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xpm2all.bsh
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xpm2all.bsh
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function xpm2xyzmat {
awk -v dat=$dat ' BEGIN{ isHB=0; ny=0; ix=1; iy=1 }
/Hydrogen Bonds/ { isHB=1; next }
/gromacs_xpm/ {
getline; gsub(/"/, " ");
nlev=$3; ncode=$4 # 每种颜色编码字符数
for(i=1; i<=nlev; i++) {
getline
if(isHB) {
v[" "]=0; v["o"]=1
} else {
gsub(/"/, " ")
v[$1]=$5 # 编码代表数值
}
}
next
}
/^"/ { sub(/^"/,""); sub(/",$/,"");
zv[ny++]=$0 # 数据颜色编码
}
/\/\* x-axis/ && ix { x0=$3; dx=$4-x0; ix=0 }
/\/\* y-axis/ && iy { y0=$3; dy=$4-y0; iy=0 }
END {
nx=length(zv[1])/ncode
if(index(dat, "xyz")) {
print "# Nx="nx" Ny="ny" X0="x0" dX="dx" Y0="y0" dY="dy
print "# x y z"
}
for(j=0; j<ny; j++) {
y = y0+j*dy
for(i=0; i<nx; i++) {
x = x0+i*dx
txt=substr(zv[ny-1-j], i*ncode+1, ncode)
if(index(dat, "mat")) printf "%12.6f", v[txt]
if(index(dat, "xyz")) printf "%12.6f %12.6f %12.6f\n", x, y, v[txt]
}
print ""
}
} ' $file.xpm > $file~.$dat
}
function xpm2gpl {
# G = "3-Helix" 3-turn helix (3/10 helix). Min length 3 residues.
# H = "A-Helix" 4-turn helix (α helix). Min length 4 residues.
# I = "5-Helix" 5-turn helix (π helix). Min length 5 residues.
# B = "B-Bridge" beta-bridge residue. residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)
# E = "B-Sheet" extended strand (in beta ladder) in parallel and/or anti-parallel β-sheet conformation. Min length 2 residues.
# T = "Turn" H-bonded turn (3, 4 or 5 turn)
# S = "Bend" bend (the only non-hydrogen-bond based assignment)
# ~ = "Coil" C, loops/coil (residues which are not in any of the above conformations)
awk -v file=$file -v minRes=$minRes -v maxRes=$maxRes -v yminRes=$yminRes \
-v ssmode=$ssmode -v color=$color ' BEGIN{
xyz=0; if(ssmode=="xyz") xyz=1;
fx=.5; if(ssmode=="box") fx=1;
ny=0; ix=1; iy=1;
vss["A-Helix" ] = 8; c["A-Helix" ,"gmx"]= "#0000FF"
vss["3-Helix" ] = 7; c["3-Helix" ,"gmx"]= "#808080"
vss["5-Helix" ] = 6; c["5-Helix" ,"gmx"]= "#800080"
vss["B-Sheet" ] = 5; c["B-Sheet" ,"gmx"]= "#FF0000"
vss["B-Bridge"] = 4; c["B-Bridge" ,"gmx"]= "#000000"
vss["Turn" ] = 3; c["Turn" ,"gmx"]= "#FFFF00"
vss["Bend" ] = 2; c["Bend" ,"gmx"]= "#008000"
vss["Coil" ] = 1; c["Coil" ,"gmx"]= "#BBBBBB"
vss["Chain_Separator"]= 0; c["Chain_Separator","gmx"]= "#E6E6E6"
c["A-Helix" ,"pdb"]="#E53535"; c["A-Helix" ,"vmd"]="#E182E1";
c["3-Helix" ,"pdb"]="#EC6262"; c["3-Helix" ,"vmd"]="#FFA0FF";
c["5-Helix" ,"pdb"]="#F28E8E"; c["5-Helix" ,"vmd"]="#E11414";
c["B-Sheet" ,"pdb"]="#FFF000"; c["B-Sheet" ,"vmd"]="#FFFF64";
c["B-Bridge" ,"pdb"]="#D4A800"; c["B-Bridge" ,"vmd"]="#B4B400";
c["Turn" ,"pdb"]="#00B266"; c["Turn" ,"vmd"]="#469696";
c["Bend" ,"pdb"]="#00CC00"; c["Bend" ,"vmd"]="#00CC00";
c["Coil" ,"pdb"]="#000000"; c["Coil" ,"vmd"]="#000000";
c["Chain_Separator","pdb"]="#FFFFFF"; c["Chain_Separator","vmd"]="#FFFFFF"
# p1: 10.1371/journal.pone.0178333 p2: 10.1371/journal.pcbi.1007487
c["A-Helix" ,"p1"]="#00FF00"; c["A-Helix" ,"p2"]="#0171B6"
c["3-Helix" ,"p1"]="#2E8B57"; c["3-Helix" ,"p2"]="#D16000"
c["5-Helix" ,"p1"]="#008000"; c["5-Helix" ,"p2"]="#FCAEE5"
c["B-Sheet" ,"p1"]="#0000FF"; c["B-Sheet" ,"p2"]="#019E73"
c["B-Bridge" ,"p1"]="#3399FF"; c["B-Bridge" ,"p2"]="#CA9261"
c["Turn" ,"p1"]="#FF8C00"; c["Turn" ,"p2"]="#C99260"
c["Bend" ,"p1"]="#FF0000"; c["Bend" ,"p2"]="#F8B0E7"
c["Coil" ,"p1"]="#000000"; c["Coil" ,"p2"]="#000000"
c["Chain_Separator","p1"]="#FFFFFF"; c["Chain_Separator","p2"]="#FFFFFF"
c["A-Helix" ,"p3"]="#FFFF00";
c["3-Helix" ,"p3"]="#FE7D6D";
c["5-Helix" ,"p3"]="#C12323";
c["B-Sheet" ,"p3"]="#000080";
c["B-Bridge" ,"p3"]="#00FFFF";
c["Turn" ,"p3"]="#006400";
c["Bend" ,"p3"]="#FF0000";
c["Coil" ,"p3"]="#BFBFBF";
c["Chain_Separator","p3"]="#FFFFFF";
}
/^"/ {
gsub(/[",\n\r]/, "")
n=split($0, arr)
if(n==1) { zv[ny++]=$0} # 数据颜色编码
else if(n==4) { ncode=$NF } # 每种颜色编码字符数
else if(n>4) { v[$1]=$5; } # 编码代表数值xyz?vss[$5]:$5
}
/x-label:/ { sub(/.*\(/,""); sub(/).*/,""); xu=$0 }
/\/\* x-axis/ && ix { x0=$3; dx=$4-x0; ix=0 }
/\/\* y-axis/ && iy { y0=$3; dy=$4-y0; iy=0; y0=yminRes }
END { Pi=4*atan2(1,1)
if(ny<maxRes) maxRes=ny
nx=length(zv[1])/ncode
if(!xyz) {
fun["A-Helix"] ="Ha"
fun["3-Helix"] ="H3"
fun["5-Helix"] ="H5"
fun["B-Sheet"] ="Bs"
fun["B-Bridge"]="Bb"
fun["Turn"] ="T"
fun["Bend"] ="B"
fun["Coil"] ="C"
print "Ha(n)=sprintf(\"set obj %d fc rgb \\\""c["A-Helix" ,color]"\\\" fs solid border lw 1;\", n)"
print "H3(n)=sprintf(\"set obj %d fc rgb \\\""c["3-Helix" ,color]"\\\" fs solid border lw 1;\", n)"
print "H5(n)=sprintf(\"set obj %d fc rgb \\\""c["5-Helix" ,color]"\\\" fs solid border lw 1;\", n)"
print "Bs(n)=sprintf(\"set obj %d fc rgb \\\""c["B-Sheet" ,color]"\\\" fs solid border lw 1;\", n)"
print "Bb(n)=sprintf(\"set obj %d fc rgb \\\""c["B-Bridge",color]"\\\" fs solid border lw 1;\", n)"
print "T(n) =sprintf(\"set obj %d fc rgb \\\""c["Turn" ,color]"\\\" fs solid border lw 1;\", n)"
print "B(n) =sprintf(\"set obj %d fc rgb \\\""c["Bend" ,color]"\\\" fs solid border lw 1;\", n)"
print "C(n) =sprintf(\"set obj %d fc rgb \\\""c["Coil" ,color]"\\\" fs solid border lw 1;\", n)"
# Nh=20; dt=2.5*Pi/Nh; t=.5*Pi-dt;
# for(i=0; i<=Nh; i++) {
# t += dt
# Hx[i]=dx*cos(t)/2.5
# Hy[i]=dy*(.5+t/Pi-sin(t))/2
# }
Nh=20; dt=1/(Nh/2); t=-dt;
for(i=0; i<=Nh/2; i++) {
t += dt
Hy[i]=Hy[Nh-i]=dy*t
Hx[i]=Hx[Nh-i]=dx*fx*.5*sin(t*2*Pi)
}
d=0.1; Nt=20; dt=1/(Nt/2); t=-dt
for(i=0; i<=Nt/2; i++) {
t += dt;
Ty[i]=Ty[Nt-i]=dy*t
Tx[i]=Tx[Nt-i]=(t<d || t>1-d) ? 0 : dx*fx*(.5*(.5-t)^2/(.5-d)^2-.5)
}
}
print "# residue index: "minRes"-"maxRes >file"~count.xvg"
print "# Time("xu") A-Helix 3-Helix 5-Helix B-Sheet B-Bridge Turn Bend Coil Chain_Separator" >file"~count.xvg"
n=0
if(xyz) print "$data <<EOD"
for(i=0; i<nx; i++) {
ftype["A-Helix"] =0
ftype["3-Helix"] =0
ftype["5-Helix"] =0
ftype["B-Sheet"] =0
ftype["B-Bridge"]=0
ftype["Turn"] =0
ftype["Bend"] =0
ftype["Coil"] =0
ftype["Chain_Separator"] =0
x = x0+i*dx
for(j=0; j<ny; j++) {
if(minRes<=j+1 && j+1<=maxRes) {
y = y0+j*dy
txt=substr(zv[ny-1-j], i*ncode+1, ncode)
type[j]=v[txt]
ftype[v[txt]]++
}
}
printf "%15.6f%9d%9d%9d%9d%9d%9d%9d%9d%9d\n", x,
ftype["A-Helix"] ,
ftype["3-Helix"] ,
ftype["5-Helix"] ,
ftype["B-Sheet"] ,
ftype["B-Bridge"],
ftype["Turn"] ,
ftype["Bend"] ,
ftype["Coil"],
ftype["Chain_Separator"] >file"~count.xvg"
for(j=0; j<ny; j++) {
if(minRes<=j+1 && j+1<=maxRes) {
if(xyz) print x, y0+j*dy, vss[type[j]]
else {
for(jj=j+1; jj<ny && type[jj]==type[j]; jj++) type[jj]=""
if(type[j]) print obj(x, y0+j*dy, y0+(jj-1)*dy, type[j], dx*fx)
}
}
}
}
if(!xyz) print "\n$data <<EOD\n0 0 0\n0 0 0\n0 0 0\n0 0 0"
print "EOD\n"
for(n=0; n<=8; n++) for(i in vss) if(vss[i]==n) print "c"n"=\""c[i, color]"\""
print "\nset pal defined( \\"
print "\t-.5 c0, 0.5 c0, 0.5 c1, 1.5 c1, 1.5 c2, 2.5 c2, \\"
print "\t2.5 c3, 3.5 c3, 3.5 c4, 4.5 c4, 4.5 c5, 5.5 c5, \\"
print "\t5.5 c6, 6.5 c6, 6.5 c7, 7.5 c7, 7.5 c8, 8.5 c8 )\n"
print "set cbtics ( \\"
print "\t\"Chain-Sep.\" 0, \\"
print "\t\"C Coil \" 1, \\"
print "\t\"S Bend \" 2, \\"
print "\t\"T Turn \" 3, \\"
print "\t\"B B-Bridge\" 4, \\"
print "\t\"E B-Sheet \" 5, \\"
print "\t\"I 5-Helix \" 6, \\"
print "\t\"G 3-Helix \" 7, \\"
print "\t\"H A-Helix \" 8 )\n"
print "set cbr [-.5:8.5]\n"
print "#set tmargin at screen 0.95"
print "#set bmargin at screen 0.2"
print "#set rmargin at screen 0.85"
print "#set label \" A-Helix \" at screen 0.85,0.92 left textcolor rgb \""c["A-Helix" ,color]"\""
print "#set label \" 3-Helix \" at screen 0.85,0.82 left textcolor rgb \""c["3-Helix" ,color]"\""
print "#set label \" 5-Helix \" at screen 0.85,0.72 left textcolor rgb \""c["5-Helix" ,color]"\""
print "#set label \" B-Sheet \" at screen 0.85,0.62 left textcolor rgb \""c["B-Sheet" ,color]"\""
print "#set label \" B-Bridge\" at screen 0.85,0.52 left textcolor rgb \""c["B-Bridge",color]"\""
print "#set label \" Turn \" at screen 0.85,0.42 left textcolor rgb \""c["Turn" ,color]"\""
print "#set label \" Bend \" at screen 0.85,0.32 left textcolor rgb \""c["Bend" ,color]"\""
print "#set label \" Coil \" at screen 0.85,0.22 left textcolor rgb \""c["Coil" ,color]"\"\n"
print "set output \"ss.png\""
print "set term pngcairo enhanced truecolor font \"HelveticaNeueLT Pro 85 Hv,85\" fontscale 1 linewidth 20 pointscale 5 size 6000,4000"
print "set tics out nomirror;"
print "set key out reverse Left spacing 2 samplen 1/2"
print "set xl\"Time("xu")\"; set yl\"#res\";"
print "plot ["x0-dx/2":"x0+(nx-1)*dx+dx/2"] ["y0+(minRes-1)*dy":"y0+(maxRes-1)*dy"] $data u 1:2:3 w imag notit"
}
function obj(x, y1, y2, type, dx, pos, i,j,k) {
if(ssmode=="box") {
n++
x1 =x-dx/2; x2 =x+dx/2
y1 -= dy/2; y2 += dy/2
return "set obj "n" poly from " \
x1","y1" to "x1","y2" to " \
x2","y2" to "x2","y1" to "x1","y1"; eval "fun[type]"("n")"
}
if(type=="A-Helix" || type=="3-Helix" || type=="5-Helix") {
str=""
for(i=y1; i<=y2; i+=dy) {
n++
str=str"set obj "n" poly from "x+Hx[0]","i+Hy[0]-dy/2
for(j=1; j<=Nh; j++) str=str" to "x+Hx[j]","i+Hy[j]-dy/2
str=str"; eval "fun[type]"("n")\n"
}
return str
}
if(type=="Turn") {
n++
y1 -= dy/2; y2 += dy/2
str="set obj "n" poly from "x+Tx[0]","y1+(y2-y1)*Ty[0]
for(j=1; j<=Nt; j++) str=str" to "x+Tx[j]","y1+(y2-y1)*Ty[j]
return str"; eval T("n")"
}
if(type=="B-Bridge") {
n++
return "set obj "n" poly from " \
x ","y1-dy/2" to "x","y2-dy/2" to " \
x-dx/2","y2-dy/2" to "x","y2 " to " \
x ","y2+dy/2" to "x","y2 " to " \
x+dx/2","y2-dy/2" to "x","y2-dy/2" to " \
x","y1-dy/2"; eval Bb("n")"
}
if(type=="B-Sheet") {
n++
return "set obj "n" poly from " \
x-dx/4","y1-dy/2" to "x-dx/4","y2-dy/2" to " \
x-dx/2","y2-dy/2" to "x ","y2 " to " \
x ","y2+dy/2" to "x ","y2 " to " \
x+dx/2","y2-dy/2" to "x+dx/4","y2-dy/2" to " \
x+dx/4","y1-dy/2" to "x-dx/4","y1-dy/2 \
"; eval Bs("n")"
}
if(type=="Bend" || type=="Coil") {
n++
return "set obj "n" poly from " \
x","y1-dy/2" to "x","y2+dy/2" to "x","y1-dy/2 \
"; eval "fun[type]"("n")"
}
}
function abs(x) { return x>0 ? x : -x }
' $file.xpm > $file~.gpl
}
function xpm2rgb {
Line=$(grep "GROMACS" $file.xpm |wc -l)
[[ $Line == 0 ]] && { cp $file.xpm $file~iv.xpm; return; }
awk -v cm=$cm ' /static/ {
print
getline; print; n=$3
for(i=1; i<=n; i++) {
getline; sub(/ \/\* .* \*\//, "")
if(length(cm)>0) $3=RGB(cm, i, 1, n, (1+n)/2)
print
}
}
/y-axis/,0 {sub(/^\/\* .* \*\//, ""); if(length($0)) print}
function abs(x) { return x>=0 ? x : -x }
function min(x, y) { return x<y ? x : y }
function max(x, y) { return x>y ? x : y }
function nint(x) { return x>=0 ? int(x+0.5) : int(x-0.5) }
function cubic(x, a0, a1, a2, a3) {return a0+a1*x+a2*x*x+a3*x*x*x}
function RGB(cm, V, Vmin, Vmax, Vcnt) {
x=(V-Vmin)/(Vmax-Vmin)
if(V<Vcnt) x=0.5*(V-Vmin)/(Vcnt-Vmin)
else x=0.5*(V-Vcnt)/(Vmax-Vcnt)+0.5
PI=4*atan2(1,1)
if(cm==1 || cm=="rgb1") { # Rainbow http://stackoverflow.com/questions/7706339
r=1; g=1; b=1
if (x<0.25) { r = 0; g = 4*x }
else if (x<0.50) { r = 0; b = 2-4*x }
else if (x<0.75) { r = 4*x-2; b = 0 }
else { g = 4-4*x; b = 0 }
} else if(cm==2 || cm=="rgb2") { # Rainbow gnuplot_33/13/10
r=abs(2*x-0.5)
g=sin(PI*x)
b=cos(.5*PI*x)
} else if(cm==3 || cm=="rgb3") { # Rainbow gnuplot_26/13/10
r=(3*x-1)/2
g=sin(PI*x)
b=cos(.5*PI*x)
} else if(cm==4 || cm=="rgb4") { # Rainbow gnuplot_22/13/-31
r=3*x-1; g=sin(PI*x); b=0.84-2*x
} else if(cm==5) { # Rainbow Mathmatica
r= x<=0.062745 ? cubic(x, 0.471375, -2.554017, -0.603914, 7.812982) : \
x<=0.152941 ? cubic(x, 0.292460, 1.809704, -31.728520, 117.994977) : \
x<=0.615686 ? cubic(x, 0.321657, -1.002195, 3.507752, -1.465506) : \
x<=0.807843 ? cubic(x, 1.060710, -5.522637, 12.504767, -7.328945) : \
x<=0.933333 ? cubic(x, 0.431446, -0.873251, 4.037986, -2.774247) : \
x<=1.000000 ? cubic(x, 5.221261, -12.772499, 12.792531, -4.383959) : 0
g= x<=0.062745 ? cubic(x, 0.108729, 0.152568, -0.600651, 7.770915) : \
x<=0.176471 ? cubic(x, 0.019507, 1.603318, -1.113349, 12.925571) : \
x<=0.364706 ? cubic(x, -0.087439, 2.477820, 0.408927, -4.700034) : \
x<=0.705882 ? cubic(x, 0.144965, 1.791961, -0.862001, -0.770124) : \
x<=0.784314 ? cubic(x, 16.562714, -66.930100, 95.145955, -45.549403) : \
x<=0.878431 ? cubic(x, -44.677970, 163.297275, -194.114854, 75.927463) : \
x<=1.000000 ? cubic(x, 2.436863, -1.845566, -0.624881, 0.164628) : 0
b= x<=0.105882 ? cubic(x, 0.526474, 2.243463, 0.792247, -31.571500) : \
x<=0.184314 ? cubic(x, 0.026914, 13.337161, -80.796176, 171.577097) : \
x<=0.254902 ? cubic(x, 0.913699, -1.400599, 7.239935, -13.759153) : \
x<=0.556863 ? cubic(x, 0.442544, 4.247120, -14.052824, 11.110080) : \
x<=0.952941 ? cubic(x, 2.960527, -9.677238, 11.755653, -4.927506) : \
x<=1.000000 ? cubic(x, 0.585773, -0.453645, 0.000000, -0.000000) : 0
} else if(cm==6) { # DarkRainbow Mathmatica
r= x<=0.309804 ? cubic(x, 0.236537, 0.246053, -1.136582, 3.202751) : \
x<=0.407843 ? cubic(x, -1.510327, 13.561592, -35.298055, 33.624234) : \
x<=0.603922 ? cubic(x, -0.599178, 2.859926, -0.741459, -0.178725) : \
x<=0.701961 ? cubic(x, 3.197059, -12.278383, 20.066775, -10.373348) : \
x<=0.901961 ? cubic(x, 0.468624, 2.127260, -2.783342, 0.824166) : \
x<=1.000000 ? cubic(x, 0.729870, 0.000000, -0.000000, 0.000000) : 0
g= x<=0.109804 ? cubic(x, 0.339471, 0.168823, -3.598735, 26.873972) : \
x<=0.309804 ? cubic(x, 0.218689, 1.512175, -3.197075, 3.440555) : \
x<=0.458824 ? cubic(x, -0.261191, 5.401505, -14.030694, 14.113778) : \
x<=0.603922 ? cubic(x, -1.534715, 10.091878, -15.985773, 9.257180) : \
x<=0.701961 ? cubic(x, 4.759391, -17.980549, 27.364646, -14.145868) : \
x<=0.815686 ? cubic(x, 18.275342, -66.730000, 86.570221, -38.633344) : \
x<=0.901961 ? cubic(x, -19.096521, 74.250435, -90.514567, 35.431661) : \
x<=1.000000 ? cubic(x, 0.239399, 0.000000, -0.000000, 0.000000) : 0
b= x<=0.101961 ? cubic(x, 0.575370, -0.214218, 1.381410, -10.814899) : \
x<=0.239216 ? cubic(x, 0.620844, 0.637717, -16.547215, 37.635934) : \
x<=0.329412 ? cubic(x, -1.404892, 21.875973, -87.291389, 110.089969) : \
x<=0.443137 ? cubic(x, -1.127449, 12.499131, -36.589253, 34.785129) : \
x<=0.717647 ? cubic(x, 0.971421, -4.438096, 8.640928, -5.173692) : \
x<=0.847059 ? cubic(x, 12.089098, -46.895840, 62.535294, -27.917903) : \
x<=0.929412 ? cubic(x, -64.437519, 225.686918, -261.540385, 100.686232) : \
x<=1.000000 ? cubic(x, 0.230961, 0.000000, -0.000000, 0.000000) : 0
} else if(cm==7) { # Rainbow CETR2
r= x<=0.137255 ? cubic(x, -0.000316, 0.038887, -0.883031, 5.101004) : \
x<=0.203922 ? cubic(x, -4.023305, 61.355168, -303.724536, 513.861584) : \
x<=0.305882 ? cubic(x, -1.622921, 20.396258, -74.241922, 90.162344) : \
x<=0.396078 ? cubic(x, 8.471779, -73.154898, 211.089180, -195.491355) : \
x<=0.623529 ? cubic(x, -0.543610, 2.677936, -0.137169, -0.445552) : \
x<=0.749020 ? cubic(x, -15.225713, 68.550324, -96.645216, 45.458704) : \
x<=1.000000 ? cubic(x, 2.274626, -4.643168, 5.626198, -2.267654) : 0
g= x<=0.207843 ? cubic(x, 0.204965, 2.709276, -7.313826, 9.194078) : \
x<=0.396078 ? cubic(x, 0.376606, 0.109729, 4.680670, -7.355355) : \
x<=0.619608 ? cubic(x, 0.865401, -1.956191, 5.447395, -3.937938) : \
x<=0.760784 ? cubic(x, -8.802577, 42.865907, -62.175709, 29.088263) : \
x<=0.992157 ? cubic(x, 7.266933, -22.020637, 25.525012, -10.575381) : \
x<=1.000000 ? cubic(x, -17.632920, 38.955075, -21.133125, 0.000000) : 0
b= x<=0.203922 ? cubic(x, 0.963162, -2.861736, 0.251083, 4.557713) : \
x<=0.313725 ? cubic(x, 0.656233, 0.043612, -5.790983, 0.106573) : \
x<=0.400000 ? cubic(x, 17.430800, -140.294221, 376.158694, -334.690862) : \
x<=0.631373 ? cubic(x, 0.328764, -2.247241, 5.614561, -3.859553) : \
x<=0.968627 ? cubic(x, -0.646066, 4.007488, -5.858817, 2.485090) : \
x<=1.000000 ? cubic(x, -0.000000, 0.000000, -0.000000, 0.000000) : 0
} else if(cm==8) { # viridis python
r= x<=0.455523 ? cubic(x, 0.282113, 0.585552, -3.199668, 3.273305) : \
x<=0.700880 ? cubic(x, -2.797136, 18.565436, -37.531934, 24.521874) : \
x<=1.000000 ? cubic(x, 4.563142, -18.410284, 23.559766, -8.759172) : 0
g= x<=0.074291 ? cubic(x, -0.000438, -0.351490, 48.354922, -360.945985) : \
x<=0.702835 ? cubic(x, -0.014997, 1.564580, -1.154700, 0.700928) : \
x<=1.000000 ? cubic(x, -0.960756, 4.427797, -3.482215, 0.926468) : 0
b= x<=0.476051 ? cubic(x, 0.327782, 1.734561, -4.300750, 3.500006) : \
x<=0.932551 ? cubic(x, 0.218208, 1.243982, -0.736753, -0.849211) : \
x<=1.000000 ? cubic(x, 348.076269, -1047.336499, 1048.282355, -348.910600) : 0
} else if(cm==9) { # BlueGreenYellow
r= x<=0.250980 ? cubic(x, 0.121646, -0.172462, -1.127437, 5.431302) : \
x<=0.392157 ? cubic(x, -0.131357, 2.516024, -9.597266, 12.395703) : \
x<=0.556863 ? cubic(x, -1.492039, 10.422082, -22.967599, 17.609067) : \
x<=0.713725 ? cubic(x, -5.895145, 28.778858, -46.038523, 25.322913) : \
x<=0.847059 ? cubic(x, -8.586891, 32.582707, -40.596624, 17.627591) : \
x<=1.000000 ? cubic(x, -1.142666, 2.057658, -0.000297, 0.000113) : 0
g= x<=0.250980 ? cubic(x, 0.009478, 1.567212, 1.134523, -5.465413) : \
x<=0.392157 ? cubic(x, 0.263542, -1.131873, 9.632994, -12.442064) : \
x<=0.592157 ? cubic(x, 0.200958, 0.462406, 1.933537, -2.125990) : \
x<=1.000000 ? cubic(x, -0.091472, 2.264930, -1.894472, 0.618395) : 0
b= x<=0.188235 ? cubic(x, 0.399324, 0.574092, 1.663684, -7.302784) : \
x<=0.407843 ? cubic(x, 0.584562, -1.180634, 5.786781, -7.789910) : \
x<=1.000000 ? cubic(x, 0.380303, 1.004679, -1.825543, 0.793271) : 0
} else if(cm==10) { # parula matlab
r= x<=0.115347 ? cubic(x, 0.209319, 0.021835, 8.049552,-184.003036) : \
x<=0.184751 ? cubic(x, 2.374031, -44.761896, 276.704512,-556.160051) : \
x<=0.317693 ? cubic(x, -0.399346, 3.459321, -4.534020, -6.611694) : \
x<=0.447703 ? cubic(x, -2.173981, 20.360889, -61.942289, 62.029278) : \
x<=0.675464 ? cubic(x, 4.243855, -25.971352, 50.451225, -29.381695) : \
x<=0.840665 ? cubic(x, 1.758620, -8.829890, 15.820527, -7.604765) : \
x<=1.000000 ? cubic(x, -47.324025, 160.987718, -178.222332, 65.537864) : 0
g= x<=0.122190 ? cubic(x, 0.166515, 1.467473, -0.294203, 23.661735) : \
x<=0.328446 ? cubic(x, 0.142739, 2.829204, -8.770193, 13.750274) : \
x<=0.695015 ? cubic(x, 0.308801, 0.881104, 0.574870, -1.368778) : \
x<=0.842620 ? cubic(x, -14.989531, 63.658741, -85.592272, 38.217482) : \
x<=1.000000 ? cubic(x, -14.773917, 50.485538, -55.874747, 21.147001) : 0
b= x<=0.109482 ? cubic(x, 0.530296, 2.857383, 6.806557, -41.144233) : \
x<=0.232649 ? cubic(x, 0.465835, 7.313556, -40.797955, 70.197547) : \
x<=0.384164 ? cubic(x, 1.953887, -11.423272, 39.003550, -44.999622) : \
x<=0.675464 ? cubic(x, -0.247051, 7.832808, -17.887612, 11.458347) : \
x<=0.862170 ? cubic(x, 9.308603, -35.135626, 47.027607, -21.482656) : \
x<=1.000000 ? cubic(x, 14.096229, -43.850498, 47.004022, -17.195887) : 0
} else if(cm==11) { # avocado
r= x<=0.254902 ? cubic(x, -0.000315, 0.019821, -0.238792, 0.738267) : \
x<=0.521569 ? cubic(x, -0.384667, 1.975454, -2.290351, 2.092677) : \
x<=0.784314 ? cubic(x, 0.251672, -2.065961, 5.852542, -3.112441) : \
x<=1.000000 ? cubic(x, -0.264265, 1.264787, -0.000831, 0.000310) : 0
g= x<=0.258824 ? cubic(x, 0.000502, 1.740189, 0.372609, -1.140405) : \
x<=0.521569 ? cubic(x, 0.294585, 0.168953, 2.224051, -2.019746) : \
x<=1.000000 ? cubic(x, 0.427054, 0.465070, 0.118419, -0.025793) : 0
b= x<=0.407843 ? cubic(x, -0.000319, 0.297254, 0.186624, -0.857099) : \
x<=0.886275 ? cubic(x, -0.121618, 1.027933, -1.611968, 0.962846) : \
x<=1.000000 ? cubic(x, -0.107974, 0.338385, 0.000000, -0.000000) : 0
} else if(cm==12) { # Diverging-CoolWarm http://www.kennethmoreland.com/color-maps/
r= x<=0.616813 ? cubic(x, 0.337271, 0.983489, 0.747265, -1.195076) : \
x<=1.000000 ? cubic(x, -0.632934, 5.066503, -4.609700, 0.870305) : 0
g= x<=0.522972 ? cubic(x, 0.283621, 1.787108, -0.273675, -1.969690) : \
x<=0.953079 ? cubic(x, 0.509720, 2.032810, -2.808791, 0.356746) : \
x<=1.000000 ? cubic(x, 1127.813666, -3504.201247, 3632.816785, -1256.425801) : 0
b= x<=0.577713 ? cubic(x, 0.753360, 1.710547, -2.941316, -0.067188) : \
x<=1.000000 ? cubic(x, 1.240366, 0.386625, -3.038613, 1.566723) : 0
} else if(cm==13) { # thermometer
r= x<=0.125490 ? cubic(x, 0.162174, 1.201690, -6.399066, 51.243518) : \
x<=0.431373 ? cubic(x, 0.148005, 0.893940, 4.075881, -6.121149) : \
x<=0.549020 ? cubic(x, -4.033245, 27.676482, -53.245771, 34.957323) : \
x<=0.682353 ? cubic(x, 6.764309, -30.526849, 52.649881, -30.087859) : \
x<=0.823529 ? cubic(x, -9.803570, 42.258774, -54.801709, 23.209690) : \
x<=0.964706 ? cubic(x, 11.780482, -36.707047, 42.042428, -16.601556) : \
x<=1.000000 ? cubic(x, 2.266182, -1.864046, 0.199584, -0.067639) : 0
g= x<=0.149020 ? cubic(x, 0.120337, 2.121807, -1.069806, 14.995654) : \
x<=0.274510 ? cubic(x, -0.223638, 7.153696, -21.865513, 31.179040) : \
x<=0.372549 ? cubic(x, 1.546500, -9.998720, 36.221021, -38.417792) : \
x<=0.466667 ? cubic(x, 4.898614, -30.601930, 76.109977, -61.896098) : \
x<=0.576471 ? cubic(x, 10.130934, -54.795573, 108.692312, -72.115484) : \
x<=0.670588 ? cubic(x, 15.937621, -74.007429, 122.359430, -68.317410) : \
x<=0.776471 ? cubic(x, 4.301756, -14.376467, 21.324263, -11.667634) : \
x<=0.960784 ? cubic(x, -11.106730, 45.205518, -56.022964, 22.036255) : \
x<=1.000000 ? cubic(x, 1.807516, -1.709471, -0.019174, 0.006442) : 0
b= x<=0.133333 ? cubic(x, 0.794128, 0.966570, 4.388059, -37.453981) : \
x<=0.286275 ? cubic(x, 0.720815, 2.417972, -8.750889, 10.817765) : \
x<=0.419608 ? cubic(x, 1.358732, -3.883291, 12.716874, -14.600037) : \
x<=1.000000 ? cubic(x, 0.636442, 2.380296, -5.193566, 2.345535) : 0
} else if(cm==14) { # redbluetones
r= x<=0.274510 ? cubic(x, 0.449268, 1.574639, -0.822878, -1.491296) : \
x<=0.403922 ? cubic(x, -0.288228, 8.474660, -22.200837, 20.561929) : \
x<=0.509804 ? cubic(x, 3.707488, -19.016191, 42.456321, -31.670207) : \
x<=0.635294 ? cubic(x, 9.680930, -46.704589, 83.339750, -50.422752) : \
x<=0.878431 ? cubic(x, -2.137951, 13.824286, -20.185904, 8.656232) : \
x<=1.000000 ? cubic(x, 34.681746, -106.281568, 110.295455, -38.557173) : 0
g= x<=0.113725 ? cubic(x, 0.156994, 1.203165, -4.497128, 33.013271) : \
x<=0.321569 ? cubic(x, 0.143463, 0.889417, 4.005165, -5.745487) : \
x<=0.435294 ? cubic(x, 2.876165, -21.447213, 64.655291, -60.582508) : \
x<=0.529412 ? cubic(x, 10.474115, -64.301217, 140.750865, -101.324183) : \
x<=0.635294 ? cubic(x, 11.899055, -59.479146, 106.631277, -63.671925) : \
x<=0.752941 ? cubic(x, 3.869591, -13.953571, 22.184265, -12.226311) : \
x<=0.905882 ? cubic(x, -7.963197, 32.488971, -39.126611, 15.003588) : \
x<=1.000000 ? cubic(x, 2.422365, -2.104851, -0.009003, 0.003156) : 0
b= x<=0.184314 ? cubic(x, 0.219042, 0.690306, 0.608545, 2.946494) : \
x<=0.529412 ? cubic(x, 0.260646, 0.314043, 2.383175, -2.250743) : \
x<=0.639216 ? cubic(x, 8.263630, -42.062465, 77.213158, -46.359035) : \
x<=0.741176 ? cubic(x, 11.232975, -48.568134, 75.137634, -38.554181) : \
x<=0.850980 ? cubic(x, 4.206315, -14.675529, 21.410637, -10.502424) : \
x<=0.929412 ? cubic(x, 72.226097, -246.169093, 283.448543, -109.133180) : \
x<=1.000000 ? cubic(x, 2.153883, -1.589228, -0.021327, 0.007324) : 0
} else if(cm==15) { # tmap
r= x<=0.184314 ? cubic(x, 0.178983, 1.552415, -0.207975, 5.223602) : \
x<=0.341176 ? cubic(x, 0.066012, 2.264477, 0.673474, -2.095856) : \
x<=0.447059 ? cubic(x, 4.749953, -33.884109, 94.216232, -83.714029) : \
x<=0.670588 ? cubic(x, -0.868992, 8.918165, -14.178095, 7.483969) : \
x<=1.000000 ? cubic(x, -0.109994, 4.838318, -6.513456, 2.604411) : 0
g= x<=0.184314 ? cubic(x, 0.303925, 1.772992, -2.122434, 6.139617) : \
x<=0.349020 ? cubic(x, 0.277610, 1.481387, 2.270264, -4.510611) : \
x<=0.450980 ? cubic(x, 4.078043, -27.598191, 76.434953, -67.732938) : \
x<=0.666667 ? cubic(x, -0.655808, 8.086928, -13.137827, 7.055502) : \
x<=0.756863 ? cubic(x, 17.528872, -67.906478, 94.487329, -44.770083) : \
x<=0.921569 ? cubic(x, 4.773772, -10.130974, 9.493433, -3.915789) : \
x<=1.000000 ? cubic(x, 3.920833, -3.780528, -0.009403, 0.003226) : 0
b= x<=0.419608 ? cubic(x, 0.935393, 0.005125, 0.678124, -0.845400) : \
x<=0.505882 ? cubic(x, 6.416300, -34.137703, 72.988688, -53.484807) : \
x<=0.588235 ? cubic(x, 11.099459, -52.804586, 93.846613, -57.963352) : \
x<=0.666667 ? cubic(x, 2.844359, -3.625769, -0.006251, 0.003290) : \
x<=0.752941 ? cubic(x, -6.371378, 32.213485, -48.309479, 22.921856) : \
x<=1.000000 ? cubic(x, 1.358718, -2.895860, 2.697215, -0.996030) : 0
} else if(cm==16) { # ltmap
r= x<=0.533333 ? cubic(x, 0.163818, 1.791632, -0.273066, -0.474513) : \
x<=0.568627 ? cubic(x, 132.161025, -731.752508, 1358.253910, -838.937696) : \
x<=1.000000 ? cubic(x, 0.374538, 2.632874, -3.441293, 1.279874) : 0
g= x<=0.121569 ? cubic(x, 0.283064, 2.509624, 3.097213, -20.814460) : \
x<=0.262745 ? cubic(x, 0.526602, -1.130885, 18.376538, -36.628242) : \
x<=0.368627 ? cubic(x, 1.975347, -13.981096, 52.456257, -59.971000) : \
x<=0.482353 ? cubic(x, 4.081605, -24.751935, 63.659714, -53.109146) : \
x<=0.607843 ? cubic(x, 3.013910, -12.490787, 25.671804, -17.528325) : \
x<=0.698039 ? cubic(x, 22.796447, -103.139979, 163.020009, -86.219083) : \
x<=0.815686 ? cubic(x, 21.113658, -80.795116, 108.914800, -49.613536) : \
x<=0.933333 ? cubic(x, 21.071994, -69.419374, 80.770813, -32.128173) : 0
x<=1.000000 ? cubic(x, 2.643322, -2.266569, -0.011028, 0.003803) : \
b= x<=0.450980 ? cubic(x, 0.936797, 0.075986, 0.411047, -0.704823) : \
x<=0.909804 ? cubic(x, 1.411502, -0.307129, -1.841263, 0.895902) : \
x<=1.000000 ? cubic(x, 1.269224, -1.085101, 0.010742, -0.003716) : 0
} else if(cm==17) { # cividis
r= x<=0.121569 ? cubic(x, -0.000426, 0.060312, -1.553906, 10.160156) : \
x<=0.196078 ? cubic(x, -1.982815, 32.605251, -172.417296, 319.227164) : \
x<=0.666667 ? cubic(x, -0.133935, 2.107203, -2.734498, 2.026416) : \
x<=0.988235 ? cubic(x, 0.321580, -0.218041, 1.387263, -0.470313) : \
x<=1.000000 ? cubic(x, 1.000001, -0.000002, 0.000002, -0.000001) : 0
g= x<=1.000000 ? cubic(x, 0.125938, 0.709731, -0.053306, 0.135030) : 0
b= x<=0.078431 ? cubic(x, 0.302000, 1.452622, 8.254845, -63.440633) : \
x<=0.509804 ? cubic(x, 0.463205, -0.353857, 0.722687, 0.040738) : \
x<=0.976471 ? cubic(x, 0.546672, -0.581206, 1.466601, -1.184898) : \
x<=0.992157 ? cubic(x, -6481.511854, 19864.890017, -20291.986582, 6908.908418) : \
x<=1.000000 ? cubic(x, 15.165100, -31.148250, 16.256250, 0.000000) : 0
} else if(cm==18) { # inferno
r= x<=0.278431 ? cubic(x, 0.000616, 0.181010, 8.784927, -16.254186) : \
x<=0.835294 ? cubic(x, 0.071163, 0.487649, 3.088135, -2.832459) : \
x<=0.972549 ? cubic(x, -35.687813, 123.643703, -138.466305, 51.482349) : \
x<=1.000000 ? cubic(x, 118.864658, -346.470291, 337.712706, -109.118711) : 0
g= x<=0.160784 ? cubic(x, -0.000172, 0.233600, 5.737230, -36.119561) : \
x<=0.372549 ? cubic(x, 0.281181, -3.267615, 13.347637, -15.212603) : \
x<=0.737255 ? cubic(x, 0.074037, 0.082848, -0.311773, 1.415728) : \
x<=0.980392 ? cubic(x, 4.496346, -17.261553, 22.700021, -8.926780) : \
x<=1.000000 ? cubic(x, -48.680714, 144.190704, -140.418049, 45.906423) : 0
b= x<=0.168627 ? cubic(x, 0.012518, 1.598834, 9.459394, -36.477360) : \
x<=0.411765 ? cubic(x, -0.026832, 3.918837, -10.497266, 8.501689) : \
x<=0.768627 ? cubic(x, 0.028600, 2.810090, -5.762656, 2.712918) : \
x<=0.878431 ? cubic(x, 67.254062, -239.175364, 281.322381, -109.217866) : \
x<=0.984314 ? cubic(x, 48.249808, -153.577768, 160.185899, -54.202907) : \
x<=1.000000 ? cubic(x, -11.485235, 17.975087, -3.061272, -2.783656) : 0
} else if(cm==19) { # magma
r= x<=0.247059 ? cubic(x, 0.000271, 0.278879, 6.004937, -8.162905) : \
x<=0.615686 ? cubic(x, 0.025335, 0.775511, 1.932576, -1.465223) : \
x<=0.972549 ? cubic(x, -2.808277, 12.812626, -14.315520, 5.304693) : \
x<=1.000000 ? cubic(x, 2.643449, -4.614285, 4.339690, -1.381797) : 0
g= x<=0.184314 ? cubic(x, -0.000638, 0.266663, 5.739256, -29.239602) : \
x<=0.403922 ? cubic(x, 0.421904, -4.277433, 15.597475, -16.366417) : \
x<=0.717647 ? cubic(x, -0.792888, 5.506012, -11.062251, 8.150197) : \
x<=1.000000 ? cubic(x, -1.225919, 3.001718, -1.168042, 0.383598) : 0
b= x<=0.180392 ? cubic(x, 0.011535, 1.658287, 5.198221, -12.392081) : \
x<=0.380392 ? cubic(x, -0.406976, 7.975221, -23.376430, 23.001029) : \
x<=0.654902 ? cubic(x, -0.110203, 3.653996, -6.568599, 3.208048) : \
x<=0.984314 ? cubic(x, 6.066511, -20.284227, 22.862804, -7.900281) : \
x<=1.000000 ? cubic(x, -79.190218, 238.092163, -238.285225, 80.132784) : 0
} else if(cm==20) { # plasma
r= x<=0.149020 ? cubic(x, 0.053555, 2.803442, -11.132236, 34.980297) : \
x<=0.796078 ? cubic(x, 0.061463, 1.996474, -1.062348, 0.024568) : \
x<=1.000000 ? cubic(x, -0.861495, 4.340974, -2.518960, -0.022154) : 0
g= x<=0.235294 ? cubic(x, 0.027025, -0.084947, -0.961318, 3.749874) : \
x<=0.423529 ? cubic(x, 0.463271, -5.279437, 18.143049, -17.011311) : \
x<=1.000000 ? cubic(x, -0.288618, 1.299266, -0.636914, 0.604317) : 0
b= x<=0.392157 ? cubic(x, 0.530119, 1.080709, -1.909092, -1.533977) : \
x<=0.878431 ? cubic(x, 0.954945, -1.020016, 0.097473, 0.022702) : \
x<=0.992157 ? cubic(x, 48.742918, -153.154434, 160.670671, -56.107107) : \
x<=1.000000 ? cubic(x, -118.047093, 239.287425, -121.109006, 0.000000) : 0
}
r=min(max(nint(r*255),0), 255)
g=min(max(nint(g*255),0), 255)
b=min(max(nint(b*255),0), 255)
return sprintf("#%02X%02X%02X", r, g, b)
} ' $file.xpm > $file~iv.xpm
}
usage="\
>>>>>>>>>>>>>>>> xpm2all <<<<<<<<<<<<<<<<
>>>>>>>>>>>>>>>> Jicun Li <<<<<<<<<<<<<<<<
>>>>>>>>>> 2023-04-19 12:33:27 <<<<<<<<<
Usage: xpm2all <File> [-xyz|-mat|-rgb <cm>|-gpl <ssmode> <color> <minRes> <maxRes> <yminRes> ]
Default: xpm2all <File> -xyz
option: -xyz: xyz datafile
-mat: matrix datafile
-rgb: regular xpm file with
colormap cm
1: Rainbow 11: avocado
2: Rainbow gnuplot_33/13/10 12: Diverging-CoolWarm
3: Rainbow gnuplot_26/13/10 13: thermometer
4: Rainbow gnuplot_22/13/-31 14: redbluetones
5: Rainbow Mathmatica 15: tmap
6: DarkRainbow Mathmatica 16: ltmap
7: Rainbow CETR2 17: cividis
8: viridis python 18: inferno
9: BlueGreenYellow 19: magma
10: parula matlab 20: plasma
-gpl: gnuplot file to plot 2nd structure
ssmode: draw method
xyz: xyz data
box: plain box
fancy: fancy helix and beta sheet
color: gmx, pdb, p1, p2, p3
minRes: initial index of residue
maxRes: final index of residue
yminRes: y value of initial residue
--------------------------------------------------------------------------------
2023-04-19: fix bug for -xyz
2023-03-09: fix bugs for -gpl
--------------------------------------------------------------------------------"
[[ $# -lt 1 ]] && { echo "$usage"; exit; }
job=xyzmat; dat=xyz; cm=1;
minRes=1; maxRes=1E9; yminRes=1; ssmode="xyz"; color="pdb"
opt=($@); N=${#opt[@]};
for((i=0; i<N; i++)); do
arg=${opt[$i]};
[[ $arg =~ (-xyz)|(-mat) ]] && { dat=${arg/-/}; opt[$i]=""; }
[[ $arg =~ -rgb ]] && {
job=${arg/-/}; opt[$i]="";
j=$((i+1)); [[ $j -lt $N ]] && { cm=${opt[$j]}; opt[$j]=""; }
}
[[ $arg =~ -gpl ]] && {
job=${arg/-/}; opt[$i]="";
j=$((i+1)); [[ $j -lt $N ]] && { ssmode=${opt[$j]}; opt[$j]=""; }
j=$((i+2)); [[ $j -lt $N ]] && { color=${opt[$j]}; opt[$j]=""; }
j=$((i+3)); [[ $j -lt $N ]] && { minRes=${opt[$j]}; opt[$j]=""; }
j=$((i+4)); [[ $j -lt $N ]] && { maxRes=${opt[$j]}; opt[$j]=""; }
j=$((i+5)); [[ $j -lt $N ]] && { yminRes=${opt[$j]}; opt[$j]=""; }
}
done
file=${opt[@]%.xpm}
xpm2$job