)],
[" H5'",11, (0.3740, -0.5366, 0.8839)],
["H5''",11, (0.3748, -0.5365, -0.8842)],
[" P ",10, (0.81940, 1.3660, 0.000)],
[" OP1", 9, (0.4669, 1.4096, 0.000)],
[" OP2", 9, (0.4615, -0.9241, 1.0676)],
[" C4 ",16, (0.8171, 1.1043, 0.0000)],
[" N3 ",16, (0.4110, 2.3918, 0.0000)],
[" C2 ",16, (1.4330, 3.2319, 0.0000)],
[" N1 ",16, (2.7493, 2.8397, 0.0000)],
[" C6 ",16, (3.1894, 1.5195, 0.0000)],
[" C5 ",16, (2.1029, 0.6070, 0.0000)],
[" N7 ",16, (2.0942, -0.7800, 0.0000)],
[" C8 ",16, (0.8285, -1.0956, 0.0000)],
[" N2 ",16, (1.2085, 4.5537, 0.0000)],
[" O6 ",16, (4.4017, 1.2743, 0.0000)],
[" H1 ",16, (3.4453, 3.5579, 0.0000)],
[" H8 ",16, (0.4623, -2.1330, 0.0000)],
[" H22",16, (0.2708, 4.9015, 0.0000)],
[" H21",16, (1.9785, 5.1920, 0.0000)],
],
[ # 25 DT
[" O4'",0, (-0.3894, 1.3649, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5186, 0.0000, 0.0000)],
[" N1 ",0, (-0.5962, -0.6345, -1.1746)],
[" H1'",0, (-0.3458, -0.5730, 0.8726)],
[" C3'",14, (0.3241, 1.4829, 0.000)],
[" H2'",14, (0.4107, -0.5097, -0.8844)],
["H2''",14, (0.4106, -0.5096, 0.8840)],
[" C4'",13, (0.3513, 1.4879, 0.000)],
[" O3'",13, (0.5035, -0.6292, 1.1839)],
[" H3'",13, (0.4310, -0.5496, -0.8502)],
[" C5'",12, (0.63111, 1.3722, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.4966, 1.3523, 0.000)],
[" H5'",11, (0.3740, -0.5366, 0.8839)],
["H5''",11, (0.3748, -0.5365, -0.8842)],
[" P ",10, (0.81940, 1.3660, 0.000)],
[" OP1", 9, (0.4669, 1.4096, 0.000)],
[" OP2", 9, (0.4615, -0.9241, 1.0676)],
[" C2 ",16, (0.6495, 1.2140, 0.0000)],
[" O2 ",16, (0.0636, 2.2854, 0.0000)],
[" N3 ",16, (2.0191, 1.1297, 0.0000)],
[" C4 ",16, (2.7859, -0.0198, 0.0000)],
[" O4 ",16, (4.0113, 0.0622, 0.0000)],
[" C5 ",16, (2.0397, -1.2580, 0.0000)],
[" C7 ",16, (2.7845, -2.5550, 0.0000)],
[" C6 ",16, (0.7021, -1.1863, 0.0000)],
[" H3 ",16, (2.5175, 1.9968, 0.0000)],
[" H71",16, (2.0680, -3.3898, 0.0000)],
[" H72",16, (3.4147, -2.6153, -0.9071)],
[" H73",16, (3.4193, -2.6153, 0.8885)],
[" H6 ",16, (0.1317, -2.1273, 0.0000)],
],
[ # 26 DX
[" O4'",0, (-0.3894, 1.3649, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5186, 0.0000, 0.0000)],
[" H1'",0, (-0.3458, -0.5730, 0.8726)],
[" C3'",14, (0.3241, 1.4829, 0.000)],
[" H2'",14, (0.4107, -0.5097, -0.8844)],
["H2''",14, (0.4106, -0.5096, 0.8840)],
[" C4'",13, (0.3513, 1.4879, 0.000)],
[" O3'",13, (0.5035, -0.6292, 1.1839)],
[" H3'",13, (0.4310, -0.5496, -0.8502)],
[" C5'",12, (0.63111, 1.3722, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.4966, 1.3523, 0.000)],
[" H5'",11, (0.3740, -0.5366, 0.8839)],
["H5''",11, (0.3748, -0.5365, -0.8842)],
[" P ",10, (0.81940, 1.3660, 0.000)],
[" OP1", 9, (0.4669, 1.4096, 0.000)],
[" OP2", 9, (0.4615, -0.9241, 1.0676)],
],
[ # 27 A
[" O4'",0, (-0.4082, 1.3525, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5292, 0.0000, 0.0000)],
[" N9 ",0, (-0.5661, -0.6642, -1.1894)],
[" H1'",0, (-0.3326, -0.4415, 0.8101)],
[" C3'",14, (0.3028, 1.4927, 0.000)],
[" H2'",14, (0.3582, -0.4393, -0.7998)],
[" O2'",14, (0.4613, -0.6189, 1.1921)],
["HO2'",14, (0.2499, -1.5749, 1.1568)],
[" C4'",13, (0.3316, 1.4845, 0.000)],
[" O3'",13, (0.5685, -0.6954, 1.0960)],
[" H3'",13, (0.3202, -0.4010, -0.8356)],
[" C5'",12, (0.6616, 1.3553, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.5217, 1.3206, 0.000)],
[" H5'",11, (0.3193, -0.4703, 0.7986)],
["H5''",11, (0.3199, -0.4711, -0.7970)],
[" P ",10, (0.8180, 1.3676, 0.000)],
[" OP1", 9, (0.4594, 1.4113, 0.000)],
[" OP2", 9, (0.4582, -0.9215, 1.0698)],
[" N1 ",16, (2.7963, 2.8824, 0.0000)],
[" C2 ",16, (1.4955, 3.2007, 0.0000)],
[" N3 ",16, (0.4333, 2.3980, 0.0000)],
[" C4 ",16, (0.8127, 1.1078, 0.0000)],
[" C5 ",16, (2.1082, 0.6254, 0.0000)],
[" C6 ",16, (3.1432, 1.5774, 0.0000)],
[" N6 ",16, (4.4400, 1.2609, 0.0000)],
[" N7 ",16, (2.1146, -0.7630, 0.0000)],
[" C8 ",16, (0.8442, -1.0830, 0.0000)],
[" H2 ",16, (1.2972, 4.1608, 0.0000)],
[" H61",16, (5.1172, 1.9697, 0.0000)],
[" H62",16, (4.7154, 0.3206, 0.0000)],
[" H8 ",16, (0.5258, -2.0104, 0.0000)],
],
[ # 28 C
[" O4'",0, (-0.4082, 1.3525, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5292, 0.0000, 0.0000)],
[" N1 ",0, (-0.5661, -0.6642, -1.1894)],
[" H1'",0, (-0.3326, -0.4415, 0.8101)],
[" C3'",14, (0.3028, 1.4927, 0.000)],
[" H2'",14, (0.3582, -0.4393, -0.7998)],
[" O2'",14, (0.4613, -0.6189, 1.1921)],
["HO2'",14, (0.2499, -1.5749, 1.1568)],
[" C4'",13, (0.3316, 1.4845, 0.000)],
[" O3'",13, (0.5685, -0.6954, 1.0960)],
[" H3'",13, (0.3202, -0.4010, -0.8356)],
[" C5'",12, (0.6616, 1.3553, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.5217, 1.3206, 0.000)],
[" H5'",11, (0.3193, -0.4703, 0.7986)],
["H5''",11, (0.3199, -0.4711, -0.7970)],
[" P ",10, (0.8180, 1.3676, 0.000)],
[" OP1", 9, (0.4594, 1.4113, 0.000)],
[" OP2", 9, (0.4582, -0.9215, 1.0698)],
[" C2 ",16, (0.6650, 1.2325, 0.0000)],
[" O2 ",16, (-0.0001, 2.2799, 0.0000)],
[" N3 ",16, (2.0175, 1.2603, 0.0000)],
[" C4 ",16, (2.7090, 0.1210, 0.0000)],
[" N4 ",16, (4.0423, 0.1969, 0.0000)],
[" C5 ",16, (2.0635, -1.1476, 0.0000)],
[" C6 ",16, (0.7250, -1.1627, 0.0000)],
[" H42",16, (4.5791, -0.6226, 0.0000)],
[" H41",16, (4.4833, 1.0723, 0.0000)],
[" H5 ",16, (2.5806, -1.9803, 0.0000)],
[" H6 ",16, (0.2622, -2.0258, 0.0000)],
],
[ # 29 G
[" O4'",0, (-0.4082, 1.3525, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5292, 0.0000, 0.0000)],
[" N9 ",0, (-0.5661, -0.6642, -1.1894)],
[" H1'",0, (-0.3326, -0.4415, 0.8101)],
[" C3'",14, (0.3028, 1.4927, 0.000)],
[" H2'",14, (0.3582, -0.4393, -0.7998)],
[" O2'",14, (0.4613, -0.6189, 1.1921)],
["HO2'",14, (0.2499, -1.5749, 1.1568)],
[" C4'",13, (0.3316, 1.4845, 0.000)],
[" O3'",13, (0.5685, -0.6954, 1.0960)],
[" H3'",13, (0.3202, -0.4010, -0.8356)],
[" C5'",12, (0.6616, 1.3553, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.5217, 1.3206, 0.000)],
[" H5'",11, (0.3193, -0.4703, 0.7986)],
["H5''",11, (0.3199, -0.4711, -0.7970)],
[" P ",10, (0.8180, 1.3676, 0.000)],
[" OP1", 9, (0.4594, 1.4113, 0.000)],
[" OP2", 9, (0.4582, -0.9215, 1.0698)],
[" N1 ",16, (2.7458, 2.8461, 0.0000)],
[" C2 ",16, (1.4286, 3.2360, 0.0000)],
[" N2 ",16, (1.1989, 4.5575, 0.0000)],
[" N3 ",16, (0.4087, 2.3932, 0.0000)],
[" C4 ",16, (0.8167, 1.1068, 0.0000)],
[" C5 ",16, (2.1036, 0.6115, 0.0000)],
[" C6 ",16, (3.1883, 1.5266, 0.0000)],
[" O6 ",16, (4.4006, 1.2842, 0.0000)],
[" N7 ",16, (2.0980, -0.7759, 0.0000)],
[" C8 ",16, (0.8317, -1.0936, 0.0000)],
[" H1 ",16, (3.4279, 3.5496, 0.0000)],
[" H22",16, (0.2781, 4.8947, 0.0000)],
[" H21",16, (1.9487, 5.1879, 0.0000)],
[" H8 ",16, (0.5085, -2.0185, 0.0000)],
],
[ # 30 U
[" O4'",0, (-0.4082, 1.3525, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5292, 0.0000, 0.0000)],
[" N1 ",0, (-0.5661, -0.6642, -1.1894)],
[" H1'",0, (-0.3326, -0.4415, 0.8101)],
[" C3'",14, (0.3028, 1.4927, 0.000)],
[" H2'",14, (0.3582, -0.4393, -0.7998)],
[" O2'",14, (0.4613, -0.6189, 1.1921)],
["HO2'",14, (0.2499, -1.5749, 1.1568)],
[" C4'",13, (0.3316, 1.4845, 0.000)],
[" O3'",13, (0.5685, -0.6954, 1.0960)],
[" H3'",13, (0.3202, -0.4010, -0.8356)],
[" C5'",12, (0.6616, 1.3553, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.5217, 1.3206, 0.000)],
[" H5'",11, (0.3193, -0.4703, 0.7986)],
["H5''",11, (0.3199, -0.4711, -0.7970)],
[" P ",10, (0.8180, 1.3676, 0.000)],
[" OP1", 9, (0.4594, 1.4113, 0.000)],
[" OP2", 9, (0.4582, -0.9215, 1.0698)],
[" C2 ",16, (0.6307, 1.2305, 0.0000)],
[" O2 ",16, (0.0260, 2.2886, 0.0000)],
[" N3 ",16, (2.0031, 1.1816, 0.0000)],
[" C4 ",16, (2.7953, 0.0532, 0.0000)],
[" O4 ",16, (4.0212, 0.1751, 0.0000)],
[" C5 ",16, (2.0746, -1.1833, 0.0000)],
[" C6 ",16, (0.7378, -1.1648, 0.0000)],
[" H3 ",16, (2.4701, 2.0428, 0.0000)],
[" H5 ",16, (2.5579, -2.0361, 0.0000)],
[" H6 ",16, (0.2681, -2.0239, 0.0000)],
],
[ # 31 RX
[" O4'",0, (-0.4082, 1.3525, 0.0000)],
[" C1'",0, (0.0000, 0.0000, 0.0000)],
[" C2'",0, (1.5292, 0.0000, 0.0000)],
[" H1'",0, (-0.3326, -0.4415, 0.8101)],
[" C3'",14, (0.3028, 1.4927, 0.000)],
[" H2'",14, (0.3582, -0.4393, -0.7998)],
[" O2'",14, (0.4613, -0.6189, 1.1921)],
["HO2'",14, (0.2499, -1.5749, 1.1568)],
[" C4'",13, (0.3316, 1.4845, 0.000)],
[" O3'",13, (0.5685, -0.6954, 1.0960)],
[" H3'",13, (0.3202, -0.4010, -0.8356)],
[" C5'",12, (0.6616, 1.3553, 0.000)],
[" H4'",12, (0.3168, -0.5077, -0.7763)],
[" O5'",11, (0.5217, 1.3206, 0.000)],
[" H5'",11, (0.3193, -0.4703, 0.7986)],
["H5''",11, (0.3199, -0.4711, -0.7970)],
[" P ",10, (0.8180, 1.3676, 0.000)],
[" OP1", 9, (0.4594, 1.4113, 0.000)],
[" OP2", 9, (0.4582, -0.9215, 1.0698)],
],
]
else:
# USE PHOSPHATE FRAME
self.aa2long=[
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), #0 ala
(" N "," CA "," C "," O "," CB "," CG "," CD "," NE "," CZ "," NH1"," NH2", None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD "," HE ","1HH1","2HH1","1HH2","2HH2"), #1 arg
(" N "," CA "," C "," O "," CB "," CG "," OD1"," ND2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD2","2HD2", None, None, None, None, None, None, None), #2 asn
(" N "," CA "," C "," O "," CB "," CG "," OD1"," OD2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ", None, None, None, None, None, None, None, None, None), #3 asp
(" N "," CA "," C "," O "," CB "," SG ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB "," HG ", None, None, None, None, None, None, None, None), #4 cys
(" N "," CA "," C "," O "," CB "," CG "," CD "," OE1"," NE2", None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HE2","2HE2", None, None, None, None, None), #5 gln
(" N "," CA "," C "," O "," CB "," CG "," CD "," OE1"," OE2", None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ", None, None, None, None, None, None, None), #6 glu
(" N "," CA "," C "," O ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H ","1HA ","2HA ", None, None, None, None, None, None, None, None, None, None), #7 gly
(" N "," CA "," C "," O "," CB "," CG "," ND1"," CD2"," CE1"," NE2", None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","2HD ","1HE ","2HE ", None, None, None, None, None, None), #8 his
(" N "," CA "," C "," O "," CB "," CG1"," CG2"," CD1", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA "," HB ","1HG2","2HG2","3HG2","1HG1","2HG1","1HD1","2HD1","3HD1", None, None), #9 ile
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB "," HG ","1HD1","2HD1","3HD1","1HD2","2HD2","3HD2", None, None), #10 leu
(" N "," CA "," C "," O "," CB "," CG "," CD "," CE "," NZ ", None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD ","1HE ","2HE ","1HZ ","2HZ ","3HZ "), #11 lys
(" N "," CA "," C "," O "," CB "," CG "," SD "," CE ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HG ","2HG ","1HE ","2HE ","3HE ", None, None, None, None), #12 met
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," CE1"," CE2"," CZ ", None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","2HD ","1HE ","2HE "," HZ ", None, None, None, None), #13 phe
(" N "," CA "," C "," O "," CB "," CG "," CD ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," HA ","1HB ","2HB ","1HG ","2HG ","1HD ","2HD ", None, None, None, None, None, None), #14 pro
(" N "," CA "," C "," O "," CB "," OG ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HG "," HA ","1HB ","2HB ", None, None, None, None, None, None, None, None), #15 ser
(" N "," CA "," C "," O "," CB "," OG1"," CG2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HG1"," HA "," HB ","1HG2","2HG2","3HG2", None, None, None, None, None, None), #16 thr
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," CE2"," CE3"," NE1"," CZ2"," CZ3"," CH2", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","1HE "," HZ2"," HH2"," HZ3"," HE3", None, None, None), #17 trp
(" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," CE1"," CE2"," CZ "," OH ", None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","1HE ","2HE ","2HD "," HH ", None, None, None, None), #18 tyr
(" N "," CA "," C "," O "," CB "," CG1"," CG2", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA "," HB ","1HG1","2HG1","3HG1","1HG2","2HG2","3HG2", None, None, None, None), #19 val
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), #20 unk
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), #21 mask
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'"," N9 "," C4 "," N3 "," C2 "," N1 "," C6 "," C5 "," N7 "," C8 "," N6 ", None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H2 "," H61"," H62"," H8 ", None, None), #22 DA
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'"," N1 "," C2 "," O2 "," N3 "," C4 "," N4 "," C5 "," C6 ", None, None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H42"," H41"," H5 "," H6 ", None, None), #23 DC
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'"," N9 "," C4 "," N3 "," C2 "," N1 "," C6 "," C5 "," N7 "," C8 "," N2 "," O6 ", None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H1 "," H22"," H21"," H8 ", None, None), #24 DG
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'"," N1 "," C2 "," O2 "," N3 "," C4 "," O4 "," C5 "," C7 "," C6 ", None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H3 "," H71"," H72"," H73"," H6 ", None), #25 DT
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'", None, None, None, None, None, None, None, None, None, None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'", None, None, None, None, None, None), #26 DX (unk DNA)
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'"," N1 "," C2 "," N3 "," C4 "," C5 "," C6 "," N6 "," N7 "," C8 "," N9 ", None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H2 "," H61"," H62"," H8 ", None, None), #27 A
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'"," N1 "," C2 "," O2 "," N3 "," C4 "," N4 "," C5 "," C6 ", None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H42"," H41"," H5 "," H6 ", None, None), #28 C
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'"," N1 "," C2 "," N2 "," N3 "," C4 "," C5 "," C6 "," O6 "," N7 "," C8 "," N9 "," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H1 "," H22"," H21"," H8 ", None, None), #29 G
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'"," N1 "," C2 "," O2 "," N3 "," C4 "," O4 "," C5 "," C6 ", None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H3 "," H5 "," H6 ", None, None, None), #30 U
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'", None, None, None, None, None, None, None, None, None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'", None, None, None, None, None, None), #31 RX (unk RNA)
(" N "," CA "," C "," O "," CB "," CG "," NE2"," CD2"," CE1"," ND1", None, None, None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","2HD ","1HE ","1HD ", None, None, None, None, None, None), #-1 his_d
]
# build the "alternate" sc mapping
self.aa2longalt=[
(" N "," CA "," C "," O "," CB ", None, None, None, None, None, None, None, None, None, 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, None, None, None, None, None, None, 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, None, None, None, 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, None, None, None, 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, None, 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, None, None, None, None, 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, None, None, None, None, 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, 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, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","2HD ","1HE ","2HE ", None, None, None, None, None, None), # his
(" N "," CA "," C "," O "," CB "," CG1"," CG2"," CD1", None, None, None, None, None, None, None, None, None, 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, None, None, None, 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, None, None, None, None, 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, None, None, None, 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, None, None, None, None, None, None, None, None, None," H ","2HD ","2HE "," HZ ","1HE ","1HD "," HA ","1HB ","2HB ", None, None, None, None), # phe
(" N "," CA "," C "," O "," CB "," CG "," CD ", None, None, None, None, None, None, None, None, None, 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, None, 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, None, None, 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"," CE2"," CE3"," NE1"," CZ2"," CZ3"," CH2", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","1HE "," HZ2"," HH2"," HZ3"," HE3", None, None, None), # trp
(" N "," CA "," C "," O "," CB "," CG "," CD2"," CD1"," CE2"," CE1"," CZ "," OH ", None, None, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","2HD ","2HE ","1HE ","1HD "," HH ", None, None, None, None), # tyr
(" N "," CA "," C "," O "," CB "," CG1"," CG2", None, None, None, None, None, None, None, None, None, 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, 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, None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","3HB ", None, None, None, None, None, None, None, None), # mask
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'"," N9 "," C4 "," N3 "," C2 "," N1 "," C6 "," C5 "," N7 "," C8 "," N6 ", None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H2 "," H61"," H62"," H8 ", None, None), #22 DA
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'"," N1 "," C2 "," O2 "," N3 "," C4 "," N4 "," C5 "," C6 ", None, None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H42"," H41"," H5 "," H6 ", None, None), #23 DC
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'"," N9 "," C4 "," N3 "," C2 "," N1 "," C6 "," C5 "," N7 "," C8 "," N2 "," O6 ", None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H1 "," H22"," H21"," H8 ", None, None), #24 DG
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'"," N1 "," C2 "," O2 "," N3 "," C4 "," O4 "," C5 "," C7 "," C6 ", None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'"," H3 "," H71"," H72"," H73"," H6 ", None), #25 DT
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C2'"," C1'", None, None, None, None, None, None, None, None, None, None, None, None,"H5''"," H5'"," H4'"," H3'","H2''"," H2'"," H1'", None, None, None, None, None, None), #26 DX (unk DNA)
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'"," N1 "," C2 "," N3 "," C4 "," C5 "," C6 "," N6 "," N7 "," C8 "," N9 ", None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H2 "," H61"," H62"," H8 ", None, None), #27 A
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'"," N1 "," C2 "," O2 "," N3 "," C4 "," N4 "," C5 "," C6 ", None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H42"," H41"," H5 "," H6 ", None, None), #28 C
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'"," N1 "," C2 "," N2 "," N3 "," C4 "," C5 "," C6 "," O6 "," N7 "," C8 "," N9 "," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H1 "," H22"," H21"," H8 ", None, None), #29 G
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'"," N1 "," C2 "," O2 "," N3 "," C4 "," O4 "," C5 "," C6 ", None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'"," H3 "," H5 "," H6 ", None, None, None), #30 U
(" OP1"," P "," OP2"," O5'"," C5'"," C4'"," O4'"," C3'"," O3'"," C1'"," C2'"," O2'", None, None, None, None, None, None, None, None, None, None, None," H5'","H5''"," H4'"," H3'"," H2'","HO2'"," H1'", None, None, None, None, None, None), #31 RX (unk RNA)
]
self.aa2type = [
("Nbb", "CAbb","CObb","OCbb","CH3", None, None, None, None, None, None, None, None, None, 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, None, None, None, None, None, None, 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, None, None, None, 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, None, None, None, 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, None, 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, None, None, None, None, 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, None, None, None, None, 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, 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, None, None, None, None, None, 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, None, None, None, 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, None, None, None, 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, None, None, None, None, 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, None, None, None, 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, None, None, None, None, None, None, 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, None, None, 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, None, 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, None, None, 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", "CH0", "aroC","Ntrp","aroC","aroC","aroC", None, None, None, None, None, None, None, None, None,"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, None, None, None, None, None, None, None, 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, None, None, 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, 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, None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None, None, None), # mask
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH2", "CH1", "Npro","aroC","Nhis","aroC","Nhis","aroC","aroC","Nhis","aroC","NH2O", None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Haro","Hpol","Hpol","Haro", None, None), # DA
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH2", "CH1", "Npro","CObb","OCbb","Nhis","aroC","NH2O","aroC","aroC", None, None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hpol","Haro","Haro", None, None), # DC
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH2", "CH1", "Npro","aroC","Nhis","aroC","Ntrp","CObb","aroC","Nhis","aroC","NH2O","OCbb", None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hpol","Hpol","Haro", None, None), # DG
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH2", "CH1", "Npro","CObb","OCbb","Ntrp","CObb","OCbb","aroC","CH3", "aroC", None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Hapo","Hapo","Haro", None), # DT
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH2", "CH1", None, None, None, None, None, None, None, None, None, None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hapo","Hapo", None, None, None, None, None, None), # DX (unk DNA)
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH1", "CH2", "OH", "Nhis","aroC","Nhis","aroC","aroC","aroC","NH2O","Nhis","aroC","Npro", None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Haro","Hpol","Hpol","Haro", None, None), # A
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH1", "CH2", "OH", "Npro","CObb","OCbb","Nhis","aroC","NH2O","aroC","aroC", None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Hpol","Hpol","Haro","Haro", None, None), # C
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH1", "CH2", "OH", "Ntrp","aroC","NH2O","Nhis","aroC","aroC","CObb","OCbb","Nhis","aroC","Npro","Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Hpol","Hpol","Hpol","Haro", None, None), # G
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH1", "CH2", "OH", "Npro","CObb","OCbb","Ntrp","CObb","OCbb","aroC","aroC", None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo","Hpol","Hapo","Haro", None, None, None), # U
("OOC","Phos", "OOC", "Oet2","CH2", "CH1", "Oet3","CH1", "Oet2","CH1", "CH2", "OH", None, None, None, None, None, None, None, None, None, None, None,"Hapo","Hapo","Hapo","Hapo","Hapo","Hpol","Hapo", None, None, None, None, None, None), # RX (unk RNA)
("Nbb", "CAbb","CObb","OCbb","CH2", "CH0", "Nhis","aroC","aroC","Ntrp", None, None, None, None, None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hpol","Hapo","Hapo", None, None, None, None, None, None), # HIS-D NOT CORRECT!!!!!!!!!!
("Nbb", "CAbb","CObb","OCbb","CH2", "CH0", "Nhis","aroC","aroC","Ntrp", None, None, None, None, None, None, None, None, None, None, None, None, None,"HNbb","Hapo","Hapo","Hapo","Hpol","Hapo","Hapo", None, None, None, None, None, None), # HIS-D NOT CORRECT!!!!!!!!!!
(None, "genAl", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Al
(None, "genAs", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # As
(None, "genAu", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Au
(None, "genB", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # B
(None, "genBe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Be
(None, "genBr", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Br
(None, "genC", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # C
(None, "genCa", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Ca
(None, "genCl", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Cl
(None, "genCo", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Co
(None, "genCr", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Cr
(None, "genCu", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Cu
(None, "genF", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # F
(None, "genFe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Fe
(None, "genHg", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Hg
(None, "genI", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # I
(None, "genIr", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Ir
(None, "genK", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # K
(None, "genLi", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Li
(None, "genMg", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Mg
(None, "genMn", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Mn
(None, "genMo", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Mo
(None, "genN", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # N
(None, "genNi", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Ni
(None, "genO", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # O
(None, "genOs", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Os
(None, "genP", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # P
(None, "genPb", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Pb
(None, "genPd", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Pd
(None, "genPr", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Pr
(None, "genPt", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Pt
(None, "genRe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Re
(None, "genRh", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Rh
(None, "genRu", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Ru
(None, "genS", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # S
(None, "genSb", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Sb
(None, "genSe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Se
(None, "genSi", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Si
(None, "genSn", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Sn
(None, "genTb", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Tb
(None, "genTe", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Te
(None, "genU", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # U
(None, "genW", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # W
(None, "genV", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # V
(None, "genY", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Y
(None, "genZn", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # Zn
(None, "genATM", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None), # ATM
]
self.aa2elt = [
("N","C","C","O","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#ala
("N","C","C","O","C","C","C","N","C","N","N",None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H","H","H"),#arg
("N","C","C","O","C","C","O","N",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H",None,None,None,None,None,None,None),#asn
("N","C","C","O","C","C","O","O",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H",None,None,None,None,None,None,None,None,None),#asp
("N","C","C","O","C","S",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#cys
("N","C","C","O","C","C","C","O","N",None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H",None,None,None,None,None),#gln
("N","C","C","O","C","C","C","O","O",None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H",None,None,None,None,None,None,None),#glu
("N","C","C","O",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H",None,None,None,None,None,None,None,None,None,None),#gly
("N","C","C","O","C","C","N","C","C","N",None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H",None,None,None,None,None,None),#his
("N","C","C","O","C","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#ile
("N","C","C","O","C","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#leu
("N","C","C","O","C","C","C","C","N",None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H","H","H"),#lys
("N","C","C","O","C","C","S","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H",None,None,None,None),#met
("N","C","C","O","C","C","C","C","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H",None,None,None,None),#phe
("N","C","C","O","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H",None,None,None,None,None,None),#pro
("N","C","C","O","C","O",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#ser
("N","C","C","O","C","O","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H",None,None,None,None,None,None),#thr
("N","C","C","O","C","C","C","C","C","C","N","C","C","C",None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H","H",None,None,None),#trp
("N","C","C","O","C","C","C","C","C","C","C","O",None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H",None,None,None,None),#tyr
("N","C","C","O","C","C","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H","H",None,None,None,None),#val
("N","C","C","O","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#unk
("N","C","C","O","C",None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H",None,None,None,None,None,None,None,None),#mask
("O","P","O","O","C","C","O","C","O","C","C","N","C","N","C","N","C","C","N","C","N",None,None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#DA
("O","P","O","O","C","C","O","C","O","C","C","N","C","O","N","C","N","C","C",None,None,None,None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#DC
("O","P","O","O","C","C","O","C","O","C","C","N","C","N","C","N","C","C","N","C","N","O",None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#DG
("O","P","O","O","C","C","O","C","O","C","C","N","C","O","N","C","O","C","C","C",None,None,None,"H","H","H","H","H","H","H","H","H","H","H","H",None),#DT
("O","P","O","O","C","C","O","C","O","C","C",None,None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H",None,None,None,None,None,None),#DX
("O","P","O","O","C","C","O","C","O","C","C","O","N","C","N","C","C","C","N","N","C","N",None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#A
("O","P","O","O","C","C","O","C","O","C","C","O","N","C","O","N","C","N","C","C",None,None,None,"H","H","H","H","H","H","H","H","H","H","H",None,None),#C
("O","P","O","O","C","C","O","C","O","C","C","O","N","C","N","N","C","C","C","O","N","C","N","H","H","H","H","H","H","H","H","H","H","H",None,None),#G
("O","P","O","O","C","C","O","C","O","C","C","O","N","C","O","N","C","O","C","C",None,None,None,"H","H","H","H","H","H","H","H","H","H",None,None,None),#U
("O","P","O","O","C","C","O","C","O","C","C","O",None,None,None,None,None,None,None,None,None,None,None,"H","H","H","H","H","H","H","H",None,None,None,None,None),#RX
]
# frames for generic FAPE
##NOTE: 1st entry must be "backbone frame"
self.frames=[
[ [" N "," CA "," C "],[" CA "," C "," O "] ], # ala
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "], [" CG "," CD "," NE "] ], # arg
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # asn
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # asp
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "] ], # cys
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "] ], # gln
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "] ], # glu
[ [" N "," CA "," C "],[" CA "," C "," O "] ], # gly
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # his
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG1"] ], # ile
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # leu
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "], [" CG "," CD "," CE "] ], # lys
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," SD "] ], # met
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # phe
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "], [" CB "," CG "," CD "]], # pro
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," OG "] ], # ser
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," OG1"] ], # thr
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # trp
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "], [" CA "," CB "," CG "] ], # tyr
[ [" N "," CA "," C "],[" CA "," C "," O "],[" N "," CA "," CB "] ], # val
[ [" N "," CA "," C "],[" CA "," C "," O "] ], # unk
[ [" N "," CA "," C "],[" CA "," C "," O "] ], # mask
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N9 "], [" C4'"," C3'"," O3'"] ], #DA
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N1 "], [" C4'"," C3'"," O3'"] ], #DC
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N9 "], [" C4'"," C3'"," O3'"] ], #DG
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N1 "], [" C4'"," C3'"," O3'"] ], #DT
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C4'"," C3'"," O3'"] ], #DX
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N9 "], [" C4'"," C3'"," O3'"] ], #A
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N1 "], [" C4'"," C3'"," O3'"] ], #C
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N9 "], [" C4'"," C3'"," O3'"] ], #G
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C2'"," C1'"," N1 "], [" C4'"," C3'"," O3'"] ], #U
[ [" OP1"," P "," OP2"], [" OP1"," P "," O5'"], [" P "," O5'"," C5'"], [" O5'"," C5'"," C4'"], [" C5'"," C4'"," C3'"], [" C5'"," C4'"," O4'"], [" C4'"," O4'"," C1'"], [" C4'"," C3'"," O3'"] ], #RX
]
#fd Rosetta ideal coords
#fd - uses same "frame-building" as AF2
# FRAMES:
# base = 0
# omega/phi/psi = 1-3 (omega unused)
# chi_1-4(prot) = 4-7
# CB_bend = 8
# NA alpha/beta/gamma/delta = 9-12 (NA epsilon/zeta no frame)
# NA nu2/nu1/nu0 = 13-15
# chi_1(NA) = 16
self.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)],
['1HE ', 5, (2.8542, 1.5693, 0.000)],
['2HD ', 5, ( 0.6584, -2.0835, 0.000) ],
[' ND1', 6, (-1.8631, -1.0722, 0.000)],
[' NE2', 6, (-1.8625, 1.0707, 0.000)],
['2HE ', 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)],
['1HD ', 5, (0.1613, 2.1362, 0.000)],
['2HD ', 5, (0.1621, -2.1360, 0.000)],
['1HE ', 5, (2.6335, 2.1384, 0.000)],
['2HE ', 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)],
['1HD ', 5, (0.4722, 2.1252, 0.000)],
['1HE ', 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)],
['1HD ', 5, (0.1485, 2.1455, 0.000)],
['2HD ', 5, (0.1484, -2.1451, 0.000)],
['1HE ', 5, (2.6200, 2.1450, 0.000)],
['2HE ', 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)],
],
[ # 22 DA
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7411, 1.2354, 0.000)],
[" C4'",10, (0.5207, 1.4178, 0.000)],
[" H5'",10, (0.3748, -0.5360, -0.8839)],
["H5''",10, (0.3744, -0.5368, 0.8842)],
[" C3'",11, ( 0.6388, 1.3889, 0.000)],
[" H4'",11, ( 0.2823, -0.5105, 0.9326)],
[" O4'",11, (0.4804, -0.6610, -1.1947)],
[" C1'",13, (0.4913, 1.3316, 0.0000)],
[" H1'",14, (0.4561, -0.4898, 0.8726)],
[" N9 ",14, (0.4467, -0.7474, -1.1746)],
[" C2'",14, (0.4167, 1.4603, 0.0000)],
[" H2'",15, (0.4107, -0.5097, -0.8844)],
["H2''",15, (0.4106, -0.5096, 0.8840)],
[" O3'",12, ( 0.4966, 1.3432, 0.000)],
[" H3'",12, (0.4359, -0.4915, -0.8827)],
[" C4 ",16, (0.8119, 1.1084, 0.0000)],
[" N3 ",16, (0.4328, 2.3976, 0.0000)],
[" C2 ",16, (1.4957, 3.1983, 0.0000)],
[" N1 ",16, (2.7960, 2.8816, 0.0000)],
[" C6 ",16, (3.1433, 1.5760, 0.0000)],
[" C5 ",16, (2.1084, 0.6255, 0.0000)],
[" N7 ",16, (2.1145, -0.7627, 0.0000)],
[" C8 ",16, (0.8438, -1.0825, 0.0000)],
[" N6 ",16, (4.4402, 1.2598, 0.0000)],
[" H2 ",16, (1.2740, 4.2755, 0.0000)],
[" H8 ",16, (0.4867, -2.1227, 0.0000)],
[" H61",16, (5.1313, 1.9828, 0.0000)],
[" H62",16, (4.7211, 0.3001, 0.0000)],
],
[ # 23 DC
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7411, 1.2354, 0.000)],
[" C4'",10, (0.5207, 1.4178, 0.000)],
[" H5'",10, (0.3748, -0.5360, -0.8839)],
["H5''",10, (0.3744, -0.5368, 0.8842)],
[" C3'",11, ( 0.6388, 1.3889, 0.000)],
[" H4'",11, ( 0.2823, -0.5105, 0.9326)],
[" O4'",11, (0.4804, -0.6610, -1.1947)],
[" C1'",13, (0.4913, 1.3316, 0.0000)],
[" H1'",14, (0.4561, -0.4898, 0.8726)],
[" N1 ",14, (0.4467, -0.7474, -1.1746)],
[" C2'",14, (0.4167, 1.4603, 0.0000)],
[" H2'",15, (0.4107, -0.5097, -0.8844)],
["H2''",15, (0.4106, -0.5096, 0.8840)],
[" O3'",12, ( 0.4966, 1.3432, 0.000)],
[" H3'",12, (0.4359, -0.4915, -0.8827)],
[" C2 ",16, (0.6758, 1.2249, 0.0000)],
[" O2 ",16, (0.0158, 2.2756, 0.0000)],
[" N3 ",16, (2.0283, 1.2334, 0.0000)],
[" C4 ",16, (2.7022, 0.0815, 0.0000)],
[" N4 ",16, (4.0356, 0.1372, 0.0000)],
[" C5 ",16, (2.0394, -1.1794, 0.0000)],
[" C6 ",16, (0.7007, -1.1745, 0.0000)],
[" H42",16, (4.5715, -0.7074, 0.0000)],
[" H41",16, (4.4992, 1.0229, 0.0000)],
[" H5 ",16, (2.6061, -2.1225, 0.0000)],
[" H6 ",16, (0.1563, -2.1302, 0.0000)],
],
[ # 24 DG
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7411, 1.2354, 0.000)],
[" C4'",10, (0.5207, 1.4178, 0.000)],
[" H5'",10, (0.3748, -0.5360, -0.8839)],
["H5''",10, (0.3744, -0.5368, 0.8842)],
[" C3'",11, ( 0.6388, 1.3889, 0.000)],
[" H4'",11, ( 0.2823, -0.5105, 0.9326)],
[" O4'",11, (0.4804, -0.6610, -1.1947)],
[" C1'",13, (0.4913, 1.3316, 0.0000)],
[" H1'",14, (0.4561, -0.4898, 0.8726)],
[" N9 ",14, (0.4467, -0.7474, -1.1746)],
[" C2'",14, (0.4167, 1.4603, 0.0000)],
[" H2'",15, (0.4107, -0.5097, -0.8844)],
["H2''",15, (0.4106, -0.5096, 0.8840)],
[" O3'",12, ( 0.4966, 1.3432, 0.000)],
[" H3'",12, (0.4359, -0.4915, -0.8827)],
[" C4 ",16, (0.8171, 1.1043, 0.0000)],
[" N3 ",16, (0.4110, 2.3918, 0.0000)],
[" C2 ",16, (1.4330, 3.2319, 0.0000)],
[" N1 ",16, (2.7493, 2.8397, 0.0000)],
[" C6 ",16, (3.1894, 1.5195, 0.0000)],
[" C5 ",16, (2.1029, 0.6070, 0.0000)],
[" N7 ",16, (2.0942, -0.7800, 0.0000)],
[" C8 ",16, (0.8285, -1.0956, 0.0000)],
[" N2 ",16, (1.2085, 4.5537, 0.0000)],
[" O6 ",16, (4.4017, 1.2743, 0.0000)],
[" H1 ",16, (3.4453, 3.5579, 0.0000)],
[" H8 ",16, (0.4623, -2.1330, 0.0000)],
[" H22",16, (0.2708, 4.9015, 0.0000)],
[" H21",16, (1.9785, 5.1920, 0.0000)],
],
[ # 25 DT
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7411, 1.2354, 0.000)],
[" C4'",10, (0.5207, 1.4178, 0.000)],
[" H5'",10, (0.3748, -0.5360, -0.8839)],
["H5''",10, (0.3744, -0.5368, 0.8842)],
[" C3'",11, ( 0.6388, 1.3889, 0.000)],
[" H4'",11, ( 0.2823, -0.5105, 0.9326)],
[" O4'",11, (0.4804, -0.6610, -1.1947)],
[" C1'",13, (0.4913, 1.3316, 0.0000)],
[" H1'",14, (0.4561, -0.4898, 0.8726)],
[" N1 ",14, (0.4467, -0.7474, -1.1746)],
[" C2'",14, (0.4167, 1.4603, 0.0000)],
[" H2'",15, (0.4107, -0.5097, -0.8844)],
["H2''",15, (0.4106, -0.5096, 0.8840)],
[" O3'",12, ( 0.4966, 1.3432, 0.000)],
[" H3'",12, (0.4359, -0.4915, -0.8827)],
[" C2 ",16, (0.6495, 1.2140, 0.0000)],
[" O2 ",16, (0.0636, 2.2854, 0.0000)],
[" N3 ",16, (2.0191, 1.1297, 0.0000)],
[" C4 ",16, (2.7859, -0.0198, 0.0000)],
[" O4 ",16, (4.0113, 0.0622, 0.0000)],
[" C5 ",16, (2.0397, -1.2580, 0.0000)],
[" C7 ",16, (2.7845, -2.5550, 0.0000)],
[" C6 ",16, (0.7021, -1.1863, 0.0000)],
[" H3 ",16, (2.5175, 1.9968, 0.0000)],
[" H71",16, (2.0680, -3.3898, 0.0000)],
[" H72",16, (3.4147, -2.6153, -0.9071)],
[" H73",16, (3.4193, -2.6153, 0.8885)],
[" H6 ",16, (0.1317, -2.1273, 0.0000)],
],
[ # 26 DX
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7411, 1.2354, 0.000)],
[" C4'",10, (0.5207, 1.4178, 0.000)],
[" H5'",10, (0.3748, -0.5360, -0.8839)],
["H5''",10, (0.3744, -0.5368, 0.8842)],
[" C3'",11, ( 0.6388, 1.3889, 0.000)],
[" H4'",11, ( 0.2823, -0.5105, 0.9326)],
[" O4'",11, (0.4804, -0.6610, -1.1947)],
[" C1'",13, (0.4913, 1.3316, 0.0000)],
[" H1'",14, (0.4561, -0.4898, 0.8726)],
[" C2'",14, (0.4167, 1.4603, 0.0000)],
[" H2'",15, (0.4107, -0.5097, -0.8844)],
["H2''",15, (0.4106, -0.5096, 0.8840)],
[" O3'",12, ( 0.4966, 1.3432, 0.000)],
[" H3'",12, (0.4359, -0.4915, -0.8827)],
],
[ # 27 A
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7289, 1.2185, 0.000)],
[" C4'",10, (0.5541, 1.4027, 0.000)],
[" H5'",10, (0.3201, -0.4698, -0.7986)],
["H5''",10, (0.3206, -0.4706, 0.7970)],
[" C3'",11, ( 0.6673, 1.3669, 0.000)],
[" H4'",11, ( 0.3173, -0.5074, 0.7763)],
[" O4'",11, ( 0.4914, -0.6338, -1.2098)],
[" C1'",13, (0.4828, 1.3277, -0.0000)],
[" H1'",14, (0.3265, -0.4460, 0.8101)],
[" N9 ",14, (0.4722, -0.7339, -1.1894)],
[" C2'",14, (0.4641, 1.4573, 0.0000)],
[" H2'",15, (0.3582, -0.4393, -0.7998)],
[" O2'",15, (0.4613, -0.6189, 1.1921)],
["HO2'",15, (0.2499, -1.5749, 1.1568)],
[" O3'",12, ( 0.5548, 1.3039, 0.000)],
[" H3'",12, ( 0.3215, -0.4857, -0.7888)],
[" N1 ",16, (2.7963, 2.8824, 0.0000)],
[" C2 ",16, (1.4955, 3.2007, 0.0000)],
[" N3 ",16, (0.4333, 2.3980, 0.0000)],
[" C4 ",16, (0.8127, 1.1078, 0.0000)],
[" C5 ",16, (2.1082, 0.6254, 0.0000)],
[" C6 ",16, (3.1432, 1.5774, 0.0000)],
[" N6 ",16, (4.4400, 1.2609, 0.0000)],
[" N7 ",16, (2.1146, -0.7630, 0.0000)],
[" C8 ",16, (0.8442, -1.0830, 0.0000)],
[" H2 ",16, (1.2972, 4.1608, 0.0000)],
[" H61",16, (5.1172, 1.9697, 0.0000)],
[" H62",16, (4.7154, 0.3206, 0.0000)],
[" H8 ",16, (0.5258, -2.0104, 0.0000)],
],
[ # 28 C
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7289, 1.2185, 0.000)],
[" C4'",10, (0.5541, 1.4027, 0.000)],
[" H5'",10, (0.3201, -0.4698, -0.7986)],
["H5''",10, (0.3206, -0.4706, 0.7970)],
[" C3'",11, ( 0.6673, 1.3669, 0.000)],
[" H4'",11, ( 0.3173, -0.5074, 0.7763)],
[" O4'",11, ( 0.4914, -0.6338, -1.2098)],
[" C1'",13, (0.4828, 1.3277, -0.0000)],
[" H1'",14, (0.3265, -0.4460, 0.8101)],
[" N1 ",14, (0.4722, -0.7339, -1.1894)],
[" C2'",14, (0.4641, 1.4573, 0.0000)],
[" H2'",15, (0.3582, -0.4393, -0.7998)],
[" O2'",15, (0.4613, -0.6189, 1.1921)],
["HO2'",15, (0.2499, -1.5749, 1.1568)],
[" O3'",12, ( 0.5548, 1.3039, 0.000)],
[" H3'",12, ( 0.3215, -0.4857, -0.7888)],
[" C2 ",16, (0.6650, 1.2325, 0.0000)],
[" O2 ",16, (-0.0001, 2.2799, 0.0000)],
[" N3 ",16, (2.0175, 1.2603, 0.0000)],
[" C4 ",16, (2.7090, 0.1210, 0.0000)],
[" N4 ",16, (4.0423, 0.1969, 0.0000)],
[" C5 ",16, (2.0635, -1.1476, 0.0000)],
[" C6 ",16, (0.7250, -1.1627, 0.0000)],
[" H42",16, (4.5791, -0.6226, 0.0000)],
[" H41",16, (4.4833, 1.0723, 0.0000)],
[" H5 ",16, (2.5806, -1.9803, 0.0000)],
[" H6 ",16, (0.2622, -2.0258, 0.0000)],
],
[ # 29 G
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7289, 1.2185, 0.000)],
[" C4'",10, (0.5541, 1.4027, 0.000)],
[" H5'",10, (0.3201, -0.4698, -0.7986)],
["H5''",10, (0.3206, -0.4706, 0.7970)],
[" C3'",11, ( 0.6673, 1.3669, 0.000)],
[" H4'",11, ( 0.3173, -0.5074, 0.7763)],
[" O4'",11, ( 0.4914, -0.6338, -1.2098)],
[" C1'",13, (0.4828, 1.3277, -0.0000)],
[" H1'",14, (0.3265, -0.4460, 0.8101)],
[" N9 ",14, (0.4722, -0.7339, -1.1894)],
[" C2'",14, (0.4641, 1.4573, 0.0000)],
[" H2'",15, (0.3582, -0.4393, -0.7998)],
[" O2'",15, (0.4613, -0.6189, 1.1921)],
["HO2'",15, (0.2499, -1.5749, 1.1568)],
[" O3'",12, ( 0.5548, 1.3039, 0.000)],
[" H3'",12, ( 0.3215, -0.4857, -0.7888)],
[" N1 ",16, (2.7458, 2.8461, 0.0000)],
[" C2 ",16, (1.4286, 3.2360, 0.0000)],
[" N2 ",16, (1.1989, 4.5575, 0.0000)],
[" N3 ",16, (0.4087, 2.3932, 0.0000)],
[" C4 ",16, (0.8167, 1.1068, 0.0000)],
[" C5 ",16, (2.1036, 0.6115, 0.0000)],
[" C6 ",16, (3.1883, 1.5266, 0.0000)],
[" O6 ",16, (4.4006, 1.2842, 0.0000)],
[" N7 ",16, (2.0980, -0.7759, 0.0000)],
[" C8 ",16, (0.8317, -1.0936, 0.0000)],
[" H1 ",16, (3.4279, 3.5496, 0.0000)],
[" H22",16, (0.2781, 4.8947, 0.0000)],
[" H21",16, (1.9487, 5.1879, 0.0000)],
[" H8 ",16, (0.5085, -2.0185, 0.0000)],
],
[ # 30 U
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7289, 1.2185, 0.000)],
[" C4'",10, (0.5541, 1.4027, 0.000)],
[" H5'",10, (0.3201, -0.4698, -0.7986)],
["H5''",10, (0.3206, -0.4706, 0.7970)],
[" C3'",11, ( 0.6673, 1.3669, 0.000)],
[" H4'",11, ( 0.3173, -0.5074, 0.7763)],
[" O4'",11, ( 0.4914, -0.6338, -1.2098)],
[" C1'",13, (0.4828, 1.3277, -0.0000)],
[" H1'",14, (0.3265, -0.4460, 0.8101)],
[" N1 ",14, (0.4722, -0.7339, -1.1894)],
[" C2'",14, (0.4641, 1.4573, 0.0000)],
[" H2'",15, (0.3582, -0.4393, -0.7998)],
[" O2'",15, (0.4613, -0.6189, 1.1921)],
["HO2'",15, (0.2499, -1.5749, 1.1568)],
[" O3'",12, ( 0.5548, 1.3039, 0.000)],
[" H3'",12, ( 0.3215, -0.4857, -0.7888)],
[" C2 ",16, (0.6307, 1.2305, 0.0000)],
[" O2 ",16, (0.0260, 2.2886, 0.0000)],
[" N3 ",16, (2.0031, 1.1816, 0.0000)],
[" C4 ",16, (2.7953, 0.0532, 0.0000)],
[" O4 ",16, (4.0212, 0.1751, 0.0000)],
[" C5 ",16, (2.0746, -1.1833, 0.0000)],
[" C6 ",16, (0.7378, -1.1648, 0.0000)],
[" H3 ",16, (2.4701, 2.0428, 0.0000)],
[" H5 ",16, (2.5579, -2.0361, 0.0000)],
[" H6 ",16, (0.2681, -2.0239, 0.0000)],
],
[ # 31 RX
[" OP1", 0, (-0.7319, 1.2920, 0.000)],
[" P ", 0, (0.000, 0.000, 0.000)],
[" OP2", 0, (1.4855, 0.000, 0.000)],
[" O5'", 0, (-0.4948, -0.8559, 1.2489)],
[" C5'", 9, (0.7289, 1.2185, 0.000)],
[" C4'",10, (0.5541, 1.4027, 0.000)],
[" H5'",10, (0.3201, -0.4698, -0.7986)],
["H5''",10, (0.3206, -0.4706, 0.7970)],
[" C3'",11, ( 0.6673, 1.3669, 0.000)],
[" H4'",11, ( 0.3173, -0.5074, 0.7763)],
[" O4'",11, ( 0.4914, -0.6338, -1.2098)],
[" C1'",13, (0.4828, 1.3277, -0.0000)],
[" H1'",14, (0.3265, -0.4460, 0.8101)],
[" C2'",14, (0.4641, 1.4573, 0.0000)],
[" H2'",15, (0.3582, -0.4393, -0.7998)],
[" O2'",15, (0.4613, -0.6189, 1.1921)],
["HO2'",15, (0.2499, -1.5749, 1.1568)],
[" O3'",12, ( 0.5548, 1.3039, 0.000)],
[" H3'",12, ( 0.3215, -0.4857, -0.7888)],
],
]
if params.get("use_cif_ordering_for_trp", False):
print("Using the cif atom ordering for TRP.")
self.aa2long[17] = (" N "," CA "," C "," O "," CB "," CG "," CD1"," CD2"," NE1"," CE2"," CE3"," CZ2"," CZ3"," CH2", None, None, None, None, None, None, None, None, None," H "," HA ","1HB ","2HB ","1HD ","1HE "," HZ2"," HH2"," HZ3"," HE3", None, None, None)
self.aabonds=[
# 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
((" 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","2HD "),(" CE1"," NE2"),(" CE1","1HE "),(" NE2","2HE ")) , # 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","1HD "),(" CD2"," CE2"),(" CD2","2HD "),(" CE1"," CZ "),(" CE1","1HE "),(" CE2"," CZ "),(" CE2","2HE "),(" 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","1HD "),(" CD2"," CE2"),(" CD2"," CE3"),(" NE1"," CE2"),(" NE1","1HE "),(" 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","1HD "),(" CD2"," CE2"),(" CD2","2HD "),(" CE1"," CZ "),(" CE1","1HE "),(" CE2"," CZ "),(" CE2","2HE "),(" 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
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'","H5''"),(" C5'"," H5'"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'","H2''"),(" C2'"," H2'"),(" C1'"," N9 "),(" C1'"," H1'"),(" N1 "," C2 "),(" N1 "," C6 "),(" C2 "," N3 "),(" C2 "," H2 "),(" N3 "," C4 "),(" C4 "," C5 "),(" C4 "," N9 "),(" C5 "," C6 "),(" C5 "," N7 "),(" C6 "," N6 "),(" N6 "," H61"),(" N6 "," H62"),(" N7 "," C8 "),(" C8 "," N9 "),(" C8 "," H8 ")) , # DA
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'","H5''"),(" C5'"," H5'"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'","H2''"),(" C2'"," H2'"),(" C1'"," N1 "),(" C1'"," H1'"),(" N1 "," C2 "),(" N1 "," C6 "),(" C2 "," O2 "),(" C2 "," N3 "),(" N3 "," C4 "),(" C4 "," N4 "),(" C4 "," C5 "),(" N4 "," H42"),(" N4 "," H41"),(" C5 "," C6 "),(" C5 "," H5 "),(" C6 "," H6 ")), # DC
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'","H5''"),(" C5'"," H5'"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'","H2''"),(" C2'"," H2'"),(" C1'"," N9 "),(" C1'"," H1'"),(" N1 "," C2 "),(" N1 "," C6 "),(" N1 "," H1 "),(" C2 "," N2 "),(" C2 "," N3 "),(" N2 "," H22"),(" N2 "," H21"),(" N3 "," C4 "),(" C4 "," C5 "),(" C4 "," N9 "),(" C5 "," C6 "),(" C5 "," N7 "),(" C6 "," O6 "),(" N7 "," C8 "),(" C8 "," N9 "),(" C8 "," H8 ")), # DG
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'","H5''"),(" C5'"," H5'"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'","H2''"),(" C2'"," H2'"),(" C1'"," N1 "),(" C1'"," H1'"),(" N1 "," C2 "),(" N1 "," C6 "),(" C2 "," O2 "),(" C2 "," N3 "),(" N3 "," C4 "),(" N3 "," H3 "),(" C4 "," O4 "),(" C4 "," C5 "),(" C5 "," C7 "),(" C5 "," C6 "),(" C7 "," H71"),(" C7 "," H72"),(" C7 "," H73"),(" C6 "," H6 ")), # DT
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'","H5''"),(" C5'"," H5'"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'","H2''"),(" C2'"," H2'"),(" C1'"," H1'")) , # DX
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'"," H5'"),(" C5'","H5''"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'"," O2'"),(" C2'"," H2'"),(" O2'","HO2'"),(" C1'"," N9 "),(" C1'"," H1'"),(" N1 "," C2 "),(" N1 "," C6 "),(" C2 "," N3 "),(" C2 "," H2 "),(" N3 "," C4 "),(" C4 "," C5 "),(" C4 "," N9 "),(" C5 "," C6 "),(" C5 "," N7 "),(" C6 "," N6 "),(" N6 "," H61"),(" N6 "," H62"),(" N7 "," C8 "),(" C8 "," N9 "),(" C8 "," H8 ")), # A
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'"," H5'"),(" C5'","H5''"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'"," O2'"),(" C2'"," H2'"),(" O2'","HO2'"),(" C1'"," N1 "),(" C1'"," H1'"),(" N1 "," C2 "),(" N1 "," C6 "),(" C2 "," O2 "),(" C2 "," N3 "),(" N3 "," C4 "),(" C4 "," N4 "),(" C4 "," C5 "),(" N4 "," H42"),(" N4 "," H41"),(" C5 "," C6 "),(" C5 "," H5 "),(" C6 "," H6 ")), # C
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'"," H5'"),(" C5'","H5''"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'"," O2'"),(" C2'"," H2'"),(" O2'","HO2'"),(" C1'"," N9 "),(" C1'"," H1'"),(" N1 "," C2 "),(" N1 "," C6 "),(" N1 "," H1 "),(" C2 "," N2 "),(" C2 "," N3 "),(" N2 "," H22"),(" N2 "," H21"),(" N3 "," C4 "),(" C4 "," C5 "),(" C4 "," N9 "),(" C5 "," C6 "),(" C5 "," N7 "),(" C6 "," O6 "),(" N7 "," C8 "),(" C8 "," N9 "),(" C8 "," H8 ")), # G
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'"," H5'"),(" C5'","H5''"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'"," O2'"),(" C2'"," H2'"),(" O2'","HO2'"),(" C1'"," N1 "),(" C1'"," H1'"),(" N1 "," C2 "),(" N1 "," C6 "),(" C2 "," O2 "),(" C2 "," N3 "),(" N3 "," C4 "),(" N3 "," H3 "),(" C4 "," O4 "),(" C4 "," C5 "),(" C5 "," C6 "),(" C5 "," H5 "),(" C6 "," H6 ")), # U
((" P "," OP2"),(" P "," OP1"),(" P "," O5'"),(" O5'"," C5'"),(" C5'"," C4'"),(" C5'"," H5'"),(" C5'","H5''"),(" C4'"," O4'"),(" C4'"," C3'"),(" C4'"," H4'"),(" O4'"," C1'"),(" C3'"," O3'"),(" C3'"," C2'"),(" C3'"," H3'"),(" C2'"," C1'"),(" C2'"," O2'"),(" C2'"," H2'"),(" O2'","HO2'"),(" C1'"," H1'")), # RX
]
self.NO_BOND = 0
self.SINGLE_BOND = 1
self.DOUBLE_BOND = 2
self.TRIPLE_BOND = 3
self.AROMATIC_BOND = 4
self.RESIDUE_BB_BOND = 5
self.RESIDUE_ATOM_BOND = 6
# BTYPES ONLY DEFINED FOR CANONICAL 20 amino acids + UNK, MAS treated as glycines
SINGLE_BOND = self.SINGLE_BOND
DOUBLE_BOND = self.DOUBLE_BOND
AROMATIC_BOND = self.AROMATIC_BOND
self.aabtypes = [
# 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # ala
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # arg
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # asn
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND), # asp
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # cys
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # gln
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND), # glu
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND), # gly
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, AROMATIC_BOND, AROMATIC_BOND, AROMATIC_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, SINGLE_BOND), # his
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # ile
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # leu
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # lys
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # met
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, AROMATIC_BOND, AROMATIC_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, SINGLE_BOND), # phe
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # pro
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # ser
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # thr
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, AROMATIC_BOND, AROMATIC_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, AROMATIC_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, SINGLE_BOND), # trp
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, AROMATIC_BOND, AROMATIC_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, AROMATIC_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # tyr
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND), # val
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND), # unk (treated as gly)
(SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, SINGLE_BOND, DOUBLE_BOND) # mask (treated as gly)
]
self.aachirals = [
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #ala
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #arg
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #asn
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #asp
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #cys
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #gln
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #glu
(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #gly
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #his
(0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #ileu
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #leu
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #lys
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #met
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #phe
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #pro
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #ser
(0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #thr
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #trp
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #tyr
(0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #val
(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #unk
(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), #mas
]
self.aachirals = torch.tensor(self.aachirals)
# tip atom
self.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
" N1 ", # DA
" N3 ", # DC
" N1 ", # DG
" N3 ", # DT
" C1'", # DX
" N1 ", # A
" N3 ", # C
" N1 ", # G
" N3 ", # U
" C1'", # RX
" NE2", # HIS_D
]
# ideal N, CA, C initial coordinates (protein)
self.init_N = torch.tensor([-0.5272, 1.3593, 0.000]).float()
self.init_CA = torch.zeros_like(self.init_N)
self.init_C = torch.tensor([1.5233, 0.000, 0.000]).float()
self.INIT_CRDS = torch.full((self.NTOTAL, 3), np.nan)
self.INIT_CRDS[:3] = torch.stack((self.init_N, self.init_CA, self.init_C), dim=0) # (3,3)
if (not params.use_phospate_frames_for_NA):
# despite the name, this uses ideal O4p,C1p,C2p initial coordinates
self.init_O1 = torch.tensor([-0.3894, 1.3649, 0.0000]).float()
self.init_P = torch.zeros_like(self.init_O1)
self.init_O2 = torch.tensor([1.5186, 0.000, 0.000]).float()
self.costgtNA = -0.2744
else:
# this uses ideal P,OP1,OP2 initial coordinates
self.init_O1 = torch.tensor([-0.7319, 1.2920, 0.000]).float()
self.init_P = torch.zeros_like(self.init_O1)
self.init_O2 = torch.tensor([1.4855, 0.000, 0.000]).float()
self.costgtNA = -0.4929
self.INIT_NA_CRDS = torch.full((self.NTOTAL, 3), np.nan)
self.INIT_NA_CRDS[:3] = torch.stack((self.init_O1, self.init_P, self.init_O2), dim=0) # (3,3)
# non-backbone torsions
# (bb torsions are hard-coded)
self.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","1HE "," 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
[ [" O4'"," C1'"," N9 "," C4 "], None, None, None ],#DA
[ [" O4'"," C1'"," N1 "," C2 "], None, None, None ],#DC
[ [" O4'"," C1'"," N9 "," C4 "], None, None, None ],#DG
[ [" O4'"," C1'"," N1 "," C2 "], None, None, None ],#DT
[ None, None, None, None ], # DX
[ [" O4'"," C1'"," N9 "," C4 "], None, None, None ],#A
[ [" O4'"," C1'"," N1 "," C2 "], None, None, None ],#C
[ [" O4'"," C1'"," N9 "," C4 "], None, None, None ],#G
[ [" O4'"," C1'"," N1 "," C2 "], None, None, None ],#U
[ None, None, None, None ], # RX
]
self.NFRAMES = max([len(f) for f in self.frames])
atomized_protein_frames = torch.load(script_dir+"atomized_protein_frames.pt")
def load_derived_data(self, params):
# resolve tip atom indices
self.tip_indices = torch.full((self.NAATOKENS,), 0)
for i in range(self.NAATOKENS):
if i > self.NNAPROTAAS-1:
# all atoms are at index 1 in the atom array
self.tip_indices[i] = 1
else:
tip_atm = self.aa2tip[i]
atm_long = self.aa2long[i]
self.tip_indices[i] = atm_long.index(tip_atm)
# resolve torsion indices
# a negative index indicates the previous residue
# order:
# omega/phi/psi: 0-2
# chi_1-4(prot): 3-6
# cb/cg bend: 7-9
# eps(p)/zeta(p): 10-11
# alpha/beta/gamma/delta: 12-15
# nu2/nu1/nu0: 16-18
# chi_1(na): 19
self.torsion_indices = torch.full((self.NAATOKENS,self.NTOTALDOFS,4),0)
self.torsion_can_flip = torch.full((self.NAATOKENS,self.NTOTALDOFS),False,dtype=torch.bool)
for i in range(self.NPROTAAS):
i_l, i_a = self.aa2long[i], self.aa2longalt[i]
# protein omega/phi/psi
self.torsion_indices[i,0,:] = torch.tensor([-1,-2,0,1]) # omega
self.torsion_indices[i,1,:] = torch.tensor([-2,0,1,2]) # phi
self.torsion_indices[i,2,:] = torch.tensor([0,1,2,3]) # psi (+pi)
# protein chis
for j in range(4):
if self.torsions[i][j] is None:
continue
for k in range(4):
a = self.torsions[i][j][k]
self.torsion_indices[i,3+j,k] = i_l.index(a)
if (i_l.index(a) != i_a.index(a)):
self.torsion_can_flip[i,3+j] = True ##bb tors never flip
# CB/CG angles (only masking uses these indices)
self.torsion_indices[i,7,:] = torch.tensor([0,2,1,4]) # CB ang1
self.torsion_indices[i,8,:] = torch.tensor([0,2,1,4]) # CB ang2
self.torsion_indices[i,9,:] = torch.tensor([0,2,4,5]) # CG ang (arg 1 ignored)
# HIS is a special case for flip
self.torsion_can_flip[8,4]=False
# DNA/RNA
if (not params.use_phospate_frames_for_NA):
# ribose frame
for i in range(self.NPROTAAS,self.NNAPROTAAS):
self.torsion_indices[i,10,:] = torch.tensor([-2,-9,-10,4]) # epsilon_prev
self.torsion_indices[i,11,:] = torch.tensor([-9,-10,4,6]) # zeta_prev
self.torsion_indices[i,12,:] = torch.tensor([7,6,4,3]) # alpha c5'-o5'-p-op1
self.torsion_indices[i,13,:] = torch.tensor([8,7,6,4]) # beta c4'-c5'-o5'-p
self.torsion_indices[i,14,:] = torch.tensor([9,8,7,6]) # gamma c3'-c4'-c5'-o5'
self.torsion_indices[i,15,:] = torch.tensor([2,9,8,7]) # delta c2'-c3'-c4'-c5'
self.torsion_indices[i,16,:] = torch.tensor([1,2,9,8]) # nu2
self.torsion_indices[i,17,:] = torch.tensor([0,1,2,9]) # nu1
self.torsion_indices[i,18,:] = torch.tensor([2,1,0,8]) # nu0
# NA chi
if self.torsions[i][0] is not None:
i_l = self.aa2long[i]
for k in range(4):
a = self.torsions[i][0][k]
self.torsion_indices[i,19,k] = i_l.index(a) # chi
else:
# phosphate frame
for i in range(self.NPROTAAS,self.NNAPROTAAS):
# NA BB tors
self.torsion_indices[i,10,:] = torch.tensor([-5,-7,-8,1]) # epsilon_prev
self.torsion_indices[i,11,:] = torch.tensor([-7,-8,1,3]) # zeta_prev
self.torsion_indices[i,12,:] = torch.tensor([0,1,3,4]) # alpha (+2pi/3)
self.torsion_indices[i,13,:] = torch.tensor([1,3,4,5]) # beta
self.torsion_indices[i,14,:] = torch.tensor([3,4,5,7]) # gamma
self.torsion_indices[i,15,:] = torch.tensor([4,5,7,8]) # delta
if (i<self.NPROTAAS+5):
# is DNA
self.torsion_indices[i,16,:] = torch.tensor([4,5,6,10]) # nu2
self.torsion_indices[i,17,:] = torch.tensor([5,6,10,9]) # nu1
self.torsion_indices[i,18,:] = torch.tensor([6,10,9,7]) # nu0
else:
# is RNA (fd: my fault since I flipped C1'/C2' order for DNA and RNA)
self.torsion_indices[i,16,:] = torch.tensor([4,5,6,9]) # nu2
self.torsion_indices[i,17,:] = torch.tensor([5,6,9,10]) # nu1
self.torsion_indices[i,18,:] = torch.tensor([6,9,10,7]) # nu0
# NA chi
if self.torsions[i][0] is not None:
i_l = self.aa2long[i]
for k in range(4):
a = self.torsions[i][0][k]
self.torsion_indices[i,19,k] = i_l.index(a) # chi
# build the mapping from atoms in the full rep (Nx27) to the "alternate" rep
self.allatom_mask = torch.zeros((self.NAATOKENS,self.NTOTAL), dtype=torch.bool)
self.long2alt = torch.zeros((self.NAATOKENS,self.NTOTAL), dtype=torch.long)
for i in range(self.NNAPROTAAS):
i_l, i_lalt = self.aa2long[i], self.aa2longalt[i]
for j,a in enumerate(i_l):
if (a is None):
self.long2alt[i,j] = j
else:
self.long2alt[i,j] = i_lalt.index(a)
self.allatom_mask[i,j] = True
for i in range(self.NNAPROTAAS, self.NAATOKENS):
for j in range(self.NTOTAL):
self.long2alt[i, j] = j
self.allatom_mask[self.NNAPROTAAS:,1] = True
# bond graph traversal
self.num_bonds = torch.zeros((self.NAATOKENS,self.NTOTAL,self.NTOTAL), dtype=torch.long)
for i in range(self.NNAPROTAAS):
num_bonds_i = np.zeros((self.NTOTAL,self.NTOTAL))
for (bnamei,bnamej) in self.aabonds[i]:
bi,bj = self.aa2long[i].index(bnamei),self.aa2long[i].index(bnamej)
num_bonds_i[bi,bj] = 1
num_bonds_i = scipy.sparse.csgraph.shortest_path (num_bonds_i,directed=False)
num_bonds_i[num_bonds_i>=4] = 4
self.num_bonds[i,...] = torch.tensor(num_bonds_i)
# atom type indices
self.idx2aatype = []
for x in self.aa2type:
for y in x:
if y and y not in self.idx2aatype:
self.idx2aatype.append(y)
self.aatype2idx = {x:i for i,x in enumerate(self.idx2aatype)}
# element indices
self.idx2elt = []
for x in self.aa2elt:
for y in x:
if y and y not in self.idx2elt:
self.idx2elt.append(y)
self.elt2idx = {x:i for i,x in enumerate(self.idx2elt)}
# LJ/LK scoring parameters
self.atom_type_index = torch.zeros((self.NAATOKENS,self.NTOTAL), dtype=torch.long)
self.element_index = torch.zeros((self.NAATOKENS,self.NTOTAL), dtype=torch.long)
self.ljlk_parameters = torch.zeros((self.NAATOKENS,self.NTOTAL,5), dtype=torch.float)
self.lj_correction_parameters = torch.zeros((self.NAATOKENS,self.NTOTAL,4), dtype=bool) # donor/acceptor/hpol/disulf
for i in range(self.NNAPROTAAS):
for j,a in enumerate(self.aa2type[i]):
if (a is not None):
self.atom_type_index[i,j] = self.aatype2idx[a]
self.ljlk_parameters[i,j,:] = torch.tensor( type2ljlk[a] )
self.lj_correction_parameters[i,j,0] = (type2hb[a]==HbAtom.DO)+(type2hb[a]==HbAtom.DA)
self.lj_correction_parameters[i,j,1] = (type2hb[a]==HbAtom.AC)+(type2hb[a]==HbAtom.DA)
self.lj_correction_parameters[i,j,2] = (type2hb[a]==HbAtom.HP)
self.lj_correction_parameters[i,j,3] = (a=="SH1" or a=="HS")
for j,a in enumerate(self.aa2elt[i]):
if (a is not None):
self.element_index[i,j] = self.elt2idx[a]
self.hbtypes = torch.full((self.NAATOKENS,self.NTOTAL,3),-1, dtype=torch.long) # (donortype, acceptortype, acchybtype)
self.hbbaseatoms = torch.full((self.NAATOKENS,self.NTOTAL,2),-1, dtype=torch.long) # (B,B0) for acc; (D,-1) for don
self.hbpolys = torch.zeros((HbDonType.NTYPES,HbAccType.NTYPES,3,15)) # weight,xmin,xmax,ymin,ymax,c9,...,c0
for i in range(self.NNAPROTAAS):
for j,a in enumerate(self.aa2type[i]):
if (a in type2dontype):
j_hs = self.donorHs(self.aa2long[i][j],self.aabonds[i],self.aa2long[i])
for j_h in j_hs:
self.hbtypes[i,j_h,0] = type2dontype[a]
self.hbbaseatoms[i,j_h,0] = j
if (a in type2acctype):
j_b, j_b0 = self.acceptorBB0(self.aa2long[i][j],type2hybtype[a],self.aabonds[i],self.aa2long[i])
self.hbtypes[i,j,1] = type2acctype[a]
self.hbtypes[i,j,2] = type2hybtype[a]
self.hbbaseatoms[i,j,0] = j_b
self.hbbaseatoms[i,j,1] = j_b0
for i in range(HbDonType.NTYPES):
for j in range(HbAccType.NTYPES):
weight = dontype2wt[i]*acctype2wt[j]
pdist,pbah,pahd = hbtypepair2poly[(i,j)]
xrange,yrange,coeffs = hbpolytype2coeffs[pdist]
self.hbpolys[i,j,0,0] = weight
self.hbpolys[i,j,0,1:3] = torch.tensor(xrange)
self.hbpolys[i,j,0,3:5] = torch.tensor(yrange)
self.hbpolys[i,j,0,5:] = torch.tensor(coeffs)
xrange,yrange,coeffs = hbpolytype2coeffs[pahd]
self.hbpolys[i,j,1,0] = weight
self.hbpolys[i,j,1,1:3] = torch.tensor(xrange)
self.hbpolys[i,j,1,3:5] = torch.tensor(yrange)
self.hbpolys[i,j,1,5:] = torch.tensor(coeffs)
xrange,yrange,coeffs = hbpolytype2coeffs[pbah]
self.hbpolys[i,j,2,0] = weight
self.hbpolys[i,j,2,1:3] = torch.tensor(xrange)
self.hbpolys[i,j,2,3:5] = torch.tensor(yrange)
self.hbpolys[i,j,2,5:] = torch.tensor(coeffs)
# cartbonded scoring parameters
# (0) inter-res
self.cb_lengths_CN = (1.32868, 369.445)
self.cb_angles_CACN = (2.02807,160)
self.cb_angles_CNCA = (2.12407,96.53)
self.cb_torsions_CACNH = (0.0,41.830) # also used for proline CACNCD
self.cb_torsions_CANCO = (0.0,38.668)
# note for the below, the extra amino acid corrsponds to cb params for HIS_D
# (1) intra-res lengths
self.cb_lengths = [[] for i in range(self.NAATOKENS+1)]
for cst in cartbonded_data_raw['lengths']:
res_idx = self.aa2num[ cst['res'] ]
self.cb_lengths[res_idx].append( (
self.aa2long[res_idx].index(cst['atm1']),
self.aa2long[res_idx].index(cst['atm2']),
cst['x0'],cst['K']
) )
ncst_per_res=max([len(i) for i in self.cb_lengths])
self.cb_length_t = torch.zeros(self.NAATOKENS+1,ncst_per_res,4)
for i in range(self.NNAPROTAAS+1):
src = i
if (self.num2aa[i]=='UNK' or self.num2aa[i]=='MAS'):
src=self.aa2num['ALA']
if (len(self.cb_lengths[src])>0):
self.cb_length_t[i,:len(self.cb_lengths[src]),:] = torch.tensor(self.cb_lengths[src])
# (2) intra-res angles
self.cb_angles = [[] for i in range(self.NAATOKENS+1)]
for cst in cartbonded_data_raw['angles']:
res_idx = self.aa2num[ cst['res'] ]
self.cb_angles[res_idx].append( (
self.aa2long[res_idx].index(cst['atm1']),
self.aa2long[res_idx].index(cst['atm2']),
self.aa2long[res_idx].index(cst['atm3']),
cst['x0'],cst['K']
) )
ncst_per_res=max([len(i) for i in self.cb_angles])
self.cb_angle_t = torch.zeros(self.NAATOKENS+1,ncst_per_res,5)
for i in range(self.NNAPROTAAS+1):
src = i
if (self.num2aa[i]=='UNK' or self.num2aa[i]=='MAS'):
src=self.aa2num['ALA']
if (len(self.cb_angles[src])>0):
self.cb_angle_t[i,:len(self.cb_angles[src]),:] = torch.tensor(self.cb_angles[src])
# (3) intra-res torsions
self.cb_torsions = [[] for i in range(self.NAATOKENS+1)]
for cst in cartbonded_data_raw['torsions']:
res_idx = self.aa2num[ cst['res'] ]
self.cb_torsions[res_idx].append( (
self.aa2long[res_idx].index(cst['atm1']),
self.aa2long[res_idx].index(cst['atm2']),
self.aa2long[res_idx].index(cst['atm3']),
self.aa2long[res_idx].index(cst['atm4']),
cst['x0'],cst['K'],cst['period']
) )
ncst_per_res=max([len(i) for i in self.cb_torsions])
self.cb_torsion_t = torch.zeros(self.NAATOKENS+1,ncst_per_res,7)
self.cb_torsion_t[...,6]=1.0 # periodicity
for i in range(self.NNAPROTAAS):
src = i
if (self.num2aa[i]=='UNK' or self.num2aa[i]=='MAS'):
src=self.aa2num['ALA']
if (len(self.cb_torsions[src])>0):
self.cb_torsion_t[i,:len(self.cb_torsions[src]),:] = torch.tensor(self.cb_torsions[src])
# kinematic parameters
self.base_indices = torch.full((self.NAATOKENS,self.NTOTAL),0, dtype=torch.long) # base frame that builds each atom
self.xyzs_in_base_frame = torch.ones((self.NAATOKENS,self.NTOTAL,4)) # coords of each atom in the base frame
self.RTs_by_torsion = torch.eye(4).repeat(self.NAATOKENS,self.NTOTALTORS,1,1) # torsion frames
self.reference_angles = torch.ones((self.NAATOKENS,self.NPROTANGS,2)) # reference values for bendable angles
## PROTEIN
for i in range(self.NPROTAAS):
i_l = self.aa2long[i]
for name, base, coords in self.ideal_coords[i]:
idx = i_l.index(name)
self.base_indices[i,idx] = base
self.xyzs_in_base_frame[i,idx,:3] = torch.tensor(coords)
# omega frame
self.RTs_by_torsion[i,0,:3,:3] = torch.eye(3)
self.RTs_by_torsion[i,0,:3,3] = torch.zeros(3)
# phi frame
self.RTs_by_torsion[i,1,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,0,:3] - self.xyzs_in_base_frame[i,1,:3],
torch.tensor([1.,0.,0.])
)
self.RTs_by_torsion[i,1,:3,3] = self.xyzs_in_base_frame[i,0,:3]
# psi frame
self.RTs_by_torsion[i,2,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,2,:3] - self.xyzs_in_base_frame[i,1,:3],
self.xyzs_in_base_frame[i,1,:3] - self.xyzs_in_base_frame[i,0,:3]
)
self.RTs_by_torsion[i,2,:3,3] = self.xyzs_in_base_frame[i,2,:3]
# chi1 frame
if self.torsions[i][0] is not None:
a0,a1,a2 = self.torsion_indices[i,3,0:3]
self.RTs_by_torsion[i,3,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,a2,:3]-self.xyzs_in_base_frame[i,a1,:3],
self.xyzs_in_base_frame[i,a0,:3]-self.xyzs_in_base_frame[i,a1,:3],
)
self.RTs_by_torsion[i,3,:3,3] = self.xyzs_in_base_frame[i,a2,:3]
# chi2/3/4 frame
for j in range(1,4):
if self.torsions[i][j] is not None:
a2 = self.torsion_indices[i,3+j,2]
if ((i==18 and j==2) or (i==8 and j==2)): # TYR CZ-OH & HIS CE1-HE1 a special case
a0,a1 = self.torsion_indices[i,3+j,0:2]
self.RTs_by_torsion[i,3+j,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,a2,:3]-self.xyzs_in_base_frame[i,a1,:3],
self.xyzs_in_base_frame[i,a0,:3]-self.xyzs_in_base_frame[i,a1,:3] )
else:
self.RTs_by_torsion[i,3+j,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,a2,:3],
torch.tensor([-1.,0.,0.]), )
self.RTs_by_torsion[i,3+j,:3,3] = self.xyzs_in_base_frame[i,a2,:3]
# CB/CG angles
NCr = 0.5*(self.xyzs_in_base_frame[i,0,:3]+self.xyzs_in_base_frame[i,2,:3])
CAr = self.xyzs_in_base_frame[i,1,:3]
CBr = self.xyzs_in_base_frame[i,4,:3]
CGr = self.xyzs_in_base_frame[i,5,:3]
self.reference_angles[i,0,:]=th_ang_v(CBr-CAr,NCr-CAr)
NCp = self.xyzs_in_base_frame[i,2,:3]-self.xyzs_in_base_frame[i,0,:3]
NCpp = NCp - torch.dot(NCp,NCr)/ torch.dot(NCr,NCr) * NCr
self.reference_angles[i,1,:]=th_ang_v(CBr-CAr,NCpp)
self.reference_angles[i,2,:]=th_ang_v(CGr,torch.tensor([-1.,0.,0.]))
## NUCLEIC ACIDS
if (not params.use_phospate_frames_for_NA):
# ribose frame
for i in range(self.NPROTAAS, self.NNAPROTAAS):
i_l = self.aa2long[i]
for name, base, coords in self.ideal_coords[i]:
idx = i_l.index(name)
self.base_indices[i,idx] = base
self.xyzs_in_base_frame[i,idx,:3] = torch.tensor(coords)
# epsilon(p)/zeta(p) - like omega in protein, not used to build atoms
# - keep as identity
self.RTs_by_torsion[i,self.NPROTTORS+0,:3,:3] = torch.eye(3)
self.RTs_by_torsion[i,self.NPROTTORS+0,:3,3] = torch.zeros(3)
self.RTs_by_torsion[i,self.NPROTTORS+1,:3,:3] = torch.eye(3)
self.RTs_by_torsion[i,self.NPROTTORS+1,:3,3] = torch.zeros(3)
# nu1
self.RTs_by_torsion[i,self.NPROTTORS+7,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,2,:3] , self.xyzs_in_base_frame[i,0,:3]
)
self.RTs_by_torsion[i,self.NPROTTORS+7,:3,3] = self.xyzs_in_base_frame[i,2,:3]
# nu0 - currently not used for atom generation
self.RTs_by_torsion[i,self.NPROTTORS+8,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,0,:3] , self.xyzs_in_base_frame[i,2,:3]
)
self.RTs_by_torsion[i,self.NPROTTORS+8,:3,3] = self.xyzs_in_base_frame[i,0,:3] # C2'
# NA chi
if self.torsions[i][0] is not None:
a0,a1,a2 = self.torsion_indices[i,19,0:3]
self.RTs_by_torsion[i,self.NPROTTORS+9,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,a2,:3], self.xyzs_in_base_frame[i,a0,:3]
)
self.RTs_by_torsion[i,self.NPROTTORS+9,:3,3] = self.xyzs_in_base_frame[i,a2,:3]
# nu2
self.RTs_by_torsion[i,self.NPROTTORS+6,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,9,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+6,:3,3] = self.xyzs_in_base_frame[i,6,:3]
# alpha
self.RTs_by_torsion[i,self.NPROTTORS+2,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,4,:3], torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+2,:3,3] = self.xyzs_in_base_frame[i,4,:3]
# beta
self.RTs_by_torsion[i,self.NPROTTORS+3,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,6,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+3,:3,3] = self.xyzs_in_base_frame[i,6,:3]
# gamma
self.RTs_by_torsion[i,self.NPROTTORS+4,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,7,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+4,:3,3] = self.xyzs_in_base_frame[i,7,:3]
# delta
self.RTs_by_torsion[i,self.NPROTTORS+5,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,8,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+5,:3,3] = self.xyzs_in_base_frame[i,8,:3]
else:
# phosphate frame
for i in range(self.NPROTAAS, self.NNAPROTAAS):
i_l = self.aa2long[i]
for name, base, coords in self.ideal_coords[i]:
idx = i_l.index(name)
self.base_indices[i,idx] = base
self.xyzs_in_base_frame[i,idx,:3] = torch.tensor(coords)
# epsilon(p)/zeta(p) - like omega in protein, not used to build atoms
# - keep as identity
self.RTs_by_torsion[i,self.NPROTTORS+0,:3,:3] = torch.eye(3)
self.RTs_by_torsion[i,self.NPROTTORS+0,:3,3] = torch.zeros(3)
self.RTs_by_torsion[i,self.NPROTTORS+1,:3,:3] = torch.eye(3)
self.RTs_by_torsion[i,self.NPROTTORS+1,:3,3] = torch.zeros(3)
# alpha
self.RTs_by_torsion[i,self.NPROTTORS+2,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,3,:3] - self.xyzs_in_base_frame[i,1,:3], # P->O5'
self.xyzs_in_base_frame[i,0,:3] - self.xyzs_in_base_frame[i,1,:3] # P<-OP1
)
self.RTs_by_torsion[i,self.NPROTTORS+2,:3,3] = self.xyzs_in_base_frame[i,3,:3] # O5'
# beta
self.RTs_by_torsion[i,self.NPROTTORS+3,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,4,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+3,:3,3] = self.xyzs_in_base_frame[i,4,:3] # C5'
# gamma
self.RTs_by_torsion[i,self.NPROTTORS+4,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,5,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+4,:3,3] = self.xyzs_in_base_frame[i,5,:3] # C4'
# delta
self.RTs_by_torsion[i,self.NPROTTORS+5,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,7,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+5,:3,3] = self.xyzs_in_base_frame[i,7,:3] # C3'
# nu2
self.RTs_by_torsion[i,self.NPROTTORS+6,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,6,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+6,:3,3] = self.xyzs_in_base_frame[i,6,:3] # O4'
# nu1
if i<self.NPROTAAS+5:
# is DNA
C1idx,C2idx = 10,9
else:
# is RNA
C1idx,C2idx = 9,10
self.RTs_by_torsion[i,self.NPROTTORS+7,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,C1idx,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+7,:3,3] = self.xyzs_in_base_frame[i,C1idx,:3] # C1'
# nu0
self.RTs_by_torsion[i,self.NPROTTORS+8,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,C2idx,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+8,:3,3] = self.xyzs_in_base_frame[i,C2idx,:3] # C2'
# NA chi
if self.torsions[i][0] is not None:
a2 = self.torsion_indices[i,19,2]
self.RTs_by_torsion[i,self.NPROTTORS+9,:3,:3] = make_frame(
self.xyzs_in_base_frame[i,a2,:3] , torch.tensor([-1.,0.,0.])
)
self.RTs_by_torsion[i,self.NPROTTORS+9,:3,3] = self.xyzs_in_base_frame[i,a2,:3]
#Small molecules
self.xyzs_in_base_frame[self.NNAPROTAAS:,1, :3] = 0
# general FAPE parameters
self.frame_indices = torch.full((self.NAATOKENS,self.NFRAMES,3,2),0, dtype=torch.long)
for i in range(self.NNAPROTAAS):
i_l = self.aa2long[i]
for j,x in enumerate(self.frames[i]):
if x is not None:
# frames are stored as (residue offset, atom position)
self.frame_indices[i,j,0] = torch.tensor((0, i_l.index(x[0])))
self.frame_indices[i,j,1] = torch.tensor((0, i_l.index(x[1])))
self.frame_indices[i,j,2] = torch.tensor((0, i_l.index(x[2])))
def seq2chars(self, seq):
out = ''.join([self.aa_321[self.num2aa[a]] for a in seq])
return out
# hbond scoring parameters
def donorHs(self, D,bonds,atoms):
dHs = []
for (i,j) in bonds:
if (i==D):
idx_j = atoms.index(j)
if (idx_j>=self.NHEAVY): # if atom j is a hydrogen
dHs.append(idx_j)
if (j==D):
idx_i = atoms.index(i)
if (idx_i>=self.NHEAVY): # if atom j is a hydrogen
dHs.append(idx_i)
assert (len(dHs)>0)
return dHs
def acceptorBB0(self, A,hyb,bonds,atoms):
if (hyb == HbHybType.SP2):
for (i,j) in bonds:
if (i==A):
B = atoms.index(j)
if (B<self.NHEAVY):
break
if (j==A):
B = atoms.index(i)
if (B<self.NHEAVY):
break
for (i,j) in bonds:
if (i==atoms[B]):
B0 = atoms.index(j)
if (B0<self.NHEAVY):
break
if (j==atoms[B]):
B0 = atoms.index(i)
if (B0<self.NHEAVY):
break
elif (hyb == HbHybType.SP3 or hyb == HbHybType.RING):
for (i,j) in bonds:
if (i==A):
B = atoms.index(j)
if (B<self.NHEAVY):
break
if (j==A):
B = atoms.index(i)
if (B<self.NHEAVY):
break
for (i,j) in bonds:
if (i==A and j!=atoms[B]):
B0 = atoms.index(j)
break
if (j==A and i!=atoms[B]):
B0 = atoms.index(i)
break
return B,B0
def load_pdb_ideal_sdf_strings(base_path: Optional[str] = script_dir, return_only_sdf_strings: bool = False):
"""
returns a dictionary of that maps all the 3letter ligand codes in the pdb to relevant information:
string of the sdf file with idealized coordinates for that molecule
atom names for the atoms in order
leaving groups if there are covalent modifications to the ligand
pdbx_align
"""
file_name = 'ligands.json.gz'
if base_path is not None:
file_name = Path(base_path) / file_name
with gzip.open(file_name,'rt') as file:
mols = json.load(file)
if return_only_sdf_strings:
mols_only_sdf = {key: value["sdf"] for key, value in mols.items()}
return mols_only_sdf
else:
return mols
def load_tanimoto_sim_matrix(base_path=script_dir):
"""
precomputed tanimoto similarities between ligands in the pdb until august 2021
returns num_molecules X num_molecules matrix of tanimoto scores and
list of names corresponding to indices in that matrix
"""
file_name = 'tanimoto_ligands.npz'
if base_path is not None:
file_name = Path(base_path) / file_name
tanimoto_data = np.load(file_name, allow_pickle=True)
sim = tanimoto_data['sim']
names = tanimoto_data['names']
return sim, names
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