python 3 compatibility for examples/*.py files

add from __future__ import
print statement -> print() function
xrange -> range
map() -> list(map())
range() -> list(range())
StandardError -> Exception

examples/group_energy.py

@@ -5,6 +5,8 @@
 
 # return distance sq between 2 atoms with PBC
 
+from __future__ import absolute_import
+
 def distance(box,x1,y1,z1,x2,y2,z2):
 
   delx = x2 - x1
@@ -37,7 +39,7 @@ def distance(box,x1,y1,z1,x2,y2,z2):
 # main script
 
 if len(argv) < 3:
-  raise StandardError,"group_energy.py data.file dump.file1 dump.file2 ..."
+  raise Exception("group_energy.py data.file dump.file1 dump.file2 ...")
 
 dt = data(argv[1])                              # data file
 q = dt.get("Atoms",4)
@@ -75,32 +77,32 @@ while 1:
   d.aselect.test("$id >= 1 and $id <= 7243 or $id >= 7274 and $id <= 14283",
                  time)
   id2,type2,x2,y2,z2 = d.vecs(time,"id","type","x","y","z")
-  id1 = map(int,id1)
+  id1 = list(map(int,id1))
-  id2 = map(int,id2)
+  id2 = list(map(int,id2))
-  type1 = map(int,type1)
+  type1 = list(map(int,type1))
-  type2 = map(int,type2)
+  type2 = list(map(int,type2))
   n1 = len(type1)
   n2 = len(type2)
-  for i in xrange(n1): 
+  for i in range(n1):
     id1[i] -= 1
     type1[i] -= 1
-  for i in xrange(n2): 
+  for i in range(n2):
     id2[i] -= 1
     type2[i] -= 1
 
   e_coul_sum = 0.0
   e_vdwl_sum = 0.0
-  for i in xrange(n1):
+  for i in range(n1):
     typei = type1[i]
     qi = q[id1[i]]
-    for j in xrange(n2):
+    for j in range(n2):
       rsq = distance(box,x1[i],y1[i],z1[i],x2[j],y2[j],z2[j])
       if rsq < maxcut_sq:
         eng_coul,eng_vdwl = p.single(rsq,typei,type2[j],qi,q[id2[j]])
         e_coul_sum += eng_coul
         e_vdwl_sum += eng_vdwl
-  print "eng_coul = %g at timestep %d" % (e_coul_sum,time)
+  print("eng_coul = %g at timestep %d" % (e_coul_sum,time))
-  print "eng_vdwl = %g at timestep %d" % (e_vdwl_sum,time)
+  print("eng_vdwl = %g at timestep %d" % (e_vdwl_sum,time))
 
   d.tselect.none()
   d.tselect.one(time)

examples/movie_flow.py

@@ -1,5 +1,7 @@
 # movie of flow around obstacle
 
+from __future__ import absolute_import
+
 d = dump("dump.flow")
 d.map(1,"id",2,"type",3,"x",4,"y",5,"z",6,"vx",7,"vy")
 d.set("$ke = sqrt($vx*$vx + $vy*$vy)")
@@ -7,8 +9,8 @@ d.spread("vx",100,"color")
 d.atype = "color"
 
 r = raster(d)
-r.acol(range(100),["red","red","red","red","yellow","green","blue","purple","purple","purple","purple"])
+r.acol(list(range(100)),["red","red","red","red","yellow","green","blue","purple","purple","purple","purple"])
-r.arad(range(100),0.5)
+r.arad(list(range(100)),0.5)
 r.rotate(0,-90)
 r.zoom(1.5)
 r.file = "flow"

examples/movie_melt.py

@@ -1,6 +1,6 @@
 # movie of melting LJ solid
 
-a = dump("dump.melt")
+a = dump("files/dump.melt")
 a.tselect.test("$t == 0")
 a.scale()
 a.set("$ix = int($x * 4)")

examples/movie_micelle.py

@@ -1,10 +1,12 @@
 # movie of self-assembling micelles
 
-d = dump("dump.micelle")
+from __future__ import absolute_import
+
+d = dump("files/dump.micelle")
 
 s = svg(d)
 s.acol([1,2,3,4],["blue","red","cyan","yellow"])
-s.arad(range(4),0.5)
+s.arad(list(range(4)),0.5)
 s.zoom(1.5)
 
 s.file = "micelle"

examples/movie_peptide.py

@@ -1,8 +1,8 @@
 # movie of solvated peptide data
 
-d = dump("dump.peptide")
+d = dump("files/dump.peptide")
 d.unwrap()
-p = pdb("peptide",d)
+p = pdbfile("files/peptide",d)
-r.file = "peptide"
+
 r = rasmol(p)
 r.all()

examples/movie_tri.py

@@ -1,6 +1,6 @@
 # movie of triangular particle data
 
-d = dump("dump.tri")
+d = dump("files/dump.tri")
 d.set("$center = ((int($id)-1)/36+1)*36")
 d.owrap("center")
 

examples/test_animate.py

@@ -11,4 +11,4 @@ a.next()
 a.previous()
 a.frame(1)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_bdump.py

@@ -9,4 +9,4 @@ dm.extra(b)
 g = gl(dm)
 v = vcr(g)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_cdata.py

@@ -31,4 +31,4 @@ c.select("A","B","C","linebox","organelle","nuchalf")
 g = gl(c)
 v = vcr(g)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_cfg.py

@@ -9,4 +9,4 @@ x.one()
 x.many()
 x.single(0,"tmp.single")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_chain.py

@@ -14,4 +14,4 @@ c.build(10,25)
 
 c.write("tmp.data.chain")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_clog.py

@@ -4,13 +4,13 @@
 
 c = log("files/log.ccell")
 
-print "# of vectors =",c.nvec
+print("# of vectors =",c.nvec)
-print "length of vectors =",c.nlen
+print("length of vectors =",c.nlen)
-print "names of vectors =",c.names
+print("names of vectors =",c.names)
 
 time,a,b = c.get("Step","prey","predator")
-print a,b
+print(a,b)
 c.write("tmp.clog")
 c.write("tmp.clog.two","Step","prey")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_data.py

@@ -2,17 +2,19 @@
 # requires files/data.micelle and dump.micelle
 # creates tmp.data
 
+from __future__ import absolute_import
+
 d = data("files/data.micelle")
 d.map(1,"id",3,"type",4,"x",5,"y",6,"z")
 coeffs = d.get("Masses")
-print "Masses",coeffs
+print("Masses",coeffs)
 x = d.get("Atoms",4)
-print "X of 1st atom",x[0]
+print("X of 1st atom",x[0])
 
 d.title = "New LAMMPS data file"
 
 natoms = d.headers["atoms"]
-vec = range(1,natoms+1)
+vec = list(range(1,natoms+1))
 vec.reverse()
 d.replace("Atoms",1,vec)
 
@@ -27,4 +29,4 @@ while 1:
 
 d.write("tmp.data")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_dump.py

@@ -27,12 +27,12 @@ d.set("$xyz = $x + $y + $z")
 d.spread("x",100,"color")
 d.clone(0,"color")
 
-print "Time",d.time()
+print("Time",d.time())
 color = d.atom(1,"color")
-print "Color of atom 1",color
+print("Color of atom 1",color)
 d.aselect.test("$id <= 10")
 color = d.vecs(1000,"color")
-print "Color of 1st 10 atoms in step 1000",color
+print("Color of 1st 10 atoms in step 1000",color)
 
 d.atype = "color"
 
@@ -42,13 +42,13 @@ while 1:
   if flag == -1: break
   time,box,atoms,bonds,tris,lines = d.viz(index)
   colors = [atom[1] for atom in atoms]
-  print time,colors
+  print(time,colors)
 
 d = dump("files/dump.peptide.*",0)
 while 1:
   time = d.next()
   if time < 0: break
 
-print "Incrementally read snaps =",d.nsnaps
+print("Incrementally read snaps =",d.nsnaps)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_ensight.py

@@ -1,4 +1,4 @@
-# simple test of xyz tool
+# simple test of ensight tool
 # requires files/dump.micelle.*
 # creates tmp*.case, etc
 
@@ -8,4 +8,4 @@ e.one()
 e.many()
 e.single(0)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_gl.py

@@ -2,6 +2,8 @@
 # requires files/dump.kinase
 # creates tmp*.png
 
+from __future__ import absolute_import
+
 d = dump("files/dump.kinase")
 g = gl(d)
 
@@ -17,7 +19,7 @@ g.all()
 from vizinfo import colors
 
 g.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
-g.arad(range(9),0.3)
+g.arad(list(range(9)),0.3)
 #g.label(0.2,0.4,'h',15,"red","test label #1")
 #g.label(-0.2,-0.4,'h',15,"yellow","test label #2")
 
@@ -25,4 +27,4 @@ g.show(0)
 g.pan(60,130,1,60,30,0.5)
 g.all(0,10,0)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_gnu.py

@@ -1,17 +1,19 @@
 # simple test of gnu tool
 # creates tmp.eps
 
+from __future__ import absolute_import
+
 g = gnu()
 
 g("plot sin(x) with lines")
 
-a = range(10)
+a = list(range(10))
 b = [3,6,2,5,7,3,6,5,3,1]
 
 g.plot(a)
 g.plot(a,b)
 g.plot(a,b,b,a)
-g.mplot(0,10,2,"tmp",a,b)
+g.mplot(2,10,2,"tmp",a,b)
 
 g.export("tmp.gnu",a,b)
 
@@ -30,4 +32,4 @@ g.ylog()
 
 g.save("tmp")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_histo.py

@@ -10,4 +10,4 @@ g.ytitle("Particle Count")
 g.title("Histogram of Particle Density")
 g.plot(x,y)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_image.py

@@ -4,6 +4,6 @@
 i = image("files/bucky*.png")
 i.convert("files/bucky*.png","tmp*.gif")
 i.montage("","files/bucky*.png","tmp*.gif","tmpnew*.png")
-i.view("")
+i.view("*.png")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_ldump.py

@@ -12,4 +12,4 @@ g.lrad(1,5)
 g.lcol(1,"green")
 v = vcr(g)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_log.py

@@ -4,13 +4,13 @@
 
 lg = log("files/log.obstacle")
 
-print "# of vectors =",lg.nvec
+print("# of vectors =",lg.nvec)
-print "length of vectors =",lg.nlen
+print("length of vectors =",lg.nlen)
-print "names of vectors =",lg.names
+print("names of vectors =",lg.names)
 
 time,temp,press = lg.get("Step","Temp","Press")
-print temp,press
+print(temp,press)
 lg.write("tmp.log")
 lg.write("tmp.log.two","Step","E_pair")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_matlab.py

@@ -1,9 +1,11 @@
 # simple test of matlab tool
 # creates tmp.eps
 
+from __future__ import absolute_import
+
 m = matlab()
 
-a = range(10)
+a = list(range(10))
 b = [3,6,2,5,7,3,6,5,3,1]
 
 m.plot(a)
@@ -30,4 +32,4 @@ m.ylog()
 
 m.save("tmp")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_mdump.py

@@ -12,7 +12,7 @@ m.tselect.all()
 m.tselect.test("$t >= 100 and $t <= 200")
 m.delete()
 
-print "Time",m.time()
+print("Time",m.time())
 
 m.map(2,"spin")
 m.etype = "spin"
@@ -23,13 +23,13 @@ while 1:
   if flag == -1: break
   time,box,atoms,bonds,tris,lines = m.viz(index)
   colors = [tri[1] for tri in tris]
-  print time,colors
+  print(time,colors)
 
 m = dump("files/mesh.grain",0)
 while 1:
   time = m.next()
   if time < 0: break
 
-print "Incrementally read snaps =",m.nsnaps
+print("Incrementally read snaps =",m.nsnaps)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_pair.py

@@ -6,6 +6,6 @@ d = data("files/data.rhodo")
 p.coeff(d)
 p.init(8.0,10.0)
 ev,ec = p.single(5.0,1,2,0.5,-0.5)
-print "Energies",ev,ec
+print("Energies",ev,ec)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_patch.py

@@ -7,4 +7,4 @@ p.build(100,"hex2",1,2,3)
 p.build(50,"tri5",4,5)
 p.write("tmp.data.patch")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_pdbfile.py

@@ -15,6 +15,6 @@ while 1:
   p.single(time,"tmp.single")
   n += 1
 
-print "Incrementally processed %d PDB files" % n
+print("Incrementally processed %d PDB files" % n)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_plotview.py

@@ -15,4 +15,4 @@ p.no(2)
 p.file("tmp.plotview")
 p.save()
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_rasmol.py

@@ -8,14 +8,14 @@ p = pdbfile("files/peptide",d)
 r = rasmol(p)
 r.file = "tmp"
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 r.show(0)
 r.all()
 
 # change RasMol settings, run all() with those settings
 
-print "change RasMol settings as desired, then type 'quit' ..."
+print("change RasMol settings as desired, then type 'quit' ...")
 r.run(0)
 r.all("tmp.rasmol")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_raster.py

@@ -2,6 +2,8 @@
 # requires files/dump.kinase
 # creates tmp*.png
 
+from __future__ import absolute_import
+
 d = dump("files/dump.kinase")
 r = raster(d)
 
@@ -10,7 +12,7 @@ r.rotate(60,130)
 r.box(1)
 r.file = "tmp"
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 r.show(0)
 r.all()
 a1 = animate("tmp0*png")
@@ -18,14 +20,14 @@ a1 = animate("tmp0*png")
 from vizinfo import colors
 
 r.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
-r.arad(range(9),0.3)
+r.arad(list(range(9)),0.3)
 r.label(0.2,0.4,'h',15,"red","test label #1")
 r.label(-0.2,-0.4,'h',15,"yellow","test label #2")
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 r.show(0)
 r.pan(60,130,1,60,30,0.5)
 r.all(0,10,0)
 a2 = animate("tmp0*png")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_svg.py

@@ -2,6 +2,8 @@
 # requires files/dump.kinase
 # creates tmp*.png
 
+from __future__ import absolute_import
+
 d = dump("files/dump.kinase")
 s = svg(d)
 
@@ -10,20 +12,20 @@ s.rotate(60,130)
 s.box(1)
 s.file = "tmp"
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 s.show(0)
 s.all()
 
 from vizinfo import colors
 
 s.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
-s.arad(range(9),0.3)
+s.arad(list(range(9)),0.3)
 s.label(0.2,0.4,'h',15,"red","test label #1")
 s.label(-0.2,-0.4,'h',15,"yellow","test label #2")
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 s.show(0)
 s.pan(60,130,1,60,30,0.5)
 s.all(0,10,0)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_vcr.py

@@ -13,4 +13,4 @@ v.clipxlo(0.2)
 v.clipxhi(0.5)
 v.play()
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_vec.py

@@ -4,13 +4,13 @@
 
 v = vec("files/vec.txt")
 
-print "# of vectors =",v.nvec
+print("# of vectors =",v.nvec)
-print "length of vectors =",v.nlen
+print("length of vectors =",v.nlen)
-print "names of vectors =",v.names
+print("names of vectors =",v.names)
 
 time,temp,press = v.get(1,"col2",6)
-print temp,press
+print(temp,press)
 v.write("tmp.vec")
 v.write("tmp.vec.two","col1",3)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_vmd.py

@@ -8,4 +8,4 @@ v.rep('VDW')
 v.new('files/peptide.pdb','pdb')
 v.flush()
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_vtk.py

@@ -8,4 +8,4 @@ v.one()
 v.many()
 v.single(0,"tmp.single")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_xyz.py

@@ -8,4 +8,4 @@ x.one()
 x.many()
 x.single(0,"tmp.single")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")