mmagnus / rna-tools

def render_x():

  rx()

def rj():

  """

  rhiju's residue-level favorite coloring of proteins

  """

  cmd.bg_color( "white" )

  AllObj=cmd.get_names("all")

  for x in AllObj:

    #print(AllObj[0],x)

    print(x)

    cmd.show( "cartoon", x )

    #cmd.hide( "line", x )

    cmd.show( "line", x )

    cmd.color( "gray", x+" and resn trp+phe+ala+val+leu+ile+pro+met" )

    cmd.color( "orange", x+" and resn gly" )

    cmd.color( "red", x+" and resn asp+glu" )

    cmd.color( "blue", x+" and resn lys+arg+his" )

    cmd.color( "purple", x+" and resn cys" )

    cmd.color( "forest", x+" and resn tyr+thr+ser+gln+asn" )

    #cmd.spectrum( "count", "rainbow", x+" and name CA" )

    cmd.show( "sticks", x +" and not elem H and not name C+N+O" )

    cmd.show( "sticks", x +" and resn PRO and name N" )

    cmd.hide( "sticks", x + " and name NR+CR+CS+CP+CQ" )

    cmd.show( "sticks", x + " and not elem H and neighbor name NR+CQ+CR+CS+CP" )

  cmd.set( "cartoon_rect_length", 0.75 )

  cmd.set( "cartoon_rect_width", 0.1 )

  cmd.set( "cartoon_oval_length", 0.6 )

  cmd.set( "cartoon_oval_width", 0.2 )

def render_rhiju():

  rj()

def render_molecules():

  rd()

def rd():

  """

  rhiju's favorite coloring of proteins and generic molecules

  side chains are all-heavy-atom and colored CPK, backbone is

  rainbow cartoon from N to C terminus.

  """

  cmd.bg_color( "white" )

  AllObj=cmd.get_names("all")

  for x in AllObj:

    #print(AllObj[0],x)

    print(x)

    cmd.show( "cartoon", x )

    cmd.hide( "line", x )

    cmd.color( "white", x+" and elem C" )

    cmd.color( "blue", x+" and elem N" )

    cmd.color( "red", x+" and elem O" )

    cmd.color( "yellow", x+" and elem S" )

    cmd.spectrum( "count", "rainbow", x+" and name CA+C" )

    cmd.show( "sticks", x +" and not elem H and not name C+N+O" )

    cmd.show( "sticks", x +" and resn PRO and name N" )

    cmd.show( "sticks", x + " and name NR+CR+CS+CP+CQ" )

    cmd.show( "sticks", x + " and not elem H and neighbor name NR+CQ+CR+CS+CP" )

    cmd.show( "sticks", x + " and not elem H and neighbor neighbor name NR+CQ+CR+CS+CP" )

    cmd.set( "cartoon_oval_width", 0.1 )

    cmd.set( "cartoon_oval_length", 0.5 )

def rx():

  """