def vis(res,
path_prefix,
c=["firebrick", "forest", 'purple', 'salmon', "gold", "red"]):
for ind, r in enumerate(res):
for a in r.atoms:
cmd.show("spheres", "id " + str(a.id))
cmd.set("sphere_color", c[ind], "id " + str(a.id))
cmd.distance("d" + str(ind), "id " + str(r.atoms[0].id),
"id " + str(r.atoms[1].id))
cmd.hide("labels")
cmd.set("grid_slot", -2, "d" + str(ind))
cmd.ray(1200)
time.sleep(2)
cmd.set("grid_mode", 0)
cmd.png(path_prefix + "_restraints.png")
#cmd.set("grid_mode", 1)
cmd.move("zoom", -10)
cmd.ray(1200, )
time.sleep(4)
cmd.png(path_prefix + "_grid_restraints.png")
cmd.set("grid_mode", 0)
cmd.hide("spheres")
cmd.delete("d*")
def images_screw(images, distance, sweep, axis):
global imagecount
global ray
global filename
global ximage
global yimage
print "... Images %s - %s:" % (imagecount, imagecount + images - 1)
print "Writing %s images moving along %s axis by %s Angstrom" % \
(images, axis, distance/images)
print " and rotating %s degrees per image" % (sweep / images)
for i in range(0, images): #cycle for number of images
# transformations
cmd.move(axis, distance / images)
cmd.turn(axis, sweep / images)
#print image
cmd.png("images/%s_%04d" % (filename, imagecount), ray=ray)
#increment imagecounter
imagecount = imagecount + 1
cmd.refresh()
def additional_camera():
# Add a rotation to the global view
cmd.scene('001', animate=0)
cmd.turn('y', -40)
cmd.mview('store', 80)
cmd.turn('y', 40)
cmd.mview('store', 140)
# Add panning to the close-up
cmd.scene('002', animate=0)
cmd.move('x', 5)
cmd.mview('store', 320)
def additional_camera():
# Add a rotation to the global view
cmd.scene('001', animate=0)
cmd.turn('y', -40)
cmd.mview('store', 80)
cmd.turn('y', 40)
cmd.mview('store', 140)
# Add panning to the close-up
cmd.scene('002', animate=0)
cmd.move('x', 5)
cmd.mview('store', 320)
def loadPackingPDB(file, name=None, native=None):
"""
usage: loadPackingPDB <file> , [<name for object>]
loads a foo_packing.pdb file and colors it all pretty-like
creates two selections along with the loaded object called
NAMEcavities and NAMEprotein which are the heteratoms representing
holes and everything else, respectively. Names can get pretty long,
by pymol lets you do good stuff like "select NA*cav*", which will
match a selection called NAMEISREALLYLONGcavities.
"""
if name is None:
name = name = os.path.basename(file)
if name.endswith('.gz'):
name = name[:-3]
if name.endswith('.pdb'):
name = name[:-4]
if name.endswith('.'):
name = name[:-1]
if name.endswith("_packing"):
name = name[:-8]
zload(file, name)
cmd.hide('everything', name)
if native is not None:
cmd.align(name, native)
cmd.zoom(native)
useRosettaRadii()
cavselname = name + "cavities"
protselname = name + "protein"
cmd.select(cavselname, "resn WSS and %s" % (name))
cmd.select(protselname, "(not resn WSS) and %s" % (name))
useTempRadii(cavselname)
useOccColors(cavselname)
cmd.color("white", protselname)
cmd.show('spheres', cavselname)
cmd.show("cartoon", protselname)
cmd.show("lines", protselname)
cmd.select("none")
cmd.delete("sele*")
cmd.move('z', -50)
return name
def loadPackingPDB(file,name=None,native=None):
"""
usage: loadPackingPDB <file> , [<name for object>]
loads a foo_packing.pdb file and colors it all pretty-like
creates two selections along with the loaded object called
NAMEcavities and NAMEprotein which are the heteratoms representing
holes and everything else, respectively. Names can get pretty long,
by pymol lets you do good stuff like "select NA*cav*", which will
match a selection called NAMEISREALLYLONGcavities.
"""
if name is None:
name = name = os.path.basename(file)
if name.endswith('.gz'):
name = name[:-3]
if name.endswith('.pdb'):
name = name[:-4]
if name.endswith('.'):
name = name[:-1]
if name.endswith("_packing"):
name = name[:-8]
zload(file,name)
cmd.hide('everything',name)
if native is not None:
cmd.align(name,native)
cmd.zoom(native)
useRosettaRadii()
cavselname = name+"cavities"
protselname = name+"protein"
cmd.select(cavselname, "resn CAV and b > 0.1 and %s"%(name) )
cmd.select(protselname,"(not resn CAV) and %s"%(name) )
useTempRadii(cavselname)
useOccColors(cavselname)
cmd.color("white",protselname)
cmd.show('spheres', cavselname )
cmd.show("cartoon",protselname)
cmd.show("lines",protselname)
cmd.select("none")
cmd.delete("sele*")
cmd.move('z',-50)
return name
def testReset(self):
# view
v = cmd.get_view()
cmd.turn('x', 10)
cmd.move('y', 10)
self.assertNotEqual(v, cmd.get_view())
cmd.reset()
self.assertEqual(v, cmd.get_view())
# object
cmd.pseudoatom("m1")
x = cmd.get_object_matrix("m1")
cmd.translate([1, 2, 3], object="m1")
self.assertNotEqual(x, cmd.get_object_matrix("m1"))
cmd.reset("m1")
self.assertEqual(x, cmd.get_object_matrix("m1"))
def testReset(self):
# view
v = cmd.get_view()
cmd.turn('x', 10)
cmd.move('y', 10)
self.assertNotEqual(v, cmd.get_view())
cmd.reset()
self.assertEqual(v, cmd.get_view())
# object
cmd.pseudoatom("m1")
x = cmd.get_object_matrix("m1")
cmd.translate([1,2,3], object="m1")
self.assertNotEqual(x, cmd.get_object_matrix("m1"))
cmd.reset("m1")
self.assertEqual(x, cmd.get_object_matrix("m1"))
def testClip(self):
for a in "xyz":
cmd.turn(a, random.random() * 10 - 5)
cmd.move(a, random.random() * 10 - 5)
v = cmd.get_view()
cmd.clip("near", -5)
self.assertAlmostEqual(v[15] + 5, cmd.get_view()[15], delta=1e-3)
cmd.clip("far", 10)
self.assertAlmostEqual(v[16] - 10, cmd.get_view()[16], delta=1e-3)
cmd.clip("move", -15)
a = cmd.get_view()
self.assertAlmostEqual(v[15], a[15] - 20, delta=1e-3)
self.assertAlmostEqual(v[16], a[16] - 5, delta=1e-3)
cmd.clip("slab", 20)
v = cmd.get_view()
self.assertAlmostEqual(v[16] - v[15], 20.0, delta=1e-3)
cmd.pseudoatom()
cmd.clip("atoms", 5, "all")
v = cmd.get_view()
self.assertAlmostEqual(v[16] - v[15], 10.0, delta=1e-3)
def testClip(self):
for a in "xyz":
cmd.turn(a, random.random() * 10 - 5)
cmd.move(a, random.random() * 10 - 5)
v = cmd.get_view()
cmd.clip("near", -5)
self.assertAlmostEqual(v[15] + 5, cmd.get_view()[15], delta=1e-3)
cmd.clip("far", 10)
self.assertAlmostEqual(v[16] - 10, cmd.get_view()[16], delta=1e-3)
cmd.clip("move", -15)
a = cmd.get_view()
self.assertAlmostEqual(v[15], a[15] - 20, delta=1e-3)
self.assertAlmostEqual(v[16], a[16] - 5, delta=1e-3)
cmd.clip("slab", 20)
v = cmd.get_view()
self.assertAlmostEqual(v[16] - v[15], 20.0, delta=1e-3)
cmd.pseudoatom()
cmd.clip("atoms", 5, "all")
v = cmd.get_view()
self.assertAlmostEqual(v[16] - v[15], 10.0, delta=1e-3)
def images_spin3_slide3(images, distance, sweep):
global imagecount
global ray
global filename
global ximage
global yimage
print "... Images %s - %s:" % (imagecount, imagecount + images - 1)
print "Writing %s images turning about:" % images
print " x axis by %s degrees, then" % (sweep[0] / images)
print " y axis by %s degrees, and" % (sweep[1] / images)
print " z axis by %s degrees per image," % (sweep[2] / images)
print " while moving along:"
print " x axis by %s Angstrom," % (distance[0] / images)
print " y axis by %s Angstrom, and" % (distance[1] / images)
print " z axis by %s Angstrom per image" % (distance[2] / images)
for i in range(0, images): #cycle for number of images
# transformations
cmd.turn("x", sweep[0] / images)
cmd.turn("y", sweep[1] / images)
cmd.turn("z", sweep[2] / images)
cmd.move("x", distance[0] / images)
cmd.move("y", distance[1] / images)
cmd.move("z", distance[2] / images)
#print image
cmd.png("images/%s_%04d" % (filename, imagecount), ray=ray)
#increment imagecounter
imagecount = imagecount + 1
cmd.refresh()
def render_to_file(fname, top=True, side=True, vesicle=False,
zoom_obj="pbcbox",
zoom_distance=10):
fname = os.path.splitext(fname)[0]
cmd.reset()
cmd.zoom(zoom_obj, zoom_distance)
if vesicle:
cmd.turn("z", -90)
cmd.move("y", -50)
if top:
cmd.ray("2048")
cmd.png("%s_top.png" % fname)
if side:
cmd.turn("x", -90)
if vesicle:
cmd.move("y", 150)
cmd.ray("2048")
cmd.png("%s_side.png" % fname)
cmd.reset()
cmd.zoom(zoom_obj, zoom_distance)
if vesicle:
cmd.turn("z", -90)
cmd.move("y", -50)
def test(self):
cmd.viewport(200, 100)
cmd.fragment('ethylene', 'm1')
cmd.remove('hydro')
cmd.pseudoatom('p1', 'index 1')
cmd.disable('p1')
cmd.ramp_new('r1', 'p1', [0.1, 1.2], ['red', 'blue'])
cmd.disable('r1')
cmd.color('r1')
cmd.show_as('sticks', 'm1')
cmd.orient('m1')
cmd.move('z', 11)
self.ambientOnly()
img = self.get_imagearray()
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
self.assertImageHasColor([.5, .0, .5], img, delta=1)
def initPymol(self):
# set stereo mode
cmd.set('stereo_mode', 3)
cmd.stereo()
# get rid of gui
cmd.set('internal_gui', 0)
# set resolution to HD for rift
cmd.viewport(1920, 1080)
# full screen?
if self.fullscreen:
cmd.full_screen('on')
# load pdb
if len(self.pdb) == 4 and self.pdb == re.match('[a-zA-Z0-9]*',
self.pdb).group(0):
cmd.fetch(self.pdb, async=0)
if self.editMolecule == True:
cmd.hide('everything', 'all')
cmd.show('cartoon', 'all')
# color each chain differently
if self.editMolecule:
util.cbc()
# set origin at camera
if self.naturalRotation:
self.setOriginAtCamera()
# move slab away to give a comfortable viewing area
cmd.clip('move', 10)
# jiggle the camera to deal with blank screen error
cmd.move('z', .0001)
def testMove(self):
for a in "xyz":
cmd.turn(a, random.random() * 10 - 5)
cmd.move(a, random.random() * 10 - 5)
v = list(cmd.get_view())
d = (2,4,6)
cmd.move("x", d[0])
cmd.move("y", d[1])
cmd.move("z", d[2])
m = cmd.get_view()
v[9] += d[0]
v[10] += d[1]
v[11] += d[2]
v[15] -= d[2]
v[16] -= d[2]
self.assertArrayEqual(v, m, delta=1e-3)
def testMove(self):
for a in "xyz":
cmd.turn(a, random.random() * 10 - 5)
cmd.move(a, random.random() * 10 - 5)
v = list(cmd.get_view())
d = (2, 4, 6)
cmd.move("x", d[0])
cmd.move("y", d[1])
cmd.move("z", d[2])
m = cmd.get_view()
v[9] += d[0]
v[10] += d[1]
v[11] += d[2]
v[15] -= d[2]
v[16] -= d[2]
self.assertArrayEqual(v, m, delta=1e-3)
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 visualize(self):
# load pdb into pymol and set up view
self.initPymol()
# TODO: check if this is necessary
self.initCamera()
# listen ...
while True:
# Rift support
self.ocudump.getPose()
#print ocudump.pose [pitch (x), yaw (z), roll (y)]
pose = self.ocudump.pose
# calculate head rotation
xRot = pose[0] - self.previousOrientation[0]
yRot = pose[1] - self.previousOrientation[1]
zRot = pose[2] - self.previousOrientation[2]
# update view
cmd.turn('x', xRot * self.rotationScaling)
cmd.turn('y', yRot * self.rotationScaling)
cmd.turn('z', zRot * self.rotationScaling)
# rift head tracking
if self.ocudump.positionTracked:
# move head if sensor detects head motion
# not tested
cmd.move('x', pose[3] - self.previousPosition[0])
cmd.move('y', pose[4] - self.previousPosition[1])
cmd.move('z', pose[5] - self.previousPosition[2])
# update camera for "natural rotation"
if self.naturalRotation:
self.setOriginAtCamera()
# record previous pose for accurate rotation diff
self.previousOrientation = pose[0:3]
time.sleep(1 / float(self.trackingRefresh))
def render_to_file(fname, top=True, side=True, vesicle=False, zoom_obj="pbcbox", zoom_distance=10):
fname = os.path.splitext(fname)[0]
cmd.reset()
cmd.zoom(zoom_obj, zoom_distance)
if vesicle:
cmd.turn("z", -90)
cmd.move("y", -50)
if top:
cmd.ray("2048")
cmd.png("%s_top.png" % fname)
if side:
cmd.turn("x", -90)
if vesicle:
cmd.move("y", 150)
cmd.ray("2048")
cmd.png("%s_side.png" % fname)
cmd.reset()
cmd.zoom(zoom_obj, zoom_distance)
if vesicle:
cmd.turn("z", -90)
cmd.move("y", -50)
cmd.load(
'/Users/choderaj/github/foldingathome/covid-moonshot/perses-figure/boronic_ester_enumeration_for_chodera_lab_FEP-permuted-dockscores-x10789.sdf',
'conformer')
cmd.set('all_states', 1)
# DEBUG
#cmd.load('nucleophilic_displacement_enumeration_for_FEP-sorted-x10789.mol2')
#cmd.load('sprint1-winners.mol2')
cmd.viewport(720, 720)
cmd.orient('N3-ligand')
cmd.turn('z', -90) # TODO: Shift camera instead
cmd.turn('y', +20) # TODO: Shift camera instead
cmd.zoom('N3-ligand')
#cmd.clip('far', -10)
cmd.move('y', +1)
cmd.show('sticks', 'not hydrogen and *-ligand')
# Hide all fragments
cmd.deselect()
cmd.disable('aminopyridines-*')
cmd.disable('quinolones-*')
cmd.disable('benzotriazoles-*')
cmd.disable('fragment-*')
if show_conformers:
cmd.hide('sticks', 'hydrogen')
cmd.hide('sticks', 'conformers')
cmd.show('lines', 'conformers and not hydrogen')
cmd.mview('store', 250)
cmd.mview('store', 400)
setup_pymol()
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
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
print "BEGIN-LOG"
print cmd.set_key('F1',lambda :cmd.turn('x',10))
print cmd.set_key('F12',lambda :cmd.turn('x',10))
print cmd.set_key('left',lambda :cmd.turn('x',10))
print cmd.set_key('right',lambda :cmd.turn('x',10))
print cmd.set_key('pgup',lambda :cmd.turn('x',10))
print cmd.set_key('pgdn',lambda :cmd.turn('x',10))
print cmd.set_key('home',lambda :cmd.turn('x',10))
print cmd.set_key('insert',lambda :cmd.turn('x',10))
print cmd.set_key('ALT-A',lambda :cmd.turn('y',10))
print cmd.set_key('CTRL-C',lambda :cmd.turn('z',10))
print cmd.set_key('SHFT-F1', lambda :cmd.turn('z',10))
print cmd.set_key('ALT-F1', lambda :cmd.turn('y',10))
print cmd.set_key('CTRL-F8', lambda :cmd.move('x',1))
print "END-LOG"
# -c
from pymol import cmd
print "BEGIN-LOG"
print cmd.set_key('F1', lambda: cmd.turn('x', 10))
print cmd.set_key('F12', lambda: cmd.turn('x', 10))
print cmd.set_key('left', lambda: cmd.turn('x', 10))
print cmd.set_key('right', lambda: cmd.turn('x', 10))
print cmd.set_key('pgup', lambda: cmd.turn('x', 10))
print cmd.set_key('pgdn', lambda: cmd.turn('x', 10))
print cmd.set_key('home', lambda: cmd.turn('x', 10))
print cmd.set_key('insert', lambda: cmd.turn('x', 10))
print cmd.set_key('ALT-A', lambda: cmd.turn('y', 10))
print cmd.set_key('CTRL-C', lambda: cmd.turn('z', 10))
print cmd.set_key('SHFT-F1', lambda: cmd.turn('z', 10))
print cmd.set_key('ALT-F1', lambda: cmd.turn('y', 10))
print cmd.set_key('CTRL-F8', lambda: cmd.move('x', 1))
print "END-LOG"
def align_allfiles(target='',
files='*.pdb',
res_sel='i. 1-',
outfile='',
name='',
cutoff=2.0,
cycles=5,
method='align'):
"""
Aligns all models in a list of files to one target using either align or super method.
Outputs: Rosetta energy terms,c-alpha, backbone, and all atom rmsd for each model
sorted by c-alpha rmsd
usage:
align_allfiles target=target name,files=name.pdb,res_sel='i. 1-,outfile='file name'
cutoff=2,cycles=5 method=align
where target specifies the model id you want to align all others against,
and cutoff and cycles are options passed to the align command.
You can specify the files to load and align using a wildcard. You should specify same
number of residues for the target and other models. if outfile is not given output is
stddount
By default all residues in the structure are aligned,cutoff is 2,number of cycles is 5, and align method is used.
Example:
pymol -cdq "run/$SCRIPTS/align_allfiles;align_allfiles <target name>,[none default
arguments eg res_sel= i. 100-120,...]"
"""
cutoff = int(cutoff)
cycles = int(cycles)
cmd.load(target) # change 1
#print outfile, cutoff,cycles,res_sel
#Define rmsd and residue selection for mobile and target
all = 'all & %s' % res_sel
ca = 'n. ca & %s' % res_sel
bb = 'n. n+c+ca+o and %s' % res_sel
#obtain files from folder and remove native
#tar=tarfile.open('*.tgz','r:tgz')
file_list = glob.glob(files)
#file_list.remove(target)
#file_list.sort()
for file in file_list:
if file == target:
file_list.remove(file)
else:
file_list.sort()
#print file_list
# print len(file_list)
extension = re.compile('(^.*[\/]|\.(pdb|ent|brk))')
object_list = []
target = extension.sub('', target) # change 3
# Define rmsd storage variables
rmsd_list = []
for i in range(len(file_list)):
obj_name1 = extension.sub('', file_list[i])
object_list.append(extension.sub('', file_list[i]))
# energy=popen('grep "total_energy"' file_list[i])
# print energy
cmd.load(file_list[i], obj_name1)
if method == 'align':
rms_ca = cmd.align('%s & %s' % (object_list[i], ca),
'%s & %s' % (target, ca),
cutoff=cutoff,
cycles=cycles)
rms_bb = cmd.align('%s & %s' % (object_list[i], bb),
'%s & %s' % (target, bb),
cutoff=cutoff,
cycles=cycles)
rms_all = cmd.align('%s & %s' % (object_list[i], all),
'%s & %s' % (target, all),
cutoff=cutoff,
cycles=cycles)
#print '%s,%6.2f,%6.2f,%6.2f' %(object_list[i],rms_bb[0],rms_ca[0],rms_all[0])
elif method == 'super':
rms_ca = cmd.super('%s & %s' % (object_list[i], ca),
'%s & %s' % (target, ca),
cutoff=cutoff,
cycles=cycles)
rms_bb = cmd.super('%s & %s' % (object_list[i], bb),
'%s & %s' % (target, bb),
cutoff=cutoff,
cycles=cycles)
rms_all = cmd.super('%s & %s' % (object_list[i], all),
'%s & %s' % (target, all),
cutoff=cutoff,
cycles=cycles)
#print '%s,%6.2f,%6.2f,%6.2f' %(object_list[i],rms_ca[0],rms_bb[0],rms_all[0])
elif method == 'cealign':
rmsdict = cmd.cealign(
'%s & %s' % (target, target_selection),
'%s & %s' % (object_list[i], mobile_selection))
rms = [rmsdict['RMSD'], rmsdict['alignment_length'], 1, 0, 0]
else:
print "only 'align', 'super' and 'cealign' are accepted as methods"
sys.exit(-1)
#rms = cmd.align('%s & %s'%(object_list[i],mobile_selection),'%s & %s'%(target,target_selection),cutoff=cutoff,cycles=cycles,object=objectname)
#else:
#rms = cmd.align('%s & %s'%(object_list[i],mobile_selection),'%s & %s'%(target,target_selection),cutoff=cutoff,cycles=cycles)
#rmsd[object_list[i]] = (rms_ca[0],rms_ca[1],rms_bb[0],rms_bb[1],rms_all[0],rms_all[1])
rmsd_list.append((object_list[i], rms_ca[0], rms_bb[0], rms_all[0]))
cmd.delete(obj_name1)
#print rmsd
rmsd_list.sort(
lambda x, y: cmp(x[2], y[2])
) #compare ca rms you can assign other rms indexes to sort i.e index 2 for bb and index 3 for all atom
# loop over dictionary and print out matrix of final rms values
outfp = outfile
table = False
out = open(outfp + '_score_vs_rmsd.csv', 'w')
out.write('model,score,ca,bb,all,fa_atr,fa_rep,fa_sol,fa_elec\n')
for r in rmsd_list:
for decoy in file_list:
model = open(decoy, 'r')
for line in model:
line_split = line.split()
if line_split[0] == '#BEGIN_POSE_ENERGIES_TABLE':
table = True
continue
if table and line_split[0] == 'pose':
score = float(line_split[-1])
fa_atr = float(line_split[1])
fa_rep = float(line_split[2])
fa_elec = float(line_split[5])
fa_sol = float(line_split[3])
if r[0] == decoy.replace('.pdb', ''):
out.write(
'%s,%6.2f,%6.2f,%6.2f,%6.2f,%6.2f,%6.2f,%6.2f,%6.2f\n'
% (decoy, score, r[1], r[2], r[3], fa_atr, fa_rep,
fa_sol, fa_elec))
print '%s,%6.2f,%6.2f,%6.2f,%6.2f,%6.2f,%6.2f,%6.2f,%6.2f\n' % (
decoy, score, r[1], r[2], r[3], fa_atr, fa_rep,
fa_sol, fa_elec)
out.close()
#generate ensemble figure
protocol = outfp.split('_')[1]
cmd.bg_color(color='white')
cmd.hide("all")
cmd.show("cartoon")
cmd.set("antialias", 1)
cmd.set("ray_trace_mode", 0)
cmd.set("depth_cue", 0)
cmd.set("ray_trace_fog", 0)
cmd.set("stick_radius", 0.1)
cmd.set("cartoon_side_chain_helper", 1)
cmd.set("cartoon_flat_sheets", 1)
# cmd.set("cartoon_transparency",0.8)
cmd.set("ray_shadow", 0)
if protocol == 'loopmodel':
cmd.rotate("x", 70)
cmd.zoom("resi 143-163")
cmd.rotate("z", 20)
cmd.rotate("y", 45)
cmd.move("y", 8)
cmd.move("x", 3)
cmd.save(outfp + 'ensemble.pse')
cmd.delete("all")
elif protocol == 'fixed' or protocol == 'backrub':
util.cbab("chain h")
util.cbac("chain l")
util.cbam("chain g")
cmd.turn("y", -140)
cmd.turn("x", -10)
cmd.turn("z", 10)
cmd.move("y", -5)
cmd.move("z", 30)
cmd.png(outfp + '_ensemble.png', 2400, 2400, dpi=300, ray=1)
cmd.save(outfp + 'ensemble.pse')
cmd.delete("all")
#generate score vs rmsd plot
scorevsrmsd(outfp + '_score_vs_rmsd.csv', name=outfp)
# Distance between hands on each axis
x=lloc[0]-rloc[0]
y=lloc[1]-rloc[1]
z=lloc[2]-rloc[2]
# Degrees to turn horizontally or vertically
hor=degrees(round(atan2(z, x), 2))-acchor
ver=degrees(round(atan2(x, y), 2))-accver
acchor+=hor
accver+=ver
cmd.turn('y', hor)
cmd.turn('z', ver)
# Zoom selection
handist=sqrt(x*x + y*y + z*z)
# print handist
zomh=handist/5-acczom
# print zomh
cmd.move('z', zomh)
acczom+=zomh
# Refresh screen and wait for next iteration
cmd.refresh()
time.sleep(0.05)
# print "x={0}, y={1}, z={2}" .format(x, y, z)