forked from jaredsampson/pymol-scripts
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quickdisplays.py
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quickdisplays.py
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'''
quickdisplays.py
Described at: http://www.pymolwiki.org/quickdisplays
##################################################
Bundled commands for quick default representations.
Type disp_list for listing of functions.
##################################################
Plugin contributed by Andreas Warnecke
(andreas.warnecke@ki.se, 4ndreas.warneck3@gmail.com)
##################################################
VERSION NOTES:
1.0 2014 First release
1.1 2016 disabled disp_surf from setting surface_carve_selection
corrected print output
'''
#-------------------------------------------------------------------------------
# IMPORT
from __future__ import print_function
from pymol import cmd
from pymol import stored
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# PRINT LIST OF FUNCTIONS
#-------------------------------------------------------------------------------
def disp_list():
print(
'''
quickdisplay - list of functions.
Enter, e.g. "help disp_ss" for more specific info.
PURPOSE FUNCTION
secondary structure cartoon......disp_ss
ball and stick representation....disp_ball_stick
mesh display.....................disp_mesh
surface display..................disp_surf
Putty b-factor sausage...........disp_putty
'''
)
cmd.extend("disp_list", disp_list)
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# PERCENTILE LIMITS (used below)
#-------------------------------------------------------------------------------
def get_b_limits(input='[0,100]', selection='all'):
from pymol import cmd, stored
import math
try:
limits = str(input)
if limits.startswith('['):
# list
limits = eval(limits)[:2]
else:
# integer
selection = str(selection)
limits = abs(float(limits))
if limits > 50:
return False
stored.temp = []
cmd.iterate(selection, 'stored.temp.append(b)')
stored.temp.sort()
kl = (len(stored.temp) - 1) * limits / 100
fl = math.floor(kl)
cl = math.ceil(kl)
kr = (len(stored.temp) - 1) * (100 - limits) / 100
fr = math.floor(kr)
cr = math.ceil(kr)
limits = [0, 0]
if fl == cl:
limits[0] = stored.temp[int(kl)]
else:
limits[0] = stored.temp[int(kl)] * (cl - kl) + stored.temp[int(kl)] * (kl - fl)
if fr == cr:
limits[1] = stored.temp[int(kr)]
else:
limits[1] = stored.temp[int(kr)] * (cr - kr) + stored.temp[int(kr)] * (kr - fr)
except:
return False
return limits
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# DISPLAY: SECONDARY STRUCTURE
#-------------------------------------------------------------------------------
def disp_ss(
selection='all',
colors='marine red white',
only=False):
'''
DESCRIPTION
Formats the passed object into secondary structure cartoon
USAGE
disp_ss [ selection [, colors [, only ]]]
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
colors='marine red white' <str> any three colors for: sheets, helices and loops
e.g. 'marine red white'
can also be set to either util.cbc, util.rainbow,
or util.chainbow (alone)
set='False' to supress coloring altogether, or enter False
for the coloring to be omitted, e.g. 'marine False green'
only <bool> if True will use show_as; else show
'''
try:
selection = '(' + selection + ')'
colors = str(colors)
only = bool(str(only) != 'False')
except:
print("Input error")
return False
if colors == 'False':
color_s = color_h = color_l = False
elif colors.startswith('util.'):
util_choices = ['util.cbc', 'util.rainbow', 'util.chainbow', 'util.ss']
if colors in util_choices:
color_s = color_h = color_l = '%s ' % util_choices[util_choices.index(colors)]
else:
print("Input error! Please check the color setting using util. is one of:", util_choices)
return False
else:
try:
color_s, color_h, color_l = colors.split()[:3]
if color_s != 'False':
cmd.color(color_s, None)
color_s = 'color %s, ' % color_s
else:
color_s = False
if color_h != 'False':
cmd.color(color_h, None)
color_h = 'color %s, ' % color_h
else:
color_h = False
if color_l != 'False':
cmd.color(color_l, None)
color_l = 'color %s, ' % color_l
else:
color_l = False
except:
print("Input error! Please check that three valid colors (or False) are provided")
return False
for p in cmd.get_object_list(selection):
cmd.set('cartoon_discrete_colors', 'on', p)
# settings
cmd.cartoon('rectangle', 'ss s and %s and %s' % (selection, p))
cmd.cartoon('dumbbell', 'ss h and %s and %s' % (selection, p))
cmd.cartoon('loop', 'ss l+"" and %s and %s' % (selection, p))
# sheets
if color_s:
print(cmd.do(color_s + '(ss s and %s and %s)' % (selection, p)))
cmd.set('cartoon_rect_length', 1.5, p)
cmd.set('cartoon_rect_width', 0.25, p)
# a-helices
if color_h:
print(cmd.do(color_h + '(ss h and %s and %s)' % (selection, p)))
cmd.set('cartoon_dumbbell_length', 1.5, p)
cmd.set('cartoon_dumbbell_width', 0.25, p)
cmd.set('cartoon_dumbbell_radius', 0.2, p)
# loops
if color_l:
print(cmd.do(color_l + '(ss l+"" and %s and %s)' % (selection, p)))
cmd.set('cartoon_loop_radius', 0.25, p)
if only:
cmd.show_as('cartoon', '%s and %s' % (selection, p))
else:
cmd.show('cartoon', '%s and %s' % (selection, p))
cmd.extend("disp_ss", disp_ss)
cmd.auto_arg[0]['disp_ss'] = [lambda: cmd.Shortcut(['all']), 'selection=', ',']
cmd.auto_arg[1]['disp_ss'] = [lambda: cmd.Shortcut(['default', 'blue', 'yellow']), 'color_s=', ',']
cmd.auto_arg[2]['disp_ss'] = [lambda: cmd.Shortcut(['default', 'red', 'blue']), 'color_h=', ',']
cmd.auto_arg[3]['disp_ss'] = [lambda: cmd.Shortcut(['color_l=default, only=False']), 'remaining (defaults)...', '']
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# DISPLAY: BALL AND STICK
#-------------------------------------------------------------------------------
def disp_ball_stick(selection='all', hydrogens=0, only=False):
'''
DESCRIPTION
Formats the passed object into ball and stick
USEAGE
disp_ball_stick [ selection [, hydrogens [, only ]]]
EXAMPLE
fetch 1hpv, async=0
disp_ball_stick
util.cbaw
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
hydrogens <int> -1: remove; 1: add; else: as is
only=False <bool> if True will use show_as; else show
'''
try:
selection = '(' + selection + ')'
hydrogens = int(hydrogens)
only = bool(str(only) != 'False')
except:
print("Input error")
return False
if hydrogens == 1:
cmd.h_add('%s' % selection)
if hydrogens == -1:
cmd.remove('%s and elem H' % selection)
for p in cmd.get_object_list(selection):
cmd.set('valence', 'on', p)
cmd.set('stick_ball', 'on', p)
cmd.set('stick_ball_ratio', 3, p)
cmd.set('stick_radius', 0.12, p)
if only:
cmd.show_as('sticks', '%s' % (selection))
else:
cmd.show('sticks', '%s' % (selection))
cmd.extend("disp_ball_stick", disp_ball_stick)
cmd.auto_arg[0]['disp_ball_stick'] = [lambda: cmd.Shortcut(['all']), 'selection=', ',']
cmd.auto_arg[1]['disp_ball_stick'] = [lambda: cmd.Shortcut(['-1', '0', '1']), 'hydrogens=', ',']
cmd.auto_arg[2]['disp_ball_stick'] = [lambda: cmd.Shortcut(['True', 'False']), 'only=', '']
#-------------------------------------------------------------------------------
def disp_stick_ball(selection='all', hydrogens=0, only=False):
'''
see help disp_stick_ball
'''
#disp_stick_ball - redirected
disp_ball_stick(selection, hydrogens, only)
cmd.extend("disp_stick_ball", disp_stick_ball)
cmd.auto_arg[0]['disp_stick_ball'] = [lambda: cmd.Shortcut(['all']), 'selection=', ',']
cmd.auto_arg[1]['disp_stick_ball'] = [lambda: cmd.Shortcut(['-1', '0', '1']), 'hydrogens=', ',']
cmd.auto_arg[2]['disp_stick_ball'] = [lambda: cmd.Shortcut(['True', 'False']), 'only=', '']
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# DISPLAY: MESH
#-------------------------------------------------------------------------------
def disp_mesh(selection='all', color_m='default', hydrogens=0, only=False, limits=5):
'''
DESCRIPTION
Adds a mesh to the object
Has advanced coloring options and automatically accounts for the hydrogens
USEAGE
disp_mesh [ selection [, color_m [, hydrogens [, only [, limits]]]]]
disp_mesh selection=all, color_m=default
disp_mesh selection=all, color_m=white
disp_mesh selection=all, color_m=putty
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
color_m='default' <str> 'default': as current
'name': colors by color or ramp called name
'putty': b-factor on surface
hydrogens=0 <int> -1: remove; 1: add; else: as is
only=False <bool> if True will use show_as; else show
limits=5 <list or flaot>
applies only if color_m=='putty'
sets the b-factor range limits
<list> [min,max] # absolute values
<float> percentile cutoff (both sides) # relative for each protein
'''
try:
selection = '(' + selection + ')'
color_m = str(color_m)
hydrogens = int(hydrogens)
only = bool(str(only) != 'False')
except:
print("Input error")
return False
if hydrogens == 1:
cmd.h_add('%s' % selection)
if hydrogens == -1:
cmd.remove('%s and elem H' % selection)
for p in cmd.get_object_list(selection):
cmd.set('mesh_width', 0.25, p)
if (color_m == 'putty'):
limits = get_b_limits(limits, p)
if not limits:
print("Input error (limits must be <list> or <float (<=50)>)!")
return False
cmd.set('mesh_color', 'default', p)
cmd.spectrum('b', 'rainbow', '(not hetatm) and %s' % p, minimum='%f' % limits[0], maximum='%f' % limits[1], byres=0)
print("disp_mesh:", p, "displayed in putty mode - mesh as putty - limits=[%.4f,%.4f]" % (limits[0], limits[1]))
else:
cmd.set('mesh_color', color_m, p)
print("disp_mesh: regular mode - mesh - " + p)
if only:
cmd.show_as('mesh', '%s and %s' % (selection, p))
else:
cmd.show('mesh', '%s and %s' % (selection, p))
cmd.rebuild()
cmd.extend("disp_mesh", disp_mesh)
cmd.auto_arg[0]['disp_mesh'] = [lambda: cmd.Shortcut(['all']), 'selection=', ',']
cmd.auto_arg[1]['disp_mesh'] = [lambda: cmd.Shortcut(['default', 'red', 'green', 'blue', 'yellow']), 'color_m=', ',']
cmd.auto_arg[2]['disp_mesh'] = [lambda: cmd.Shortcut(['-1', '0', '1']), 'hydrogens=', ',']
cmd.auto_arg[3]['disp_mesh'] = [lambda: cmd.Shortcut(['only=False, limits=5']), 'remaining (defaults)...', '']
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# DISPLAY: SURFACE AND SURFACE AS PUTTY
#-------------------------------------------------------------------------------
def disp_surf(
selection='all',
color_s='default',
transparency=0,
hydrogens=0,
solvent=0,
ramp_above=1,
only=False,
limits=5):
'''
DESCRIPTION
Advanced surface representation (cf. examples)
USAGE
disp_surf [ selection [, color_s [, transparency [, hydrogens [, solvent [, ramp_above [, only [, limits]]]]]]]]
EXAMPLES
disp_surf # opaque surface with default colors
disp_surf all, white, 0.5 # half-transparent white surface
disp_surf all, putty # b-factor on surface
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
color_s='default' <str> 'default': as current
'name': colors by color or ramp called name
'putty': b-factor on surface (by resi)
transparency=0 <float> set surface transparency
hydrogens=0 <int> -1: remove; 1: add; else: as is
solvent=0 <int> defines 'surface_solvent'
ramp_above=1 <int> defines 'surface_ramp_above_mode'
only=False <bool> if True will use show_as; else show
limits=5 <list or flaot>
applies only if color_s=='putty'
sets the b-factor range limits
<list> [min,max] # absolute values
<float> percentile cutoff (both sides) # relative for each protein
'''
try:
selection = '(' + selection + ')'
color_s = str(color_s)
transparency = float(transparency)
hydrogens = int(hydrogens)
solvent = int(solvent)
ramp_above = int(ramp_above)
only = bool(str(only) != 'False')
except:
print("Input error")
return False
for p in cmd.get_object_list(selection):
if hydrogens == -1:
cmd.remove('%s and elem H' % p)
if hydrogens == 1:
cmd.h_add(p)
# if hydrogens==0: as is
# some defaults (settings can be changed later, too)
cmd.set('surface_carve_cutoff', '4.5', p)
cmd.set('surface_quality', '2', p)
cmd.set('solvent_radius', '1.5', p)
cmd.set('cavity_cull', '2', p)
#cmd.set('surface_carve_selection', p)
# this causes issues when using the command on different objects
# it is better to define surface_carve_selection manually
# defined
cmd.set('surface_solvent', solvent, p)
cmd.set('surface_ramp_above_mode', ramp_above, p)
cmd.set('transparency', transparency, p)
if (color_s == 'putty'):
limits = get_b_limits(limits, p)
if not limits:
print("Input error (limits must be <list> or <float (<=50)>)!")
return False
cmd.set('surface_color', 'default', p)
cmd.spectrum('b', 'rainbow',
'(not hetatm) and %s' % p, minimum='%f' % limits[0],
maximum='%f' % limits[1], byres=0)
print("disp_surf:", p, "displayed in putty mode - surface as putty - limits=[%.4f,%.4f]" % (limits[0], limits[1]))
else:
cmd.set('surface_color', color_s, selection)
print("disp_surf:", p, "displayed as regular surface")
if only:
cmd.show_as('surface', '(%s and %s)' % (selection, p))
else:
cmd.show('surface', '(%s and %s)' % (selection, p))
cmd.extend("disp_surf", disp_surf)
cmd.auto_arg[0]['disp_surf'] = [lambda: cmd.Shortcut(['all']), 'selection=', ',']
cmd.auto_arg[1]['disp_surf'] = [lambda: cmd.Shortcut(['default', 'red', 'green', 'blue', 'yellow']), 'color_s=', ',']
cmd.auto_arg[2]['disp_surf'] = [lambda: cmd.Shortcut(['0', '0.10', '0.20', '0.30', '0.40', '0.50', '0.60', '0.70', '0.80', '0.90', '1.00']), 'transparency=', ',']
cmd.auto_arg[3]['disp_surf'] = [lambda: cmd.Shortcut(['hydrogens=0, solvent=0, ramp_above=1, only=False, limits=5']), 'remaining (deafults)...', ',']
#cmd.auto_arg[4]['disp_surf']=[lambda: cmd.Shortcut(['0']), 'solvent=', ',']
#cmd.auto_arg[5]['disp_surf']=[lambda: cmd.Shortcut(['1']), 'ramp_above=', ',']
#cmd.auto_arg[6]['disp_surf']=[lambda: cmd.Shortcut(['True','False']), 'only=', '']
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# DISPLAY: PUTTY
#-------------------------------------------------------------------------------
def disp_putty(selection='all', limits=10, only=True):
'''
DESCRIPTION
Formats the passed object into a Putty b-factor sausage
USEAGE
disp_putty [ selection ]
selection <str> input selection
limits=10 <list or flaot>
applies only if color_m=='putty'
sets the b-factor range limits (by protein)
<list> [min,max]
<float> percentile cutoff (both sides)
only=True <bool> if True will use show_as; else show
'''
try:
selection = '(' + selection + ')'
only = bool(str(only) != 'False')
except:
print("Input error")
return False
for p in cmd.get_object_list(selection):
limits = get_b_limits(limits, p)
if not limits:
print("Input error (limits must be <list> or <float (<=50)>)!")
return False
# settings
cmd.set('cartoon_discrete_colors', 'off', p)
cmd.set('cartoon_putty_scale_max', 5, p)
cmd.set('cartoon_putty_scale_min', 1, p)
# normalized nonlinear scaling
cmd.set('cartoon_putty_transform', 0, p)
cmd.spectrum('b', 'rainbow', '(not hetatm) and %s' % p, minimum='%f' % limits[0], maximum='%f' % limits[1], byres=1)
cmd.cartoon('putty', '(%s and %s)' % (selection, p))
if only:
cmd.show_as('cartoon', '(%s and %s)' % (selection, p))
else:
cmd.show('cartoon', '(%s and %s)' % (selection, p))
cmd.extend("disp_putty", disp_putty)
cmd.auto_arg[0]['disp_putty'] = [lambda: cmd.Shortcut(['all', 'all and visible']), 'selection=', ',']
cmd.auto_arg[1]['disp_putty'] = [lambda: cmd.Shortcut('0', '5', '10', '[10,50]'), 'limits=', ',']
cmd.auto_arg[2]['disp_putty'] = [lambda: cmd.Shortcut(['True', 'False']), 'only=', '']
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------