Nothing
R/atom_nom.R
In edmcr: Euclidean Distance Matrix Completion Tools
Defines functions
atom_nom
atom_nom <- function(residuetype, atom, mode){
delta <- -1
natom <- ""
switch(mode,
full = switch(residuetype,
ALA = switch(atom,
HB1 = {natom = "QB"
delta=1},
HB2 = {natom = "QB"
delta=1},
HB3 = {natom = "QB"
delta=1},
QB = c()),
ARG = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HD2 = c(),
HD3 = c(),
QD = c(),
HH11 = c(),
HH12 = c(),
QH1 = c(),
HH21 = c(),
HH22 = c(),
QH2 = c()),
ASN = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD21 = c(),
HD22 = c(),
QD2 = c()),
ASP = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c()),
CYS = switch(atom,
HB2 = c(),
HB3 = c(),
HG = c(),
QB = c()),
CYSS = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c()),
GLN = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HE21 = c(),
HE22 = c(),
QE2 = c()),
GLU = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c()),
GLY = switch(atom,
HA2 = c(),
HA3 = c(),
QA = c()),
HIS = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD1 = c(),
HD2 = c(),
HE1 = c()),
ILE = switch(atom,
HB = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
HG12 = c(),
HG13 = c(),
QG1 = c(),
HD11 = {natom = "QD1"
delta=1},
HD12 = {natom = "QD1"
delta=1},
HD13 = {natom = "QD1"
delta=1},
QD1 = c()),
LEU = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG = c(),
HD11 = {natom = "QD1"
delta=1},
HD12 = {natom = "QD1"
delta=1},
HD13 = {natom = "QD1"
delta=1},
QD1 = c(),
HD21 = {natom = "QD2"
delta=1},
HD22 = {natom = "QD2"
delta=1},
HD23 = {natom = "QD2"
delta=1},
QD2 = c(),
QQD = c()),
LYS = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HD2 = c(),
HD3 = c(),
QD = c(),
HE2 = c(),
HE3 = c(),
QE = c(),
HZ1 = {natom = "QZ"
delta=1},
HZ2 = {natom = "QZ"
delta=1},
HZ3 = {natom = "QZ"
delta=1},
QZ = c()),
MET = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HE1 = {natom = "QE"
delta=1},
HE2 = {natom = "QE"
delta=1},
HE3 = {natom = "QE"
delta=1},
QE = c()),
PHE = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD1 = c(),
HD2 = c(),
QD = c(),
HB2 = c(),
HB3 = c(),
QB = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HZ = c()),
PRO = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HD2 = c(),
HD3 = c(),
QD = c()),
SER = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG = c()),
THR = switch(atom,
HB = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
HG1 = c()),
TRP = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD1 = c(),
HE1 = c(),
HE3 = c(),
HZ2 = c(),
HZ3 = c(),
HH2 = c()),
TYR = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD1 = c(),
HD2 = c(),
QD = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HH = c()),
VAL = switch(atom,
HB = c(),
HG11 = {natom = "QG1"
delta=1},
HG12 = {natom = "QG1"
delta=1},
HG13 = {natom = "QG1"
delta=1},
QG1 = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
QQG = c())),
homitted = switch(residuetype,
ALA = switch(atom,
HB1 = {natom = "CB"
delta=1},
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = c()),
ARG = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1},
HD2 = {natom = "CD"
delta=1},
HD3 = {natom = "CD"
delta=1},
QD = {natom = "CD"
delta=1},
HH11 = c(),
HH12 = c(),
QH1 = c(),
HH21 = c(),
HH22 = c(),
QH2 = c()),
ASN = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD21 = c(),
HD22 = c(),
QD2 = c()),
ASP = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1}),
CYS = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
HG = {natom = "SG"
delta=1},
QB = {natom = "CB"
delta=1}),
CYSS = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1}),
GLN = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1},
HE21 = c(),
HE22 = c(),
QE2 = c()),
GLU = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1}),
GLY = switch(atom,
HA2 = c(),
HA3 = c(),
QA = c()),
HIS = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD1 = c(),
HD2 = c(),
HE1 = c()),
ILE = switch(atom,
HB = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
HG12 = {natom = "CG1"
delta=1},
HG13 = {natom = "CG1"
delta=1},
QG1 = {natom = "CG1"
delta=1},
HD11 = {natom = "QD1"
delta=1},
HD12 = {natom = "QD1"
delta=1},
HD13 = {natom = "QD1"
delta=1},
QD1 = c()),
LEU = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG = c(),
HD11 = {natom = "QD1"
delta=1},
HD12 = {natom = "QD1"
delta=1},
HD13 = {natom = "QD1"
delta=1},
QD1 = c(),
HD21 = {natom = "QD2"
delta=1},
HD22 = {natom = "QD2"
delta=1},
HD23 = {natom = "QD2"
delta=1},
QD2 = c(),
QQD = c()),
LYS = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1},
HD2 = {natom = "CD"
delta=1},
HD3 = {natom = "CD"
delta=1},
QD = {natom = "CD"
delta=1},
HE2 = {natom = "CE"
delta=1},
HE3 = {natom = "CE"
delta=1},
QE = {natom = "CE"
delta=1},
HZ1 = {natom = "QZ"
delta=1},
HZ2 = {natom = "QZ"
delta=1},
HZ3 = {natom = "QZ"
delta=1},
QZ = c()),
MET = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1},
HE1 = {natom = "QE"
delta=1},
HE2 = {natom = "QE"
delta=1},
HE3 = {natom = "QE"
delta=1},
QE = c()),
PHE = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD1 = c(),
HD2 = c(),
QD = c(),
HB2 = c(),
HB3 = c(),
QB = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HZ = c()),
PRO = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HD2 = c(),
HD3 = c(),
QD = c()),
SER = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG = {natom = "OG"
delta=1}),
THR = switch(atom,
HB = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
HG1 = {natom = "OG1"
delta=1}),
TRP = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD1 = c(),
HE1 = c(),
HE3 = c(),
HZ2 = c(),
HZ3 = c(),
HH2 = c()),
TYR = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD1 = c(),
HD2 = c(),
QD = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HH = {natom = "OH"
delta=1}),
VAL = switch(atom,
HB = c(),
HG11 = {natom = "QG1"
delta=1},
HG12 = {natom = "QG1"
delta=1},
HG13 = {natom = "QG1"
delta=1},
QG1 = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
QQG = c())),
xplor = switch(residuetype,
ALA = switch(atom,
HB1 = c(),
HB2 = c(),
HB3 = c(),
QB = c()),
ARG = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HD2 = c(),
HD1 = {natom="HD3"
delta=-1},
QD = c(),
HH11 = c(),
HH12 = c(),
QH1 = c(),
HH21 = c(),
HH22 = c(),
QH2 = c()),
ASN = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD21 = c(),
HD22 = c(),
QD2 = c()),
ASP = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c()),
CYS = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
HG = c(),
QB = c()),
CYSS = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c()),
GLN = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HE21 = c(),
HE22 = c(),
QE2 = c()),
GLU = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c()),
GLY = switch(atom,
HA2 = c(),
HA1 = {natom="HA3"
delta=-1},
QA = c()),
HIS = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD1 = c(),
HD2 = c(),
HE1 = c()),
ILE = switch(atom,
HB = c(),
HG21 = c(),
HG22 = c(),
HG23 = c(),
QG2 = c(),
HG12 = c(),
HG11 = {natom="HG13"
delta=-1},
QG1 = c(),
HD11 = c(),
HD12 = c(),
HD13 = c(),
QD1 = c()),
LEU = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG = c(),
HD11 = c(),
HD12 = c(),
HD13 = c(),
QD1 = c(),
HD21 = c(),
HD22 = c(),
HD23 = c(),
QD2 = c(),
QQD = c()),
LYS = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HD2 = c(),
HD1 = {natom="HD3"
delta=-1},
QD = c(),
HE2 = c(),
HE1 = {natom="HE3"
delta=-1},
QE = c(),
HZ1 = c(),
HZ2 = c(),
HZ3 = c(),
QZ = c()),
MET = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HE1 = c(),
HE2 = c(),
HE3 = c(),
QE = c()),
PHE = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD1 = c(),
HD2 = c(),
QD = c(),
HB2 = c(),
HB3 = c(),
QB = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HZ = c()),
PRO = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HD2 = c(),
HD1 = {natom="HD3"
delta=-1},
QD = c()),
SER = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG = c()),
THR = switch(atom,
HB = c(),
HG21 = c(),
HG22 = c(),
HG23 = c(),
QG2 = c(),
HG1 = c()),
TRP = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD1 = c(),
HE1 = c(),
HE3 = c(),
HZ2 = c(),
HZ3 = c(),
HH2 = c()),
TYR = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD1 = c(),
HD2 = c(),
QD = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HH = c()),
VAL = switch(atom,
HB = c(),
HG11 = c(),
HG12 = c(),
HG13 = c(),
QG1 = c(),
HG21 = c(),
HG22 = c(),
HG23 = c(),
QG2 = c(),
QQG = c())))
return(list(natom=natom, delta=delta))
}
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Defines functions atom_nom
atom_nom <- function(residuetype, atom, mode){
delta <- -1
natom <- ""
switch(mode,
full = switch(residuetype,
ALA = switch(atom,
HB1 = {natom = "QB"
delta=1},
HB2 = {natom = "QB"
delta=1},
HB3 = {natom = "QB"
delta=1},
QB = c()),
ARG = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HD2 = c(),
HD3 = c(),
QD = c(),
HH11 = c(),
HH12 = c(),
QH1 = c(),
HH21 = c(),
HH22 = c(),
QH2 = c()),
ASN = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD21 = c(),
HD22 = c(),
QD2 = c()),
ASP = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c()),
CYS = switch(atom,
HB2 = c(),
HB3 = c(),
HG = c(),
QB = c()),
CYSS = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c()),
GLN = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HE21 = c(),
HE22 = c(),
QE2 = c()),
GLU = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c()),
GLY = switch(atom,
HA2 = c(),
HA3 = c(),
QA = c()),
HIS = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD1 = c(),
HD2 = c(),
HE1 = c()),
ILE = switch(atom,
HB = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
HG12 = c(),
HG13 = c(),
QG1 = c(),
HD11 = {natom = "QD1"
delta=1},
HD12 = {natom = "QD1"
delta=1},
HD13 = {natom = "QD1"
delta=1},
QD1 = c()),
LEU = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG = c(),
HD11 = {natom = "QD1"
delta=1},
HD12 = {natom = "QD1"
delta=1},
HD13 = {natom = "QD1"
delta=1},
QD1 = c(),
HD21 = {natom = "QD2"
delta=1},
HD22 = {natom = "QD2"
delta=1},
HD23 = {natom = "QD2"
delta=1},
QD2 = c(),
QQD = c()),
LYS = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HD2 = c(),
HD3 = c(),
QD = c(),
HE2 = c(),
HE3 = c(),
QE = c(),
HZ1 = {natom = "QZ"
delta=1},
HZ2 = {natom = "QZ"
delta=1},
HZ3 = {natom = "QZ"
delta=1},
QZ = c()),
MET = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HE1 = {natom = "QE"
delta=1},
HE2 = {natom = "QE"
delta=1},
HE3 = {natom = "QE"
delta=1},
QE = c()),
PHE = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD1 = c(),
HD2 = c(),
QD = c(),
HB2 = c(),
HB3 = c(),
QB = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HZ = c()),
PRO = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HD2 = c(),
HD3 = c(),
QD = c()),
SER = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG = c()),
THR = switch(atom,
HB = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
HG1 = c()),
TRP = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD1 = c(),
HE1 = c(),
HE3 = c(),
HZ2 = c(),
HZ3 = c(),
HH2 = c()),
TYR = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HD1 = c(),
HD2 = c(),
QD = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HH = c()),
VAL = switch(atom,
HB = c(),
HG11 = {natom = "QG1"
delta=1},
HG12 = {natom = "QG1"
delta=1},
HG13 = {natom = "QG1"
delta=1},
QG1 = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
QQG = c())),
homitted = switch(residuetype,
ALA = switch(atom,
HB1 = {natom = "CB"
delta=1},
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = c()),
ARG = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1},
HD2 = {natom = "CD"
delta=1},
HD3 = {natom = "CD"
delta=1},
QD = {natom = "CD"
delta=1},
HH11 = c(),
HH12 = c(),
QH1 = c(),
HH21 = c(),
HH22 = c(),
QH2 = c()),
ASN = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD21 = c(),
HD22 = c(),
QD2 = c()),
ASP = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1}),
CYS = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
HG = {natom = "SG"
delta=1},
QB = {natom = "CB"
delta=1}),
CYSS = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1}),
GLN = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1},
HE21 = c(),
HE22 = c(),
QE2 = c()),
GLU = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1}),
GLY = switch(atom,
HA2 = c(),
HA3 = c(),
QA = c()),
HIS = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD1 = c(),
HD2 = c(),
HE1 = c()),
ILE = switch(atom,
HB = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
HG12 = {natom = "CG1"
delta=1},
HG13 = {natom = "CG1"
delta=1},
QG1 = {natom = "CG1"
delta=1},
HD11 = {natom = "QD1"
delta=1},
HD12 = {natom = "QD1"
delta=1},
HD13 = {natom = "QD1"
delta=1},
QD1 = c()),
LEU = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG = c(),
HD11 = {natom = "QD1"
delta=1},
HD12 = {natom = "QD1"
delta=1},
HD13 = {natom = "QD1"
delta=1},
QD1 = c(),
HD21 = {natom = "QD2"
delta=1},
HD22 = {natom = "QD2"
delta=1},
HD23 = {natom = "QD2"
delta=1},
QD2 = c(),
QQD = c()),
LYS = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1},
HD2 = {natom = "CD"
delta=1},
HD3 = {natom = "CD"
delta=1},
QD = {natom = "CD"
delta=1},
HE2 = {natom = "CE"
delta=1},
HE3 = {natom = "CE"
delta=1},
QE = {natom = "CE"
delta=1},
HZ1 = {natom = "QZ"
delta=1},
HZ2 = {natom = "QZ"
delta=1},
HZ3 = {natom = "QZ"
delta=1},
QZ = c()),
MET = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG2 = {natom = "CG"
delta=1},
HG3 = {natom = "CG"
delta=1},
QG = {natom = "CG"
delta=1},
HE1 = {natom = "QE"
delta=1},
HE2 = {natom = "QE"
delta=1},
HE3 = {natom = "QE"
delta=1},
QE = c()),
PHE = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD1 = c(),
HD2 = c(),
QD = c(),
HB2 = c(),
HB3 = c(),
QB = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HZ = c()),
PRO = switch(atom,
HB2 = c(),
HB3 = c(),
QB = c(),
HG2 = c(),
HG3 = c(),
QG = c(),
HD2 = c(),
HD3 = c(),
QD = c()),
SER = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HG = {natom = "OG"
delta=1}),
THR = switch(atom,
HB = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
HG1 = {natom = "OG1"
delta=1}),
TRP = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD1 = c(),
HE1 = c(),
HE3 = c(),
HZ2 = c(),
HZ3 = c(),
HH2 = c()),
TYR = switch(atom,
HB2 = {natom = "CB"
delta=1},
HB3 = {natom = "CB"
delta=1},
QB = {natom = "CB"
delta=1},
HD1 = c(),
HD2 = c(),
QD = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HH = {natom = "OH"
delta=1}),
VAL = switch(atom,
HB = c(),
HG11 = {natom = "QG1"
delta=1},
HG12 = {natom = "QG1"
delta=1},
HG13 = {natom = "QG1"
delta=1},
QG1 = c(),
HG21 = {natom = "QG2"
delta=1},
HG22 = {natom = "QG2"
delta=1},
HG23 = {natom = "QG2"
delta=1},
QG2 = c(),
QQG = c())),
xplor = switch(residuetype,
ALA = switch(atom,
HB1 = c(),
HB2 = c(),
HB3 = c(),
QB = c()),
ARG = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HD2 = c(),
HD1 = {natom="HD3"
delta=-1},
QD = c(),
HH11 = c(),
HH12 = c(),
QH1 = c(),
HH21 = c(),
HH22 = c(),
QH2 = c()),
ASN = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD21 = c(),
HD22 = c(),
QD2 = c()),
ASP = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c()),
CYS = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
HG = c(),
QB = c()),
CYSS = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c()),
GLN = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HE21 = c(),
HE22 = c(),
QE2 = c()),
GLU = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c()),
GLY = switch(atom,
HA2 = c(),
HA1 = {natom="HA3"
delta=-1},
QA = c()),
HIS = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD1 = c(),
HD2 = c(),
HE1 = c()),
ILE = switch(atom,
HB = c(),
HG21 = c(),
HG22 = c(),
HG23 = c(),
QG2 = c(),
HG12 = c(),
HG11 = {natom="HG13"
delta=-1},
QG1 = c(),
HD11 = c(),
HD12 = c(),
HD13 = c(),
QD1 = c()),
LEU = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG = c(),
HD11 = c(),
HD12 = c(),
HD13 = c(),
QD1 = c(),
HD21 = c(),
HD22 = c(),
HD23 = c(),
QD2 = c(),
QQD = c()),
LYS = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HD2 = c(),
HD1 = {natom="HD3"
delta=-1},
QD = c(),
HE2 = c(),
HE1 = {natom="HE3"
delta=-1},
QE = c(),
HZ1 = c(),
HZ2 = c(),
HZ3 = c(),
QZ = c()),
MET = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HE1 = c(),
HE2 = c(),
HE3 = c(),
QE = c()),
PHE = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD1 = c(),
HD2 = c(),
QD = c(),
HB2 = c(),
HB3 = c(),
QB = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HZ = c()),
PRO = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG2 = c(),
HG1 = {natom="HG3"
delta=-1},
QG = c(),
HD2 = c(),
HD1 = {natom="HD3"
delta=-1},
QD = c()),
SER = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HG = c()),
THR = switch(atom,
HB = c(),
HG21 = c(),
HG22 = c(),
HG23 = c(),
QG2 = c(),
HG1 = c()),
TRP = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD1 = c(),
HE1 = c(),
HE3 = c(),
HZ2 = c(),
HZ3 = c(),
HH2 = c()),
TYR = switch(atom,
HB2 = c(),
HB1 = {natom="HB3"
delta=-1},
QB = c(),
HD1 = c(),
HD2 = c(),
QD = c(),
HE1 = c(),
HE2 = c(),
QE = c(),
QR = c(),
HH = c()),
VAL = switch(atom,
HB = c(),
HG11 = c(),
HG12 = c(),
HG13 = c(),
QG1 = c(),
HG21 = c(),
HG22 = c(),
HG23 = c(),
QG2 = c(),
QQG = c())))
return(list(natom=natom, delta=delta))
}
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