build.rna_tools.tools.PyMOL4RNA.PyMOL4Spliceosome.spl_help() - Code Metrics - mmagnus/rna-tools - Measure and Improve Code Quality continuously with Scrutinizer

spl_help() A
last analyzed 2025-03-19 22:26 UTC

↳ Parent: build.rna_tools.tools.PyMOL4RNA.PyMOL4Spliceosome

Complexity

Conditions

Size

Total Lines	2
Code Lines	2

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	2
nop	0
dl	0
loc	2
rs	10
c	0
b	0
f	0

"""
See the PyMOL Sessions processed with this code here <https://github.com/mmagnus/PyMOL4Spliceosome>
"""
from pymol import cmd
from rna_tools.tools.PyMOL4RNA import code_for_color_spl
from rna_tools.tools.PyMOL4RNA import code_for_spl

try:
    from pymol import cmd
except ImportError:
    print("PyMOL Python lib is missing")
    # sys.exit(0)

def spl_help():
    print("""
PyMOL4Spliceosome
-----------------------
extract all (ea)  - show
colors            - list all colors

spl hprp8
spl prp8
spl yprp8 - "color skyblue, PRP8_* and resi 885-1251"
spl hprp28

spl chains
 color blue, chain 5
 color red, chain 6
 color forest, chain 2

set cartoon_ring_mode to 3 ...

""")
spl_help()

print("""
spl g2 # coloring for 6chr g2 introns
""")

cmd.set('transparency', 0.25)
cmd.set('cartoon_ring_mode', 3)
# colors taken from https://github.com/maxewilkinson/Spliceosome-PyMOL-sessions
cmd.set_color('lightgreen', [144, 238, 144])
cmd.set_color('darkgreen', [0, 100, 0])
cmd.set_color('darkseagreen', [143, 188, 143])
cmd.set_color('greenyellow', [173, 255, 47])
cmd.set_color('coral', [255, 127, 80])
cmd.set_color('darkorange', [255, 140, 0])
cmd.set_color('gold', [255, 215, 0])
cmd.set_color('lemonchiffon', [255,250,205])
cmd.set_color('moccasin', [255,228,181])
cmd.set_color('skyblue', [135,206,235])
cmd.set_color('lightyellow', [255,255,224])
cmd.set_color('powderblue', [176,224,230])
cmd.set_color('royalblue', [65,105,225])
cmd.set_color('cornflowerblue', [100,149,237])
cmd.set_color('steelblue', [70,130,180])
cmd.set_color('lightsteelblue', [176,196,222])
cmd.set_color('violetBlue', [40, 0, 120])
cmd.set_color('mediumpurple', [147,112,219])
cmd.set_color('lavenderblush', [255,240,245])
cmd.set_color('lavender', [230,230,250])
cmd.set_color('thistle', [216,191,216])



def color_by_text(txt):
    """Helper function used for color-coding based on residue indexes ranges."""
    for t in txt.strip().split('\n'):
        print(t)
        color, resi = t.replace('color ', '').split(',')
        print((color, resi))
        cmd.color(color.strip(), resi.strip())

def spl(arg=''):
    """
    action='', name=''
    """
    #reload()
    print(arg)
    if ' ' in arg:
        action, name = arg.split()
        name = name.lower()
    else:
        action = arg
        name = ''
    #import pandas as pd
    #df = pd.read_excel("/home/magnus/Desktop/pyMoL_colors-EMX.xlsx")
    if not action or action == 'help':
        spl_help()
        cmd.do('color red, chain A')        
        cmd.do('color forest, chain B')
        cmd.do('color grey, chain C')        
        cmd.do('color grey, chain D')

        cmd.do('color grey, chain I')        
        cmd.do('color grey, chain J')

        cmd.do('color purple, chain D and resi 4')        
        cmd.do('color purple, resn MG')
        # exon
        cmd.do('color yellow, chain G')
        cmd.do('color yellow, chain E')
        
        cmd.do('color blue, chain H')
        cmd.do('color blue, chain U')

        cmd.show("spheres", "inorganic")
        cmd.set('sphere_scale', '1', '(all)')
        #cmd.set('sphere_scale', '1', '(all)')
        cmd.color("yellow", "inorganic")

    elif arg == 'g22':
        print('g22')
        t = """
        color gray, resi 1-600;
        color red, resi 550-586;
        color pink, resi 587-630;
        color brown, resi 507-549;
        color marine, resi 350-424;
        color yellow, resi 425-507;
        color forest, resi 1-26;
        color forest, resi 327-350;
        color yellow, chain B;
        """
        color_by_text(t)

    elif arg == 'g21':
        print('g21')
        t = """
        color gray, resi 1-600;
        color red, resi 300-400
        color marine, resi 288-289;
        """
        color_by_text(t)

    elif action == 'color' or arg=='c':
        code_for_color_spl.spl_color()
    elif arg == 'extract all' or arg == 'ea' or arg == 'e':
        code_for_spl.spl_extract()
    elif arg == 'cc': # colorchains
        cmd.do('color blue, chain 5')
        cmd.do('color red, chain 6')        
        cmd.do('color forest, chain 2')

        cmd.do('color red, chain V')        
        cmd.do('color forest, chain Z')

    elif arg == 'ab': # colorchains
        cmd.do('color red, chain B')        
        cmd.do('color forest, chain A')
        cmd.do('color grey, chain C')        
        cmd.do('color grey, chain D')
        cmd.do('color purple, chain D and resi 4')        
        cmd.do('color purple, resn MG')

    elif arg == 'trim':
        cmd.do("""    	remove chain 5;
	remove chain 2 and resi 1-19;
	remove chain 2 and resi 50-200;
	remove chain 6 and resi 87-200;
	remove chain 6 and resi 1-40;
	remove chain P and resi 45-200;
    """)

    elif arg == 'trim2':  # keep super small
        cmd.do("""    	remove chain 5;
	remove chain 2 and resi 1-19;
	remove chain 2 and resi 30-200;

	remove chain 6 and resi 87-200;
	remove chain 6 and resi 1-50;

	remove chain P and resi 45-200;

	remove chain I;
	remove chain E;
    """)

    elif arg == 't5':
        cmd.set('transparency', 0.5)
    elif arg == 't1':
        cmd.set('transparency', 1)
    elif arg.startswith('hprp28'):
        print("""
purple, resi 240-361  # RecA1
blue, resi 361-631    # RecA1
orange, resi 631-811  # RecA2
""")
        cmd.do("color purple, PRP28_h* and resi 240-361") # RecA1
        cmd.do("color blue, PRP28_h* and resi 361-631") # RecA1
        cmd.do("color orange, PRP28_h* and resi 631-811")  # RecA2
    elif arg.startswith('hprp8'):
        print("""

RT finger/palm, skyblue, 812-1303
Thumb/X, cyan, 1257-1375
linker smudge, 1304-1577
Endonuclease yellow, 1581-1752
RNaseH-like wheat, 1767-2020
JAB salmon, 2103-2234

""")
        cmd.do("color yellow, PRP8_h* and resi 1581-1752")  # rt
        cmd.do("color wheat, PRP8_h* and resi 1767-2020")   # rh
        cmd.do("color salmon, PRP8_h* and resi 2103-2234")  # jab
        cmd.do("color smudge, PRP8_h* and resi 1304-1577")  # linker
        cmd.do("color skyblue, PRP8_h* and resi 812-1303")  # rt
    elif arg.startswith('prp8'):
        print(
"""
select Prp8N, Prp8 and resi 1-870
select Prp8Large, Prp8 and resi 871-1827
select Prp8RH, Prp8 and resi 1828-2106
select Prp8RT, Prp8 and resi 871-1375
select Prp8linker, Prp8 and resi 1376-1652
select Prp8EN, Prp8 and resi 1653-1824
select Prp8afinger, Prp8 and resi 1583-1610
""")
        cmd.do("color skyblue, PRP8_y* and resi 885-1251")  # rt
        cmd.do("color cyan, PRP8_y* and resi 1257-1375")    # thumb/x
        cmd.do("color smudge, PRP8_y* and resi 1376-1649")  # linker
        cmd.do("color wheat, PRP8_y* and resi  1840-2090")  # rh
        cmd.do("color salmon, PRP8_y* and resi 2150-2395")  # jab
        cmd.do("color yellow, PRP8_y* and resi 1650-1840")  # endo
    elif arg.startswith('yprp8'):
        print(
"""
select Prp8N, Prp8 and resi 1-870
select Prp8Large, Prp8 and resi 871-1827
select Prp8RH, Prp8 and resi 1828-2106
select Prp8RT, Prp8 and resi 871-1375
select Prp8linker, Prp8 and resi 1376-1652
select Prp8EN, Prp8 and resi 1653-1824
select Prp8afinger, Prp8 and resi 1583-1610
""")
        cmd.do("color skyblue, PRP8_* and resi 885-1251")  # rt
        cmd.do("color cyan, PRP8_* and resi 1257-1375")    # thumb/x
        cmd.do("color smudge, PRP8_* and resi 1376-1649")  # linker
        cmd.do("color wheat, PRP8_* and resi  1840-2090")  # rh
        cmd.do("color salmon, PRP8_* and resi 2150-2395")  # jab
        cmd.do("color yellow, PRP8_* and resi 1650-1840")  # endo
    elif arg.startswith(''):
        if 'hjab' in arg.lower():
            cmd.select('PRP8_h* and resi 2103-2234')
        if 'hlinker' in arg.lower():
            cmd.select('PRP8_h* and resi 1304-1577')
        if 'hrt' in arg.lower():
            cmd.select('PRP8_h* and resi 812-1303')
        if 'hrh' in arg.lower():
            cmd.select('PRP8_h* and resi 1767-2020')
        if 'he' in arg.lower():
            cmd.select('PRP8_h* and resi 1581-1752')
    elif arg == 'align' or arg=='a':
        cmd.do("""
    align /5gm6//6, /5lj3//V;
    align /5mps//6, /5lj3//V;
    align /6exn//6, /5lj3//V;
    align /5y88//D, /5lj3//V;
    align /5ylz//D, /5lj3//V;
    """)
    else:
        spl_help()

cmd.extend('spl', spl)

def g2():
    txt = """color gray, all;
    color yellow, chain B;
    color red, resi 788-824;
    color yellow, resi 828-866;
    color forest, resi 476-490;
    """
    color_by_text(txt)
    cmd.color('pink', 'resi 120')
    cmd.color('pink', 'resi 2')

def __spl_color():
    for m in mapping:

        protein = m[0]
        chain = m[1]
        color = m[2]
        print('\_' + ' '.join([protein, chain, color]))
        cmd.do('color ' + color + ', chain ' + chain)
        # cmd.do('color firebrick, chain V') # U6

def _spl_color():
    """Color spl RNAs (for only color spl RNA and use 4-color code for residues see `spl2`)
    """
    AllObj = cmd.get_names("all")
    for name in AllObj:
        if 'Exon' in name or 'exon' in name:
            cmd.color('yellow', name)
        if 'Intron' in name or 'intron' in name or '5splicing-site' in name:
            cmd.color('gray40', name)
        if '3exon-intron' in name.lower():
            cmd.color('gray20', name)
        if name.startswith("U2_snRNA"):
            cmd.color('forest', name)
        if name.startswith("U5_snRNA"):
            cmd.color('blue', name)
        if name.startswith("U4_snRNA"):
            cmd.color('orange', name)
        if name.startswith("U6_snRNA"):
            cmd.color('red', name)

    cmd.do('color gray')

    # trisnrp
    cmd.do('color orange, chain V') # conflict
    cmd.do('color red, chain W')
    cmd.do('color blue, chain U')
    #
    cmd.do('color blue, chain 5')
    cmd.do('color forest, chain 2')
    cmd.do('color red, chain 6')
    cmd.do('color orange, chain 4')
    cmd.do('color yellow, chain Y')
    # shi
    cmd.do('color blue, chain D') # u5
    cmd.do('color forest, chain L') # u2
    cmd.do('color red, chain E') # u6
    cmd.do('color yellow, chain M')
    cmd.do('color yellow, chain N')
    # afte branch
    cmd.do('color blue, chain U') # u5
    cmd.do('color forest, chain Z') # u2
    cmd.do('color red, chain V') # u6
    cmd.do('color yellow, chain E')
    cmd.do('color black, chain I')
    # 5WSG
    # Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution
    cmd.do('color blue, chain D') # u5
    #cmd.do('color forest, chain L') # u2
    cmd.do('color yellow, chain B')
    cmd.do('color yellow, chain b')
    cmd.do('color black, chain N')
    cmd.do('color black, chain M')

    cmd.do('color black, chain 3') # orange
    cmd.do('color black, chain E') # yellow
    cmd.do('color black, chain i')
    cmd.do('color black, chain e')

    cmd.do('color black, chain e')

    cmd.do('color dirtyviolet, chain L') # bud31
    cmd.do('color rasberry, chain L') # CERF1

    cmd.do('color skyblue, chain A') # PRP8
    cmd.do('color grey60, chain B') # BRR2
    cmd.do('color dirtyiolet, chain L') # BUD31
    cmd.do('color rasberry, chain O') # CEF1
    cmd.do('color rasberry, chain S') # CLF1
    cmd.do('color dirtyviolet, chain P') # CWC15
    cmd.do('color lightteal, chain D') # CWC16/YJU2
    cmd.do('color ruby, chain M') # CWC2
    cmd.do('color violetpurple, chain R') # CWC21
    cmd.do('color bluewhite, chain H') # CWC22
    cmd.do('color deepteal, chain F') # CWC25
    cmd.do('color black, chain I') # Intron
    cmd.do('color dirtyviolet, chain G') # ISY1
    cmd.do('color palegreen, chain W') # LEA1
    cmd.do('color palegreen, chain Y') # Msl1
    cmd.do('color lightpink, chain K') # PRP45
    cmd.do('color smudge, chain Q') # Prp16
    cmd.do('color grey70, chain t') # Prp19
    cmd.do('color lightblue, chain J') # PRP46
    cmd.do('color chocolate, chain N') # SLT11/ECM2
    cmd.do('color grey70, chain s') # Snt309
    cmd.do('color slate, chain C') # SNU114
    cmd.do('color brightorange, chain T') # SYF1
    cmd.do('color forest, chain Z') # U2
    cmd.do('color density, chain U') # U5
    cmd.do('color deepblue, chain b') # U5_Sm

    cmd.do('bg gray')
    # cmd.do('remove (polymer.protein)')

    cmd.set("cartoon_tube_radius", 1.0)
    ino()


def spl2():
    """Color spl RNAs and use 4-color code for residues (for only color spl RNA see `spl`)
    """

    AllObj = cmd.get_names("all")
    for name in AllObj:
        if 'Exon' in name or 'exon' in name:
            cmd.color('yellow', name)
        if 'Intron' in name or 'intron' in name or '5splicing-site' in name:
            cmd.color('gray40', name)
        if '3exon-intron' in name.lower():
            cmd.color('gray20', name)
        if name.startswith("U2_snRNA"):
            cmd.color('forest', name)
        if name.startswith("U5_snRNA"):
            cmd.color('blue', name)
        if name.startswith("U4_snRNA"):
            cmd.color('orange', name)
        if name.startswith("U6_snRNA"):
            cmd.color('red', name)

    cmd.do('color gray')

    # trisnrp
    cmd.do('color orange, chain V') # conflict
    cmd.do('color red, chain W')
    cmd.do('color blue, chain U')
    #
    cmd.do('color blue, chain 5')
    cmd.do('color forest, chain 2')
    cmd.do('color red, chain 6')
    cmd.do('color orange, chain 4')
    cmd.do('color yellow, chain Y')
    # shi
    cmd.do('color blue, chain D') # u5
    cmd.do('color forest, chain L') # u2
    cmd.do('color red, chain E') # u6
    cmd.do('color yellow, chain M')
    cmd.do('color yellow, chain N')
    # afte branch
    cmd.do('color blue, chain U') # u5
    cmd.do('color forest, chain Z') # u2
    cmd.do('color red, chain V') # u6
    cmd.do('color yellow, chain E')
    cmd.do('color black, chain I')
    # 5WSG
    # Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution
    cmd.do('color blue, chain D') # u5
    #cmd.do('color forest, chain L') # u2
    cmd.do('color yellow, chain B')
    cmd.do('color yellow, chain b')
    cmd.do('color black, chain N')
    cmd.do('color black, chain M')

    cmd.do('color black, chain 3') # orange
    cmd.do('color black, chain E') # yellow
    cmd.do('color black, chain i')
    cmd.do('color black, chain e')

    cmd.do('bg gray')
    cmd.do('remove (polymer.protein)')

    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.set("cartoon_tube_radius", 1.0)
    ino()



def x():
    spl_extract()

    spl_color()

cmd.extend("x", x)

def _spli():
    """
    # this trick is taken from Rhiju's Das code
    color red,resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2
    color forest,resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6
    color orange, resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2
    color blue, resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2

    #
    #cmd.color("yellow", "*intron*")
    #cmd.color("yellow", "*exon*")

    #cmd.show("spheres", "inorganic")
    #cmd.color("yellow", "inorganic")
    """
    cmd.color("orange", "U4_snRNA*")
    cmd.color("red", "U6_snRNA*")
    cmd.color("blue", "U5_snRNA*")
    cmd.color("green", "U2_snRNA*")
    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')

try:
    from pymol import cmd
except ImportError:
    print("PyMOL Python lib is missing")
else:

    #cmd.extend("spl", spl)
    cmd.extend("spl2", spl2)



1			"""
2			See the PyMOL Sessions processed with this code here <https://github.com/mmagnus/PyMOL4Spliceosome>
3			"""
4			from pymol import cmd
5			from rna_tools.tools.PyMOL4RNA import code_for_color_spl
6			from rna_tools.tools.PyMOL4RNA import code_for_spl
7
8			try:
9			from pymol import cmd
10			except ImportError:
11			print("PyMOL Python lib is missing")
12			# sys.exit(0)
13
14			def spl_help():
15			print("""
16			PyMOL4Spliceosome
17			-----------------------
18			extract all (ea) - show
19			colors - list all colors
20
21			spl hprp8
22			spl prp8
23			spl yprp8 - "color skyblue, PRP8_* and resi 885-1251"
24			spl hprp28
25
26			spl chains
27			color blue, chain 5
28			color red, chain 6
29			color forest, chain 2
30
31			set cartoon_ring_mode to 3 ...
32
33			""")
34			spl_help()
35
36			print("""
37			spl g2 # coloring for 6chr g2 introns
38			""")
39
40			cmd.set('transparency', 0.25)
41			cmd.set('cartoon_ring_mode', 3)
42			# colors taken from https://github.com/maxewilkinson/Spliceosome-PyMOL-sessions
43			cmd.set_color('lightgreen', [144, 238, 144])
44			cmd.set_color('darkgreen', [0, 100, 0])
45			cmd.set_color('darkseagreen', [143, 188, 143])
46			cmd.set_color('greenyellow', [173, 255, 47])
47			cmd.set_color('coral', [255, 127, 80])
48			cmd.set_color('darkorange', [255, 140, 0])
49			cmd.set_color('gold', [255, 215, 0])
50			cmd.set_color('lemonchiffon', [255,250,205])
51			cmd.set_color('moccasin', [255,228,181])
52			cmd.set_color('skyblue', [135,206,235])
53			cmd.set_color('lightyellow', [255,255,224])
54			cmd.set_color('powderblue', [176,224,230])
55			cmd.set_color('royalblue', [65,105,225])
56			cmd.set_color('cornflowerblue', [100,149,237])
57			cmd.set_color('steelblue', [70,130,180])
58			cmd.set_color('lightsteelblue', [176,196,222])
59			cmd.set_color('violetBlue', [40, 0, 120])
60			cmd.set_color('mediumpurple', [147,112,219])
61			cmd.set_color('lavenderblush', [255,240,245])
62			cmd.set_color('lavender', [230,230,250])
63			cmd.set_color('thistle', [216,191,216])
64
65
66
67			def color_by_text(txt):
68			"""Helper function used for color-coding based on residue indexes ranges."""
69			for t in txt.strip().split('\n'):
70			print(t)
71			color, resi = t.replace('color ', '').split(',')
72			print((color, resi))
73			cmd.color(color.strip(), resi.strip())
74
75			def spl(arg=''):
76			"""
77			action='', name=''
78			"""
79			#reload()
80			print(arg)
81			if ' ' in arg:
82			action, name = arg.split()
83			name = name.lower()
84			else:
85			action = arg
86			name = ''
87			#import pandas as pd
88			#df = pd.read_excel("/home/magnus/Desktop/pyMoL_colors-EMX.xlsx")
89			if not action or action == 'help':
90			spl_help()
91			cmd.do('color red, chain A')
92			cmd.do('color forest, chain B')
93			cmd.do('color grey, chain C')
94			cmd.do('color grey, chain D')
95
96			cmd.do('color grey, chain I')
97			cmd.do('color grey, chain J')
98
99			cmd.do('color purple, chain D and resi 4')
100			cmd.do('color purple, resn MG')
101			# exon
102			cmd.do('color yellow, chain G')
103			cmd.do('color yellow, chain E')
104
105			cmd.do('color blue, chain H')
106			cmd.do('color blue, chain U')
107
108			cmd.show("spheres", "inorganic")
109			cmd.set('sphere_scale', '1', '(all)')
110			#cmd.set('sphere_scale', '1', '(all)')
111			cmd.color("yellow", "inorganic")
112
113			elif arg == 'g22':
114			print('g22')
115			t = """
116			color gray, resi 1-600;
117			color red, resi 550-586;
118			color pink, resi 587-630;
119			color brown, resi 507-549;
120			color marine, resi 350-424;
121			color yellow, resi 425-507;
122			color forest, resi 1-26;
123			color forest, resi 327-350;
124			color yellow, chain B;
125			"""
126			color_by_text(t)
127
128			elif arg == 'g21':
129			print('g21')
130			t = """
131			color gray, resi 1-600;
132			color red, resi 300-400
133			color marine, resi 288-289;
134			"""
135			color_by_text(t)
136
137			elif action == 'color' or arg=='c':
138			code_for_color_spl.spl_color()
139			elif arg == 'extract all' or arg == 'ea' or arg == 'e':
140			code_for_spl.spl_extract()
141			elif arg == 'cc': # colorchains
142			cmd.do('color blue, chain 5')
143			cmd.do('color red, chain 6')
144			cmd.do('color forest, chain 2')
145
146			cmd.do('color red, chain V')
147			cmd.do('color forest, chain Z')
148
149			elif arg == 'ab': # colorchains
150			cmd.do('color red, chain B')
151			cmd.do('color forest, chain A')
152			cmd.do('color grey, chain C')
153			cmd.do('color grey, chain D')
154			cmd.do('color purple, chain D and resi 4')
155			cmd.do('color purple, resn MG')
156
157			elif arg == 'trim':
158			cmd.do(""" remove chain 5;
159			remove chain 2 and resi 1-19;
160			remove chain 2 and resi 50-200;
161			remove chain 6 and resi 87-200;
162			remove chain 6 and resi 1-40;
163			remove chain P and resi 45-200;
164			""")
165
166			elif arg == 'trim2': # keep super small
167			cmd.do(""" remove chain 5;
168			remove chain 2 and resi 1-19;
169			remove chain 2 and resi 30-200;
170
171			remove chain 6 and resi 87-200;
172			remove chain 6 and resi 1-50;
173
174			remove chain P and resi 45-200;
175
176			remove chain I;
177			remove chain E;
178			""")
179
180			elif arg == 't5':
181			cmd.set('transparency', 0.5)
182			elif arg == 't1':
183			cmd.set('transparency', 1)
184			elif arg.startswith('hprp28'):
185			print("""
186			purple, resi 240-361 # RecA1
187			blue, resi 361-631 # RecA1
188			orange, resi 631-811 # RecA2
189			""")
190			cmd.do("color purple, PRP28_h* and resi 240-361") # RecA1
191			cmd.do("color blue, PRP28_h* and resi 361-631") # RecA1
192			cmd.do("color orange, PRP28_h* and resi 631-811") # RecA2
193			elif arg.startswith('hprp8'):
194			print("""
195
196			RT finger/palm, skyblue, 812-1303
197			Thumb/X, cyan, 1257-1375
198			linker smudge, 1304-1577
199			Endonuclease yellow, 1581-1752
200			RNaseH-like wheat, 1767-2020
201			JAB salmon, 2103-2234
202
203			""")
204			cmd.do("color yellow, PRP8_h* and resi 1581-1752") # rt
205			cmd.do("color wheat, PRP8_h* and resi 1767-2020") # rh
206			cmd.do("color salmon, PRP8_h* and resi 2103-2234") # jab
207			cmd.do("color smudge, PRP8_h* and resi 1304-1577") # linker
208			cmd.do("color skyblue, PRP8_h* and resi 812-1303") # rt
209			elif arg.startswith('prp8'):
210			print(
211			"""
212			select Prp8N, Prp8 and resi 1-870
213			select Prp8Large, Prp8 and resi 871-1827
214			select Prp8RH, Prp8 and resi 1828-2106
215			select Prp8RT, Prp8 and resi 871-1375
216			select Prp8linker, Prp8 and resi 1376-1652
217			select Prp8EN, Prp8 and resi 1653-1824
218			select Prp8afinger, Prp8 and resi 1583-1610
219			""")
220			cmd.do("color skyblue, PRP8_y* and resi 885-1251") # rt
221			cmd.do("color cyan, PRP8_y* and resi 1257-1375") # thumb/x
222			cmd.do("color smudge, PRP8_y* and resi 1376-1649") # linker
223			cmd.do("color wheat, PRP8_y* and resi 1840-2090") # rh
224			cmd.do("color salmon, PRP8_y* and resi 2150-2395") # jab
225			cmd.do("color yellow, PRP8_y* and resi 1650-1840") # endo
226			elif arg.startswith('yprp8'):
227			print(
228			"""
229			select Prp8N, Prp8 and resi 1-870
230			select Prp8Large, Prp8 and resi 871-1827
231			select Prp8RH, Prp8 and resi 1828-2106
232			select Prp8RT, Prp8 and resi 871-1375
233			select Prp8linker, Prp8 and resi 1376-1652
234			select Prp8EN, Prp8 and resi 1653-1824
235			select Prp8afinger, Prp8 and resi 1583-1610
236			""")
237			cmd.do("color skyblue, PRP8_* and resi 885-1251") # rt
238			cmd.do("color cyan, PRP8_* and resi 1257-1375") # thumb/x
239			cmd.do("color smudge, PRP8_* and resi 1376-1649") # linker
240			cmd.do("color wheat, PRP8_* and resi 1840-2090") # rh
241			cmd.do("color salmon, PRP8_* and resi 2150-2395") # jab
242			cmd.do("color yellow, PRP8_* and resi 1650-1840") # endo
243			elif arg.startswith(''):
244			if 'hjab' in arg.lower():
245			cmd.select('PRP8_h* and resi 2103-2234')
246			if 'hlinker' in arg.lower():
247			cmd.select('PRP8_h* and resi 1304-1577')
248			if 'hrt' in arg.lower():
249			cmd.select('PRP8_h* and resi 812-1303')
250			if 'hrh' in arg.lower():
251			cmd.select('PRP8_h* and resi 1767-2020')
252			if 'he' in arg.lower():
253			cmd.select('PRP8_h* and resi 1581-1752')
254			elif arg == 'align' or arg=='a':
255			cmd.do("""
256			align /5gm6//6, /5lj3//V;
257			align /5mps//6, /5lj3//V;
258			align /6exn//6, /5lj3//V;
259			align /5y88//D, /5lj3//V;
260			align /5ylz//D, /5lj3//V;
261			""")
262			else:
263			spl_help()
264
265			cmd.extend('spl', spl)
266
267			def g2():
268			txt = """color gray, all;
269			color yellow, chain B;
270			color red, resi 788-824;
271			color yellow, resi 828-866;
272			color forest, resi 476-490;
273			"""
274			color_by_text(txt)
275			cmd.color('pink', 'resi 120')
276			cmd.color('pink', 'resi 2')
277
278			def __spl_color():
279			for m in mapping:
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-08-03 20:10 UTC by Report Bug Copy Issue Report The variable `mapping` does not seem to be defined. Loading history...
280			protein = m[0]
281			chain = m[1]
282			color = m[2]
283			print('\_' + ' '.join([protein, chain, color]))
284			cmd.do('color ' + color + ', chain ' + chain)
285			# cmd.do('color firebrick, chain V') # U6
286
287			def _spl_color():
288			"""Color spl RNAs (for only color spl RNA and use 4-color code for residues see `spl2`)
289			"""
290			AllObj = cmd.get_names("all")
291			for name in AllObj:
292			if 'Exon' in name or 'exon' in name:
293			cmd.color('yellow', name)
294			if 'Intron' in name or 'intron' in name or '5splicing-site' in name:
295			cmd.color('gray40', name)
296			if '3exon-intron' in name.lower():
297			cmd.color('gray20', name)
298			if name.startswith("U2_snRNA"):
299			cmd.color('forest', name)
300			if name.startswith("U5_snRNA"):
301			cmd.color('blue', name)
302			if name.startswith("U4_snRNA"):
303			cmd.color('orange', name)
304			if name.startswith("U6_snRNA"):
305			cmd.color('red', name)
306
307			cmd.do('color gray')
308
309			# trisnrp
310			cmd.do('color orange, chain V') # conflict
311			cmd.do('color red, chain W')
312			cmd.do('color blue, chain U')
313			#
314			cmd.do('color blue, chain 5')
315			cmd.do('color forest, chain 2')
316			cmd.do('color red, chain 6')
317			cmd.do('color orange, chain 4')
318			cmd.do('color yellow, chain Y')
319			# shi
320			cmd.do('color blue, chain D') # u5
321			cmd.do('color forest, chain L') # u2
322			cmd.do('color red, chain E') # u6
323			cmd.do('color yellow, chain M')
324			cmd.do('color yellow, chain N')
325			# afte branch
326			cmd.do('color blue, chain U') # u5
327			cmd.do('color forest, chain Z') # u2
328			cmd.do('color red, chain V') # u6
329			cmd.do('color yellow, chain E')
330			cmd.do('color black, chain I')
331			# 5WSG
332			# Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution
333			cmd.do('color blue, chain D') # u5
334			#cmd.do('color forest, chain L') # u2
335			cmd.do('color yellow, chain B')
336			cmd.do('color yellow, chain b')
337			cmd.do('color black, chain N')
338			cmd.do('color black, chain M')
339
340			cmd.do('color black, chain 3') # orange
341			cmd.do('color black, chain E') # yellow
342			cmd.do('color black, chain i')
343			cmd.do('color black, chain e')
344
345			cmd.do('color black, chain e')
346
347			cmd.do('color dirtyviolet, chain L') # bud31
348			cmd.do('color rasberry, chain L') # CERF1
349
350			cmd.do('color skyblue, chain A') # PRP8
351			cmd.do('color grey60, chain B') # BRR2
352			cmd.do('color dirtyiolet, chain L') # BUD31
353			cmd.do('color rasberry, chain O') # CEF1
354			cmd.do('color rasberry, chain S') # CLF1
355			cmd.do('color dirtyviolet, chain P') # CWC15
356			cmd.do('color lightteal, chain D') # CWC16/YJU2
357			cmd.do('color ruby, chain M') # CWC2
358			cmd.do('color violetpurple, chain R') # CWC21
359			cmd.do('color bluewhite, chain H') # CWC22
360			cmd.do('color deepteal, chain F') # CWC25
361			cmd.do('color black, chain I') # Intron
362			cmd.do('color dirtyviolet, chain G') # ISY1
363			cmd.do('color palegreen, chain W') # LEA1
364			cmd.do('color palegreen, chain Y') # Msl1
365			cmd.do('color lightpink, chain K') # PRP45
366			cmd.do('color smudge, chain Q') # Prp16
367			cmd.do('color grey70, chain t') # Prp19
368			cmd.do('color lightblue, chain J') # PRP46
369			cmd.do('color chocolate, chain N') # SLT11/ECM2
370			cmd.do('color grey70, chain s') # Snt309
371			cmd.do('color slate, chain C') # SNU114
372			cmd.do('color brightorange, chain T') # SYF1
373			cmd.do('color forest, chain Z') # U2
374			cmd.do('color density, chain U') # U5
375			cmd.do('color deepblue, chain b') # U5_Sm
376
377			cmd.do('bg gray')
378			# cmd.do('remove (polymer.protein)')
379
380			cmd.set("cartoon_tube_radius", 1.0)
381			ino()
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-08-03 20:10 UTC by Report Bug Copy Issue Report The variable `ino` does not seem to be defined. Loading history...
382
383			def spl2():
384			"""Color spl RNAs and use 4-color code for residues (for only color spl RNA see `spl`)
385			"""
386
387			AllObj = cmd.get_names("all")
388			for name in AllObj:
389			if 'Exon' in name or 'exon' in name:
390			cmd.color('yellow', name)
391			if 'Intron' in name or 'intron' in name or '5splicing-site' in name:
392			cmd.color('gray40', name)
393			if '3exon-intron' in name.lower():
394			cmd.color('gray20', name)
395			if name.startswith("U2_snRNA"):
396			cmd.color('forest', name)
397			if name.startswith("U5_snRNA"):
398			cmd.color('blue', name)
399			if name.startswith("U4_snRNA"):
400			cmd.color('orange', name)
401			if name.startswith("U6_snRNA"):
402			cmd.color('red', name)
403
404			cmd.do('color gray')
405
406			# trisnrp
407			cmd.do('color orange, chain V') # conflict
408			cmd.do('color red, chain W')
409			cmd.do('color blue, chain U')
410			#
411			cmd.do('color blue, chain 5')
412			cmd.do('color forest, chain 2')
413			cmd.do('color red, chain 6')
414			cmd.do('color orange, chain 4')
415			cmd.do('color yellow, chain Y')
416			# shi
417			cmd.do('color blue, chain D') # u5
418			cmd.do('color forest, chain L') # u2
419			cmd.do('color red, chain E') # u6
420			cmd.do('color yellow, chain M')
421			cmd.do('color yellow, chain N')
422			# afte branch
423			cmd.do('color blue, chain U') # u5
424			cmd.do('color forest, chain Z') # u2
425			cmd.do('color red, chain V') # u6
426			cmd.do('color yellow, chain E')
427			cmd.do('color black, chain I')
428			# 5WSG
429			# Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution
430			cmd.do('color blue, chain D') # u5
431			#cmd.do('color forest, chain L') # u2
432			cmd.do('color yellow, chain B')
433			cmd.do('color yellow, chain b')
434			cmd.do('color black, chain N')
435			cmd.do('color black, chain M')
436
437			cmd.do('color black, chain 3') # orange
438			cmd.do('color black, chain E') # yellow
439			cmd.do('color black, chain i')
440			cmd.do('color black, chain e')
441
442			cmd.do('bg gray')
443			cmd.do('remove (polymer.protein)')
444
445			cmd.color("red",'resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2')
446			cmd.color("forest",'resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6')
447			cmd.color("orange",'resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2')
448			cmd.color("blue",'resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2')
449			cmd.set("cartoon_tube_radius", 1.0)
450			ino()
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-08-03 20:10 UTC by Report Bug Copy Issue Report The variable `ino` does not seem to be defined. Loading history...
451
452
453			def x():
454			spl_extract()
			0 ignored issues – show Comprehensibility Best Practice introduced 2024-04-16 18:55 UTC by Report Bug Copy Issue Report The variable `spl_extract` does not seem to be defined. Loading history...
455			spl_color()
			0 ignored issues – show Comprehensibility Best Practice introduced 2024-04-16 18:55 UTC by Report Bug Copy Issue Report The variable `spl_color` does not seem to be defined. Loading history...
456			cmd.extend("x", x)
457
458			def _spli():
459			"""
460			# this trick is taken from Rhiju's Das code
461			color red,resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2
462			color forest,resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6
463			color orange, resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2
464			color blue, resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2
465
466			#
467			#cmd.color("yellow", "intron")
468			#cmd.color("yellow", "exon")
469
470			#cmd.show("spheres", "inorganic")
471			#cmd.color("yellow", "inorganic")
472			"""
473			cmd.color("orange", "U4_snRNA*")
474			cmd.color("red", "U6_snRNA*")
475			cmd.color("blue", "U5_snRNA*")
476			cmd.color("green", "U2_snRNA*")
477			cmd.color("red",'resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2')
478			cmd.color("forest",'resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6')
479			cmd.color("orange",'resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2')
480			cmd.color("blue",'resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2')
481
482			try:
483			from pymol import cmd
484			except ImportError:
485			print("PyMOL Python lib is missing")
486			else:
487
488			#cmd.extend("spl", spl)
489			cmd.extend("spl2", spl2)
490
491

mmagnus / rna-tools

spl_help() A last analyzed 2025-03-19 22:26 UTC

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spl_help() A
last analyzed 2025-03-19 22:26 UTC