build.rna_tools.tools.PyMOL4RNA.libs.pymol_daslab

Complexity

Total Complexity

75

Size/Duplication

Total Lines	625
Duplicated Lines	40.32 %

Importance

Changes

0

30 Functions

Rating	Name	Duplication	Size	Complexity
A	render_cartoon()	0	2	1
A	rr2()	0	9	1
C	align_all()	0	45	11
A	render_rna_sticks()	0	2	1
A	render_rhiju()	0	2	1
A	render_rna()	0	2	1
A	rcd()	0	7	1
A	render_molecules()	0	2	1
A	superimpose_all()	0	2	1
A	sa()	0	16	4
A	rx()	0	27	3
A	atomcolor()	0	11	1
A	chainbow()	0	8	2
A	render_x()	0	2	1
A	rr()	65	65	2
A	rcm()	35	35	2
A	render_rna2()	0	2	1
A	source_pymol_rhiju()	0	5	1
A	bx()	0	12	2
A	color_by_text()	0	5	2
A	spr()	0	6	1
F	color_by_data()	0	51	17
A	rb()	0	16	2
A	rj()	28	28	2
A	get_residue_colors()	0	14	3
A	rc()	33	33	2
A	rg()	65	65	2
A	rd()	26	26	2
A	rrs()	0	7	1
A	loop_color()	0	43	3

from pymol import cmd,util
import inspect
import tempfile
from glob import glob
from tempfile import NamedTemporaryFile
# Pymol commands used by the Das Lab
# (C) R. Das 2010-2013.
#
# Some documentation and sample images available at:
#
# https://docs.google.com/document/d/1uWeEEGPjAceaw07ESf9bec-FrxW4Bx6jGaBqoHbSXuo/edit
#

print('rp06() -- colors for helices of rp06')
print('rp14() -- colors for helices of rp14')
print('sa -- superimpose all')
print('aa -- align all -- full atom RMSD!')
print('rcd() # flat ribbon with sticks')

def sa(intra=False,rainbow=True):
  """
  Superimpose all open models onto the first one.
  This may not work well with selections.
  Option intra can be set to True to enable intra_fit first, for working with multi-state (nmr) pdbs.
  [Thanks to Kyle Beauchamp for this one]
  """
  AllObj=cmd.get_names("all")
  for x in AllObj:
    print(AllObj[0],x)
    if intra==True:
      cmd.intra_fit(x)
    if rainbow==True:
      cmd.util.chainbow(x)
    cmd.align(x,AllObj[0])
    cmd.zoom()

def superimpose_all(intra=False,rainbow=True):
  sa( intra, rainbow );

def chainbow():
  """
  run chainbow on all molecules, one by one.
  """
  AllObj=cmd.get_names("all")
  for x in AllObj:
    print(AllObj[0],x)
    cmd.util.chainbow(x)

def color_by_data( filename, offset = 0, min_val=-1.0, max_val = 0.0 ):
  """
  Read in a text file with rows like:

  125 0.12
  126 1.50

  and color specified residue numbers by scalar values.
  Takes advantage of B-factor column, and color by temperature
  function in pymol. Note that coloring is scaled/offset based
  on lowest/highest scalar value.
  """
  lines = open( filename ).readlines()
  data = {}
  data_backbone = {}

  avg_data = 0.0
  min_data = 0.0
  max_data = 0.0
  for line in lines:
    cols = string.split( line )

The variable string does not seem to be defined.

    dataval = float( cols[1] )
    if min_val >= 0 and dataval < min_val: dataval = min_val
    if max_val > 0 and dataval > max_val: dataval = max_val
    data[ int( cols[0] )  ] = dataval

The variable int does not seem to be defined.

    avg_data = avg_data + dataval
    if ( dataval < min_data ): min_data = dataval
    if ( dataval > max_data ): max_data = dataval

    if len( cols ) > 2:
      dataval2 = float( cols[2] )
      if min_val >= 0 and dataval2 < min_val: dataval2 = min_val
      if max_val > 0 and dataval2 > max_val: dataval2 = max_val
      data_backbone[ int( cols[0] ) ] = dataval2


  avg_data /= len( data.keys() )

  cmd.alter( 'all', 'b=%6.3f' % avg_data )

  for i in data.keys():
    cmd.alter( 'resi  \\%d' % (i+int(offset)),  'b=%6.3f' % data[i] )

  backbone_tag = " and (name o1p+o2p+o3p+p+op1+op2+'c1*'+'c2*'+'c3*'+'c5*'+'o2*'+'o3*'+'o4*'+'o5*'+'c1*'+'c2*'+'c3*'+'c4*'+'o2*'+'o4*'+c1'+c2'+c3'+c5'+o2'+o3'+o4'+o5'+c1'+c2'+c3'+c4'+o2'+o4') and (not name c1+c2+c3+c4+c5+o2+o3+o4+o5)"
  for i in data_backbone.keys():
    cmd.alter( 'resi  \\%d %s' % (i+int(offset),backbone_tag),  'b=%6.3f' % data_backbone[i] )

  if ( min_val < 0 ): min_val = min_data
  if ( max_val < 0 ): max_val = max_data

  cmd.spectrum( "b", "rainbow","all",min_val,max_val )
  #cmd.ramp_new("ramp_obj", "1gid_RNAA", range=[0, 0, max_val], color="[blue, white, red ]")

def align_all( subset = [] ):
  """
  Superimpose all open models onto the first one.
  This may not work well with selections.
  """
  PATH_BAR_CHAT = '/Users/magnus/Documents/GTD/software/data_hacks/bar_chart.py'

  print("""This returns a list with 7 items:

    RMSD after refinement
    Number of aligned atoms after refinement
    Number of refinement cycles
    RMSD before refinement
    Number of aligned atoms before refinement
    Raw alignment score
    Number of residues aligned """)

  AllObj=cmd.get_names("all")
  report = []
  for x in AllObj[1:]:
    #print(AllObj[0],x)
    subset_tag = ''
    if isinstance( subset, int ):
      subset_tag = ' and resi %d' % subset
    elif isinstance( subset, list ) and len( subset ) > 0:
      subset_tag = ' and resi %d' % (subset[0])
      for m in range( 1,len(subset)): subset_tag += '+%d' % subset[m]
    elif isinstance( subset, str ) and len( subset ) > 0:
      subset_tag = ' and %s' % subset
    values = cmd.align(x+subset_tag,AllObj[0]+subset_tag)
    print(AllObj[0], x, ' '.join([str(v) for v in values]), '-- RMSD', values[3], ' of ', values[6], 'residues')
    print(AllObj[0], x, 'RMSD: ', values[3], ' of ', values[6], 'residues')
    report.append([AllObj[0], x, values[3], values[6]])
    cmd.zoom()


  print('==== SUMMARY =====')
  f = NamedTemporaryFile(delete=False)
  for i in report:
    if not i[1].startswith('_align'):
      # rp14_5ddp_bound_clean_ligand rp14_farna_eloop_nol2fixed_cst.out.1 RMSD:  4.49360132217 of 52 residues
      if i[1] not in ['sele', 'rov_pc']: # skip them
        print(i[0], i[1], 'RMSD:', round(i[2],2), str(i[3]) + 'nt')
        #f.write(i[0] + '-' + i[1] + ' ' + str(i[2]) + '\n')
  print()
  #print f.name
  #x = 'cat ' + f.name + ' | python ' + PATH_BAR_CHAT + ' -A -k -v --dot ='
  #f.close()
  #print x
  #print commands.getoutput(x)


def render_molecules():
  rd()

def rd():

This code seems to be duplicated in your project.

  """
  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():
  """
  rhiju's favorite coloring of proteins, more details --
  no cartoon; heavy backbone
  """
  cmd.bg_color( "white" )
  AllObj=cmd.get_names("all")

  for x in AllObj:
    #print(AllObj[0],x)
    print(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.select('backbone','name o+c+ca+n')
    cmd.show('sticks','not elem H')

    if not x.count( 'BACKBONE' ):
      cmd.create( x+"_BACKBONE", x+" and not element H and backbone" )


    cmd.set('stick_radius', '0.5', "*BACKBONE" )

def render_x():
  rx()

def rj():

This code seems to be duplicated in your project.

  """
  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 rg(rainbow=False):

This code seems to be duplicated in your project.

  """
  rhiju's favorite coloring of RNA
  with 2' OH as spheres,
  bases as filled rings, and backbone as cartoon
  ribbons, rainbow colored from 5' to 3'. No hydrogens,

  change: don't color the backbone
  """
  # cmd.bg_color( "white" )

  # cmd.hide('everything' ) # don't hide
  cmd.show('sticks','not elem H')

  #cmd.color( 'red','resn rG+G+DG')
  #cmd.color( 'forest','resn rC+C+DC')
  #cmd.color( 'orange','resn rA+A+DA')
  #cmd.color( 'blue','resn rU+U+DT+BRU')

  #cmd.set( 'cartoon_ring_color',  'red','resn rG+G+DG')
  #cmd.set( 'cartoon_ring_color',  'forest','resn rC+C+DC')
  #cmd.set( 'cartoon_ring_color',  'orange','resn rA+A+DA')
  #cmd.set( 'cartoon_ring_color',  'blue','resn rU+U+DT+BRU')

  #cmd.set( 'cartoon_ring_color',  'red','resn RG+G+DG+RG3+RG5')
  #cmd.set( 'cartoon_ring_color',  'forest','resn rC+C+DC+RC+RC3+RC5')
  #cmd.set( 'cartoon_ring_color',  'orange','resn rA+A+DA+RA+RA3+RA5')
  #cmd.set( 'cartoon_ring_color',  'blue','resn rU+U+DT+BRU+RU+RU3+RU5')

  cmd.select('bases','name c2+c4+c5+c6+c8+n1+n2+n3+n4+n6+n7+n9+o2+o4+o6+n1p')
  cmd.select('backbone_', 'name o1p+o2p+o3p+p+c1*+c2*+c3*+c5*+o2*+o3*+o4*+o5*')
  cmd.select('sugar', 'name c1*+c2*+c3*+c4*+o2*+o4*')
  AllObj=cmd.get_names("all")

  cmd.color( 'gray','resn RG+G+RG3+RG5 and name N1+C6+O6+C5+C4+N7+C8+N9+N3+C2+N1+N2')
  cmd.color( 'gray','resn rC+C+RC+RC3+RC5 and name N1+C2+O2+N3+C4+N4+C5+C6')
  cmd.color( 'gray','resn rA+A+RA+RA3+RA5 and name N1+C6+N6+C5+N7+C8+N9+C4+N3+C2')
  cmd.color( 'gray','resn rU+U+RU+RU3+RU5 and name N3+C4+O4+C5+C6+N1+C2+O2')
  cmd.color('gray', "name c1*+c2*+c3*+c4*+o2*+o4*+C1'+C2'+C3'+C4'+O2'+O4'")
  cmd.select( 'backbone_', " (name o1p+o2p+o3p+p+op1+op2+'c1*'+'c2*'+'c3*'+'c5*'+'o2*'+'o3*'+'o4*'+'o5*'+'c1*'+'c2*'+'c3*'+'c4*'+'o2*'+'o4*'+c1'+c2'+c3'+c5'+o2'+o3'+o4'+o5'+c1'+c2'+c3'+c4'+o2'+o4') and (not name c1+c2+c3+c4+c5+o2+o3+o4+o5) ")

  for x in AllObj:
    cmd.show( "cartoon", x )
    #cmd.spectrum( "count", "rainbow", x+" and backbone" )
    #cmd.color( 'white', 'backbone' )

  cmd.cartoon("tube", "backbone" )

  cmd.set( "cartoon_ring_mode", 3 )
  cmd.set( "cartoon_ring_transparency", 0.0 )
  #CMD.set( "cartoon_tube_radius", 0.8)

  cmd.hide( "sticks", "backbone" )
  cmd.alter( "name o2*","vdw=0.5" )
  cmd.show( "spheres", "name o2'+'o2*' and not name o2" )
  cmd.show( "sticks", "name 'o2*'+'c2*'" )

  cmd.alter( "resn mg", "vdw=1.0")
  cmd.alter( "resn hoh", "vdw=0.5")
  cmd.show( "spheres", "resn mg+sr+co+zn")

  # clean up
  cmd.delete('backbone_')
  cmd.delete('bases')
  cmd.delete('sugar')

cmd.extend('rg', rg)

def rr(rainbow=False):

This code seems to be duplicated in your project.

  """
  rhiju's favorite coloring of RNA
  with 2' OH as spheres,
  bases as filled rings, and backbone as cartoon
  ribbons, rainbow colored from 5' to 3'. No hydrogens,

  change: don't color the backbone
  """
  # cmd.bg_color( "white" )

  # cmd.hide('everything' ) # don't hide
  cmd.show('sticks','not elem H')

  #cmd.color( 'red','resn rG+G+DG')
  #cmd.color( 'forest','resn rC+C+DC')
  #cmd.color( 'orange','resn rA+A+DA')
  #cmd.color( 'blue','resn rU+U+DT+BRU')

  #cmd.set( 'cartoon_ring_color',  'red','resn rG+G+DG')
  #cmd.set( 'cartoon_ring_color',  'forest','resn rC+C+DC')
  #cmd.set( 'cartoon_ring_color',  'orange','resn rA+A+DA')
  #cmd.set( 'cartoon_ring_color',  'blue','resn rU+U+DT+BRU')

  #cmd.set( 'cartoon_ring_color',  'red','resn RG+G+DG+RG3+RG5')
  #cmd.set( 'cartoon_ring_color',  'forest','resn rC+C+DC+RC+RC3+RC5')
  #cmd.set( 'cartoon_ring_color',  'orange','resn rA+A+DA+RA+RA3+RA5')
  #cmd.set( 'cartoon_ring_color',  'blue','resn rU+U+DT+BRU+RU+RU3+RU5')

  cmd.select('bases','name c2+c4+c5+c6+c8+n1+n2+n3+n4+n6+n7+n9+o2+o4+o6+n1p')
  cmd.select('backbone_', 'name o1p+o2p+o3p+p+c1*+c2*+c3*+c5*+o2*+o3*+o4*+o5*')
  cmd.select('sugar', 'name c1*+c2*+c3*+c4*+o2*+o4*')
  AllObj=cmd.get_names("all")

  cmd.color( 'red','resn RG+G+RG3+RG5 and name N1+C6+O6+C5+C4+N7+C8+N9+N3+C2+N1+N2')
  cmd.color( 'forest','resn rC+C+RC+RC3+RC5 and name N1+C2+O2+N3+C4+N4+C5+C6')
  cmd.color( 'orange','resn rA+A+RA+RA3+RA5 and name N1+C6+N6+C5+N7+C8+N9+C4+N3+C2')
  cmd.color( 'blue','resn rU+U+RU+RU3+RU5 and name N3+C4+O4+C5+C6+N1+C2+O2')

  cmd.select( 'backbone_', " (name o1p+o2p+o3p+p+op1+op2+'c1*'+'c2*'+'c3*'+'c5*'+'o2*'+'o3*'+'o4*'+'o5*'+'c1*'+'c2*'+'c3*'+'c4*'+'o2*'+'o4*'+c1'+c2'+c3'+c5'+o2'+o3'+o4'+o5'+c1'+c2'+c3'+c4'+o2'+o4') and (not name c1+c2+c3+c4+c5+o2+o3+o4+o5) ")

  for x in AllObj:
    cmd.show( "cartoon", x )
    #cmd.spectrum( "count", "rainbow", x+" and backbone" )
    #cmd.color( 'white', 'backbone' )

  cmd.cartoon("tube", "backbone" )

  cmd.set( "cartoon_ring_mode", 3 )
  cmd.set( "cartoon_ring_transparency", 0.0 )
  #CMD.set( "cartoon_tube_radius", 0.8)

  cmd.hide( "sticks", "backbone" )
  cmd.alter( "name o2*","vdw=0.5" )
  cmd.show( "spheres", "name o2'+'o2*' and not name o2" )
  cmd.show( "sticks", "name 'o2*'+'c2*'" )

  cmd.alter( "resn mg", "vdw=1.0")
  cmd.alter( "resn hoh", "vdw=0.5")
  cmd.show( "spheres", "resn mg+sr+co+zn")

  # clean up
  cmd.delete('backbone_')
  cmd.delete('bases')
  cmd.delete('sugar')

def render_rna():
  rr()
  
def rrs():
  """)
  rhiju's favorite coloring of RNA, showing
  all heavy atoms as sticks -- more detail than rr().
  """
  rr()
  cmd.show( 'sticks', 'not elem H' )

def render_rna_sticks():
  rr()

def rr2():
  """
  rhiju's favorite coloring of RNA, showing
  all heavy atoms as sticks -- more detail than rr().
  """
  rr()
  cmd.hide( 'spheres' )
  cmd.hide( 'sticks' )
  cmd.set( "cartoon_ring_mode", 0 )

def render_rna2():
  rr2()


def get_residue_colors( sele ):
  """
  Get RGB color values associated with a selection.
  Useful if you want to exactly match coloring of 3D models
  with coloring in, say, a MATLAB script.
  """
  pymol.stored.colors = []

The variable pymol does not seem to be defined.

  cmd.iterate( sele, "stored.colors.append( (chain, resi, name, color))")
  res_colors = {}
  for chain, resi, name, color in pymol.stored.colors:
    if name == 'CA': # c-alpha atom
      res_colors[(chain, resi)] = cmd.get_color_tuple(color)
  print(res_colors)
  return res_colors

def spr():
  """
  Load up these commands again after, say, an edit.
  """

  cmd.do( 'run '+inspect.getfile(inspect.currentframe()) )

def source_pymol_rhiju():
  """
  Load up these commands again after, say, an edit.
  """
  spr()


def loop_color( start, end, native=None, zoom=False ):
  """
  Used for rendering protein loop modeling puzzles.
  White in background, colored red/blue over loop.
  """

  rd()

  cmd.color( "white", "not resi %d-%d" % (start,end) )
  #cmd.hide( "cartoon", "resi %d-%d" % (start,end) )
  #cmd.show( "sticks", "not elem H and resi %d-%d" % (start,end) )

  #before_start = start - 1
  #cmd.show( "sticks", "name C and resi %d" % (before_start) )
  #after_end = end + 1
  #cmd.show( "sticks", "name N and resi %d" % (after_end) )

  cmd.color( "salmon",  "elem C and resi %d-%d" % (start,end) )

  #cmd.show( "lines", "not elem H" )
  #cmd.hide( "cartoon",  "resi %d-%d" % (start,end) )
  #cmd.show( "sticks",  "name C+N+CA+O and resi %d-%d" % (start,end) )
  cmd.hide( "sticks", "resi %d-%d and name C+N+O" % (start,end) )
  cmd.show( "sticks", "resn PRO and name N")
  cmd.show( "sticks", x +" and ( not elem H and neighbor name NR+CR+CS+CP+CQ )" )

The variable x does not seem to be defined.

  if native:

    # reassign colors based on native -- spectrum colors by atom count and
    # messes up loop coloring on small loop subsegments.
    #colors = get_residue_colors( "%s and resi %d-%d" % (native,start,end) )
    #for x in AllObj:
      #for m in range( start, end+1):
        #cmd.set_color( 'color%d' % m, colors[ ('','%d' % m) ] )
        #cmd.color( 'color%d' % m, 'elem C and resi %d' % m )


    cmd.color( "white", native + " and not resi %d-%d" % (start,end) )
    #cmd.color( "palecyan", native+" and not name C+N+CA+O")
    cmd.color( "skyblue", native+" and elem C and resi %d-%d" % (start,end) )

  if zoom: cmd.zoom( "resi %d-%d" % (start,end) )


def rb():
  """
  basic cartoon coloring
  """

  AllObj=cmd.get_names("all")
  cmd.bg_color( "white" )
  cmd.hide( "ev" )
  cmd.show( "cartoon" )
  cmd.cartoon( "rectangle" )
  cmd.set( "cartoon_ring_mode", 1 )
  cmd.set( "cartoon_rect_length", 0.7 )
  cmd.set( "cartoon_rect_width", 0.2 )
  for x in AllObj:
    print(AllObj[0],x)
    cmd.spectrum( "count", "rainbow", x )

def atomcolor():
  """
  atom coloring
  """

  cmd.bg_color( "white" )
  cmd.hide( "ev" )
  cmd.show( "sticks", "not elem H" )
  cmd.show( "lines", "elem H" )
  util.cbag()
  cmd.color( "white", "elem C" )

def rc():

This code seems to be duplicated in your project.

  """
  tube coloring for large RNA comparisons
  """
  cmd.bg_color( "white" )
  cmd.hide( 'everything' )

  cmd.color( 'red','resn rG+G+DG')
  cmd.color( 'forest','resn rC+C+DC')
  cmd.color( 'orange','resn rA+A+DA')
  cmd.color( 'blue','resn rU+U+DT+BRU')

  AllObj=cmd.get_names("all")

  cmd.select( 'backbone', " (name o1p+o2p+o3p+p+op1+op2+'c1*'+'c2*'+'c3*'+'c5*'+'o2*'+'o3*'+'o4*'+'o5*'+'c1*'+'c2*'+'c3*'+'c4*'+'o2*'+'o4*'+c1'+c2'+c3'+c5'+o2'+o3'+o4'+o5'+c1'+c2'+c3'+c4'+o2'+o4') and (not name c1+c2+c3+c4+c5+o2+o3+o4+o5) ")

  for x in AllObj:
    print(x)
    cmd.show( "cartoon", x )
    cmd.spectrum( "count", "rainbow", x+" and backbone" )

  cmd.cartoon( "tube", "backbone" )

  cmd.set( "cartoon_ring_mode", 0 )
  cmd.set( "cartoon_ring_transparency", 0.0 )
  cmd.set( "cartoon_tube_radius", 1.0 )

  cmd.color( 'red','resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2')
  cmd.color( 'forest','resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6')
  cmd.color( 'orange','resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2')
  cmd.color( 'blue','resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2')

  cmd.delete('backbone')

def rcm():

This code seems to be duplicated in your project.

  """
  tube coloring for large RNA comparisons
  """
  #cmd.bg_color( "white" )
  cmd.hide( 'everything' )

  cmd.set('cartoon_ladder_mode', 0 )

  cmd.color( 'red','resn rG+G+DG')
  cmd.color( 'forest','resn rC+C+DC')
  cmd.color( 'orange','resn rA+A+DA')
  cmd.color( 'blue','resn rU+U+DT+BRU')

  AllObj=cmd.get_names("all")

  cmd.select( 'backbone', " (name o1p+o2p+o3p+p+op1+op2+'c1*'+'c2*'+'c3*'+'c5*'+'o2*'+'o3*'+'o4*'+'o5*'+'c1*'+'c2*'+'c3*'+'c4*'+'o2*'+'o4*'+c1'+c2'+c3'+c5'+o2'+o3'+o4'+o5'+c1'+c2'+c3'+c4'+o2'+o4') and (not name c1+c2+c3+c4+c5+o2+o3+o4+o5) ")

  for x in AllObj:
    print(x)
    cmd.show( "cartoon", x )
    cmd.spectrum( "count", "rainbow", x+" and backbone" )

  cmd.cartoon( "tube", "backbone" )

  cmd.set( "cartoon_ring_mode", 0 )
  cmd.set( "cartoon_ring_transparency", 0.0 )
  cmd.set( "cartoon_tube_radius", 1.0 )

  cmd.color( 'red','resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2')
  cmd.color( 'forest','resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6')
  cmd.color( 'orange','resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2')
  cmd.color( 'blue','resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2')

  cmd.delete('backbone')


def rcd():
  """
  fancy ribbon coloring for large RNA comparisons
  """
  rc()
  cmd.cartoon( 'dumbbell')
  cmd.set( 'cartoon_dumbbell_radius', 0.5 )

def render_cartoon():
  rc()

def bx():
  txt = """color black, all
color pink, resi 3-5+132-134 # p1
color forest, resi 12-13+129-130 # p3
color orange, resi 17-33 # p4
color green, resi 36-45  # p5
color blue, resi 47-124 # p6color
  """
  for t in txt.split('\n'):
    color, resi = t.replace('color ', '').split(',')
    print(color, resi)
    cmd.color(color.strip(), resi.strip())

def color_by_text(txt):
  for t in txt.strip().split('\n'):
    color, resi = t.replace('color ', '').split(',')
    print(color, resi)
    cmd.color(color.strip(), resi.strip())




from multiprocessing import Process

cmd.extend('rib', rcm)
#cmd.extend('clr_', clr)
cmd.extend('aaa', align_all)
cmd.extend('rr', rr)
cmd.extend('rcd', rcd)