I have Mac PyMOL 1.7.4.4, and I have attempted to run the attached program. I
know the program works on older versions, but I get the following error:
AttributeError: 'module' object has no attribute 'extend'
Does anyone know how to fix this?
'''
In pymol terminal, change directory to where RNA_coloring_pymol.py is stored, then:
run RNA_coloring_pymol.py
color_structure 2QBG
'''
import sys
import cmd
import csv
import urllib2
def split_range(nt_range):
'''
Imput :' 1 -- 9 / 35 -- 38 '
Output : [('1','9'), ('35','38')]
'''
nt_range = nt_range.strip()
if nt_range=="Not Present":
return ''
if len(nt_range)==0:
return ''
if '0' <= nt_range[0] <='9':
split1= nt_range.split('/')
split2= '\n'.join(split1)
nt_number = ''.join(split2.split('--'))
a= nt_number.split()
it = iter(a)
d= zip(it, it)
return d
else:
return ''
def convert_color_RGB(colorr):
'''
RGB colors are not defined in pymol.
convert_color_RBG function defines RGB colors
Input : '#3300FF'
Output : "RGB_blue" ( which we have defined to be [51 , 0 , 255] )
'''
cmd.set_color( 'RGB_blue' , [51 , 0 , 255] )
cmd.set_color( 'RGB_green' , [51 , 153 , 51] )
cmd.set_color( 'RGB_Lblue' , [51 , 153 , 255] )
cmd.set_color( 'RGB_grey' , [128 , 128 , 128] )
cmd.set_color( 'RGB_brown' , [139 , 69 , 19] )
cmd.set_color( 'RGB_purple' , [153 , 30 , 255] )
cmd.set_color( 'RGB_gold' , [205 , 173 , 0] )
cmd.set_color( 'RGB_red' , [255 , 0 , 51] )
cmd.set_color( 'RGB_orange' , [255 , 102 , 0] )
if colorr == "#3300FF":
return "RGB_blue"
elif colorr == "#339933":
return "RGB_green"
elif colorr == "#3399FF":
return "RGB_Lblue"
elif colorr == "#808080":
return "RGB_grey"
elif colorr == "#8B4513":
return "RGB_brown"
elif colorr == "#991EFF":
return "RGB_purple"
elif colorr == "#CDAD00":
return "RGB_gold"
elif colorr == "#FF0033":
return "RGB_red"
elif colorr == "#FF6600":
return 'RGB_orange'
else:
return 'white'
# ntd = [('1', '9'), ('2886', '2897')]
# ntdList = (data) = [('31_32', 'blue'), ('57_70', 'Purple'),....]
def nt_ranges(reader):
'''
This function gives a list of tuples with the range of nucletides and their corresponding defined color
ntd = [('1', '9'), ('2886', '2897'), ...]
Output : ntdList = (data) = [('31_32', 'blue', 'A'), ('57_70', 'Purple'), 'B',....]
'''
ntdList=[]
for i, line in enumerate(reader):
ntd = split_range(line[1])
ntd_color = convert_color_RGB(line[0])
chain = line[2]
if len(ntd)==1: # just one range [('1', '9')]
ntdList += [((ntd[0][0])+'-'+(ntd[0][1]), ntd_color, line[2])]
if len(ntd)==2:
ntdList += [((ntd[0][0])+'-'+(ntd[0][1]), ntd_color, line[2])]
ntdList += [((ntd[1][0])+'-'+(ntd[1][1]), ntd_color, line[2])]
#print len(ntdList)
return ntdList
def color_structure(pdb_file):
'''
this function colors each nucleotide in pymol
>>>print (data[1][0])
2886_2897
2QBG must match the name of pdb file which is open
data[i][1] = color
data[i][0] = range of nucleotide
data[i][2] = chain
'''
pdb_file = pdb_file.upper()
url = 'https://raw.githubusercontent.com/BGSU-RNA/3D-structure-coloring/master/csv_files/%s.csv' % pdb_file
response = urllib2.urlopen(url)
reader = csv.reader(response, delimiter=",")
data = nt_ranges(reader)
for i in range(0,len(data)):
if (data[i][2]) != '':
cmd.color(data[i][1], "%s and resi %s in chain %s" % ( pdb_file, data[i][0], data[i][2]))
elif(data[i][2]) == '':
cmd.color(data[i][1], "%s and resi %s " % ( pdb_file, data[i][0]))
print(cmd)
print(dir(cmd.Cmd))
cmd.extend('color_structure', color_structure)
------------------------------------------------------------------------------
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