def frag(state=state, obj=obj):
pwd, mutations, orig_sequence = setup(obj)
#get_positions_in_selection(sub, distance)
# Run over all sites where to mutate, optionally add and retain hydrogens.
for site in mutations.keys():
variants = mutations[site]
# Run over all variants.
for variant in variants:
cmd.load(obj)
cmd.do('wizard mutagenesis')
cmd.do('refresh_wizard')
cmd.get_wizard().set_hyd("keep")
cmd.get_wizard().set_mode(variant)
#cmd.get_wizard().do_select(site + '/')
# Get the number of available rotamers at that site.
# Introduce a condition here to check if rotamers are requested.
# <<OPTIONAL>>
nRots = getRots(site, variant)
#if nRots > 3:
# nRots = 3
nRots=1
cmd.rewind()
for i in range(1, nRots + 1):
cmd.get_wizard().do_select("(" + site + "/)")
cmd.frame(i)
cmd.get_wizard().apply()
# Optimize the mutated sidechain
#<<OPTION>>
#print "Sculpting."
local_sculpt(obj, variant, site)
# Protonation of the N.
#cmd.do("select n%d, name n and %d/" % (int(site), int(site)))
#cmd.edit("n%d" % int(site), None, None, None, pkresi=0, pkbond=0)
#cmd.do("h_fill")
# Protonation of the C.
#cmd.do("select c%d, name c and %d/" % (int(site), int(site)))
#cmd.edit("c%d" % int(site), None, None, None, pkresi=0, pkbond=0)
#cmd.do("h_fill")
# Definition of saveString
#saveString = '%s/' % pwd
#saveString += 'frag-' + get_one(orig_sequence[site]).lower() +\
# site + get_one(variant).lower() + '-%s.pdb, ' % state +\
# '((%s/))' % site
save_string_rot = '%s/' % pwd
save_string_rot += 'frag-' + get_one(orig_sequence[site]).lower() +\
site + get_one(variant).lower() + '-%02d-%s.pdb, ' % (i, state) +\
'((%s/))' % site
#print saveString
#cmd.do('save %s' % saveString.lower())
cmd.do('save %s' % save_string_rot.lower())
cmd.do('delete all')
cmd.set_wizard('done')
def testRewind(self):
self.prep_movie()
cmd.frame(30)
self.assertEquals(cmd.get_frame(), 30)
cmd.rewind()
self.assertEquals(cmd.get_frame(), 1)
def testRewind(self):
self.prep_movie()
cmd.frame(30)
self.assertEquals(cmd.get_frame(), 30)
cmd.rewind()
self.assertEquals(cmd.get_frame(), 1)
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.set_title('pdb',1,os.path.split(file)[-1])
cmd.rewind()
cmd.orient('pdb')
cmd.refresh()
cmd.show_as("ribbon")
cmd.refresh()
cmd.show_as("sticks")
cmd.refresh()
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
if n>1:
cmd.rewind()
sys.__stderr__.write(file+"\n")
sys.__stderr__.flush()
for a in range(1,n+1):
cmd.forward()
cmd.refresh()
except:
traceback.print_exc()
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.set_title('pdb',1,os.path.split(file)[-1])
cmd.rewind()
cmd.orient('pdb')
cmd.refresh()
cmd.zoom('center',16)
cmd.label("polymer and (name ca or elem P)","'//%s/%s/%s`%s/%s'%(segi,chain,resn,resi,name)")
cmd.refresh()
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
if n>1:
cmd.rewind()
sys.__stderr__.write(file+"\n")
sys.__stderr__.flush()
for a in range(1,n+1):
cmd.forward()
cmd.refresh()
except:
traceback.print_exc()
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
cmd.delete('pdb')
cmd.load(file, 'pdb')
cmd.set_title('pdb', 1, os.path.split(file)[-1])
cmd.rewind()
cmd.orient('pdb')
cmd.refresh()
cmd.show_as("ribbon")
cmd.refresh()
cmd.show_as("sticks")
cmd.refresh()
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
if n > 1:
cmd.rewind()
sys.__stderr__.write(file + "\n")
sys.__stderr__.flush()
for a in range(1, n + 1):
cmd.forward()
cmd.refresh()
except:
traceback.print_exc()
def load():
global last1, last2
list = glob("pdb/*/*")
list = map(lambda x: (random.random(), x), list)
list.sort()
list = map(lambda x: x[1], list)
l = len(list)
c = 0
for file in list:
c = c + 1
try:
cmd.set("suspend_updates", "1")
cmd.delete("pdb")
print file, last1, last2, c, "of", l
last2 = last1
last1 = file
cmd.load(file, "pdb")
cmd.set_title("pdb", 1, os.path.split(file)[-1])
cmd.rewind()
# cmd.refresh()
# cmd.hide()
cmd.show("cartoon")
cmd.color("auto", "ss h")
cmd.color("auto", "ss s")
cmd.orient("pdb")
cmd.color("auto", "organic and elem c")
cmd.show("spheres", "organic")
cmd.move("z", -50.0)
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
finally:
cmd.set("suspend_updates", "0")
if cmd.count_atoms():
start = time.time()
if n > 1:
while (time.time() - start) < cycle_time:
for a in range(1, n + 1):
cmd.refresh()
cmd.frame(a)
cmd.move("z", 2)
cmd.turn("y", 1)
time.sleep(0.025)
sys.__stderr__.write(" %d of %d" % (c, l))
sys.__stderr__.write("\n")
sys.__stderr__.flush()
else:
cmd.refresh()
while (time.time() - start) < cycle_time:
for a in range(1, n + 1):
time.sleep(0.05)
cmd.move("z", 1.0)
cmd.turn("y", 1)
def load():
global last1, last2
list = glob("pdb/*/*")
list = map(lambda x: (random.random(), x), list)
list.sort()
list = map(lambda x: x[1], list)
l = len(list)
c = 0
for file in list:
c = c + 1
try:
cmd.set("suspend_updates", "1")
cmd.delete('pdb')
print file, last1, last2, c, "of", l
last2 = last1
last1 = file
cmd.load(file, 'pdb')
cmd.set_title('pdb', 1, os.path.split(file)[-1])
cmd.rewind()
# cmd.refresh()
# cmd.hide()
cmd.show('cartoon')
cmd.color('auto', 'ss h')
cmd.color('auto', 'ss s')
cmd.orient('pdb')
cmd.color('auto', 'organic and elem c')
cmd.show('spheres', 'organic')
cmd.move('z', -50.0)
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
finally:
cmd.set("suspend_updates", "0")
if cmd.count_atoms():
start = time.time()
if n > 1:
while (time.time() - start) < cycle_time:
for a in range(1, n + 1):
cmd.refresh()
cmd.frame(a)
cmd.move('z', 2)
cmd.turn('y', 1)
time.sleep(0.025)
sys.__stderr__.write(" %d of %d" % (c, l))
sys.__stderr__.write("\n")
sys.__stderr__.flush()
else:
cmd.refresh()
while (time.time() - start) < cycle_time:
for a in range(1, n + 1):
time.sleep(0.05)
cmd.move('z', 1.0)
cmd.turn('y', 1)
def set_browse(self,browse):
# allow user to focus on only a subset of the compounds
self.browse = browse
if self.browse == 1:
print(" Filter: Browsing all compounds.")
cmd.mset() # all states visible
elif self.object is None:
print(" Filter-Error: please choose an object first")
else:
self.check_object_dict()
if self.browse == 2:
print(" Filter: Browsing accepted compounds.")
target = accept_str
elif self.browse == 3:
print(" Filter: Browsing rejected compounds.")
target = reject_str
elif self.browse == 4:
print(" Filter: Browsing deferred compounds.")
target = defer_str
lst = []
sd = self.state_dict
sdo = self.dict[self.object]
if self.browse<5:
for a in list(sdo.keys()):
if sdo[a]==target:
lst.append(sd[a])
else:
print(" Filter: Browsing remaining compounds")
for a in sd.keys():
if a not in sdo:
lst.append(sd[a])
lst.sort()
if len(lst)==0:
print(" Filter-Error: No matching compounds.")
cmd.mset(' '.join(map(str,lst)))
cmd.rewind()
cmd.refresh_wizard()
def set_browse(self,browse):
# allow user to focus on only a subset of the compounds
self.browse = browse
if self.browse == 1:
print " Filter: Browsing all compounds."
cmd.mset() # all states visible
elif self.object==None:
print " Filter-Error: please choose an object first"
else:
self.check_object_dict()
if self.browse == 2:
print " Filter: Browsing accepted compounds."
target = accept_str
elif self.browse == 3:
print " Filter: Browsing rejected compounds."
target = reject_str
elif self.browse == 4:
print " Filter: Browsing deferred compounds."
target = defer_str
lst = []
sd = self.state_dict
sdo = self.dict[self.object]
if self.browse<5:
for a in sdo.keys():
if sdo[a]==target:
lst.append(sd[a])
else:
print " Filter: Browsing remaining compounds"
for a in sd.keys():
if not sdo.has_key(a):
lst.append(sd[a])
lst.sort()
if len(lst)==0:
print " Filter-Error: No matching compounds."
cmd.mset(' '.join(map(str,lst)))
cmd.rewind()
cmd.refresh_wizard()
"""
Generate a movie from atom-by-atom proposal PMF and placement PDB files.
Run with `run movie.py` in PyMOL
"""
iteration = 6
from pymol import cmd, movie
#cmd.mclear()
#cmd.mset('1')
cmd.set('sphere_scale', 0.02)
cmd.rewind()
cmd.delete('all')
cmd.load('geometry-%d-forward-proposal.pdb' % iteration)
cmd.hide('all')
cmd.show('spheres', 'name Ar')
cmd.spectrum(expression='b', selection='name Ar', palette='blue_white_red', minimum=0, maximum=6)
cmd.load('geometry-%d-forward-stages.pdb' % iteration)
nframes = 30
specification = ''
for i in range(15):
specification += '%d x%d ' % (i, nframes)
cmd.mset(specification)
frame = 0
for i in range(15):
movie.rock(frame, frame+nframes)
frame += nframes
def set_up_scenes():
"""Set up the scenes for a global view and a close-up on the binding site"""
cmd.zoom('Cathepsin', 10) # Zoom out to get a view on the whole complex
cmd.scene('001', 'store', message='This is the first scene with a view on the complex!')
cmd.set_view(closeup) # Get a close-up of the ligand by using the manually chosen viewpoint
cmd.scene('002', 'store', message='This is the second scene with a close-up on the ligand!')
setup_pymol()
cmd.load('../../input-files/Cathepsin.pdb') # Load the PDB file
initial_representations()
set_up_scenes()
# With the scenes ready, we need to assign them to frames, i.e. set how long a scene should appear in the animation
cmd.scene('001', animate=0) # First, select the scene to assign
cmd.mview('store', 1) # We assign it to the first frame, i.e. the movie should start showing the first scene
cmd.mview('store', 150) # Also assign it to frame 200. Scene 001 is now shown for 150 frames
cmd.scene('002', animate=0) # Now, choose the close-up scene
cmd.mview('store', 250) # Assign it to frame 250
cmd.mview('store', 400) # Also assign it to frame 400
# Using scenes, we don't have to bother about transitions (the camera flights) between scenes.
# PyMOL takes care of that. It interpolates a smooth transition between the scenes.
# Let's rewind to frame 1 and see how the animation looks. To get a fast preview, we have to turn off ray tracing.
cmd.rewind() # Rewind the movie to frame 1
cmd.set('ray_trace_frames', 0) # Turn ray-tracing for frames off
# By default, PyMOL shows the video in a loop and also takes care of the transition of the last to the first scene.
# This setting is perfect for producing videos for presentations that should loop over and over again.
def frag(state=state, obj=obj):
pwd, mutations, orig_sequence = setup(obj)
# Add and retain hydrogens
cmd.get_wizard().set_hyd("keep")
# Run over all sites where to mutate
for site in mutations.keys():
variants = mutations[site]
# Run over all variants.
for variant in variants:
cmd.load(obj)
cmd.do("wizard mutagenesis")
cmd.do("refresh_wizard")
cmd.get_wizard().set_mode(variant)
cmd.get_wizard().do_select(site + "/")
# Get the number of available rotamers at that site
# Introduce a condition here to check if
# rotamers are requested.
# <<OPTION>>
# nRots = getRots(site, variant)
# if nRots > 3:
# nRots = 3
nRots = 1
cmd.rewind()
for i in range(1, nRots + 1):
cmd.get_wizard().do_select("(" + site + "/)")
cmd.frame(i)
cmd.get_wizard().apply()
# Optimize the mutated sidechain
# <<OPTION>>
# print "Sculpting."
# localSculpt(obj, site)
# Protonation of the N.
cmd.do("select n%d, name n and %d/" % (int(site), int(site)))
cmd.edit("n%d" % int(site), None, None, None, pkresi=0, pkbond=0)
cmd.do("h_fill")
# Protonation of the C.
cmd.do("select c%d, name c and %d/" % (int(site), int(site)))
cmd.edit("c%d" % int(site), None, None, None, pkresi=0, pkbond=0)
cmd.do("h_fill")
# Definition of saveString
# saveString = '%s/' % pwd
# saveString += 'frag-' + getOne(orig_sequence[site]).lower() +\
# site + getOne(variant).lower() + '-%s.pdb, ' % state +\
# '((%s/))' % site
saveStringRot = "%s/" % pwd
saveStringRot += (
"frag-"
+ getOne(orig_sequence[site]).lower()
+ site
+ getOne(variant).lower()
+ "-%02d-%s.pdb, " % (i, state)
+ "((%s/))" % site
)
# print saveString
# cmd.do('save %s' % saveString.lower())
cmd.do("save %s" % saveStringRot.lower())
cmd.do("delete all")
cmd.set_wizard("done")
def rewind():
cmd.mstop()
cmd.rewind()
def growProtein():
cmd.mstop()
cmd.mclear()
cmd.mset()
glb.update()
objects = cmd.get_names('all')
if 'protein' in objects:
cmd.bg_color('black')
# create the objects to be used in this movie
cmd.create('helix', 'ss h and protein')
cmd.create('sheets', 'ss s and protein')
cmd.create('surface', objects[0])
cmd.mset('1', '1400')
# dna and rna will be represented as sticks
# to make them stand out from the protein
if 'dna' in objects:
glb.procolor('dna','sticks','cpk',None)
if 'rna' in objects:
glb.procolor('rna','sticks','cpk',None)
# coloring the protein and secondary structures
cmd.color('white', 'protein')
cmd.color('purple', 'helix')
cmd.color('teal', 'sheets')
cmd.cartoon('loop', 'protein')
cmd.cartoon('automatic', 'helix')
cmd.cartoon('automatic', 'sheets')
cmd.hide('all')
cmd.show('cartoon', 'protein')
#cmd.mdo(1,'hide cartoon, helix; hide cartoon, sheets;')
cmd.util.mrock('2', '200', '90', '1', '1')
cmd.mdo(201,'show cartoon, helix;')
cmd.util.mrock('202', '400', '90', '1', '1')
cmd.mdo(401,'show cartoon, sheets;')
cmd.util.mrock('402', '600', '90', '1', '1')
if 'ligands' in objects:
cmd.color('hotpink', 'ligands')
cmd.mdo(600, 'show spheres, ligands; show sticks, ligands;'+
' set sphere_transparency = 0.5, ligands;')
cmd.util.mroll('601', '800', '1', axis = "x")
cmd.color('blue', 'surface')
cmd.mview('store', '800')
cmd.turn('z', 180)
cmd.mview('store' , '1000')
cmd.turn('z', 180)
cmd.mdo(800, 'show surface, surface; '+
'set transparency = 0.8, surface;')
cmd.mdo(850,'set transparency = 0.7, surface;')
cmd.mdo(900,'set transparency = 0.6, surface;')
cmd.mdo(950,'set transparency = 0.5, surface;')
cmd.mdo(1000,'set transparency = 0.4, surface;')
cmd.mdo(1050,'set transparency = 0.3, surface;')
cmd.mdo(1100,'set transparency = 0.2, surface;')
cmd.mdo(1150,'set transparency = 0.1, surface;')
cmd.mdo(1200,'set transparency = 0.0, surface;')
cmd.mview('store', '1200')
cmd.util.mrock('1201', '1399', '180', '1', '1')
cmd.hide('everything', 'surface')
cmd.hide('everything', 'helix')
cmd.hide('everything', 'sheets')
cmd.reset()
cmd.orient()
cmd.mdo(1400,'hide everything, all; show cartoon, protein;')
cmd.mdo(1400,'mstop')
cmd.mview('interpolate')
cmd.rewind()
def frag(state=state, obj=obj3):
pwd, orig_sequence = setup(obj)
stored.rotamerDict = {}
# Add and retain hydrogens
cmd.get_wizard().set_hyd("keep")
# Run over all sites where to mutate
for site in mutations.keys():
variants = mutations[site]
# Run over all variants.
for variant in variants:
cmd.load(obj)
cmd.do('wizard mutagenesis')
cmd.do('refresh_wizard')
cmd.get_wizard().do_select("(%s/)" % site)
cmd.do("cmd.get_wizard().set_mode('%s')"%variant)
# Get the number of available rotamers at that site
# Introduce a condition here to check if
# rotamers are requested.
# <<OPTION>>
print variant, "variant"
nRots = getRots(site, variant)
nRots = 2
stored.rotamerDict[str(site)+getOne(variant)] = nRots
cmd.rewind()
for i in range(1, nRots + 1):
cmd.get_wizard().do_select("(" + site + "/)")
cmd.frame(i)
cmd.get_wizard().apply()
# Optimize the mutated sidechain
#<<OPTION>>
print "Sculpting."
localSculpt(obj, site)
# Protonation of the N.
cmd.do("select n%d, name n and %d/" % (int(site), int(site)))
cmd.edit("n%d" % int(site), None, None, None, pkresi=0, pkbond=0)
cmd.do("h_fill")
# Protonation of the C.
cmd.do("select c%d, name c and %d/" % (int(site), int(site)))
cmd.edit("c%d" % int(site), None, None, None, pkresi=0, pkbond=0)
cmd.do("h_fill")
# Definition of saveString
saveString = '%s/' % pwd
saveString += 'frag-' + getOne(orig_sequence[site]).lower() +\
site + getOne(variant).lower() + '-rot%i-%s.pdb, ' \
% (i,state) +'((%s/))' % site
#print saveString
cmd.do('save %s' % saveString)
cmd.do('delete all')
cmd.set_wizard('done')
print "Frag is all done"
#import __main__
#__main__.pymol_argv = [ 'pymol', '-qc']
#import pymol
#pymol.finish_launching()
# DEBUG: ANALYSIS PATH IS HARD-CODED FOR NOW
source_directory = 'experiments'
reference_pdbfile = 'setup/systems/Abl-STI/complex.pdb'
phase = 'complex'
replica = 0 # replica index to render
#replica = 15 # replica index to render
# Load PDB file.
cmd.rewind()
cmd.delete('all')
cmd.reset()
cmd.load(reference_pdbfile, 'complex')
cmd.remove('resn WAT') # remove waters
cmd.select('receptor', '(not resn MOL) and (not resn WAT) and (not hydrogen)')
cmd.select('ligand', 'resn MOL and not hydrogen')
cmd.select('ions', 'resn Na\+ or resn Cl\-')
cmd.deselect()
cmd.hide('all')
cmd.show('cartoon', 'receptor')
cmd.show('spheres', 'ligand')
cmd.show('spheres', 'ions')
util.cbay('ligand')
cmd.color('green', 'receptor')
cmd.load('../../input-files/Cathepsin.pdb') # Load the PDB file
initial_representations()
set_up_scenes()
scenes_to_frames()
# Apart from moving between scenes, independent camera movements can be added to the animation
# One of them, the zoom (cmd.zoom) was already used
# Two other movements are rotation (cmd.turn) and panning (cmd.move)
# Let's add a rotation to the global view and a panning to the close-up to make them more interesting
cmd.scene(
'001', animate=0
) # Select the first scene again (we need the camera view as a starting point)
cmd.turn('y', -40) # Turn the camera 40 degrees left around the y-axis
cmd.mview('store', 80) # Store the changed view/assign it to frame 60
cmd.turn(
'y',
40) # Turn the camera 40 degrees in the other direction around the y-axis
cmd.mview('store', 140) # Assign the view to frame 120
cmd.scene('002', animate=0) # Select the second scene
cmd.move('x', 5) # Move along the x-axis
cmd.mview('store', 320) # Assign the view to frame 320
# Rewind and turn off ray-tracing
cmd.rewind() # Rewind the movie to frame 1
cmd.set('ray_trace_frames', 0) # Turn ray-tracing for frames off
# Running the script, you should now see the additional camera movements additional to the scene transitions
# Note that there are also transitions back to original scene 001 and scene 002 views after the movements
