def save_flip_selections():
'''Save the user-selected flips to a new PDB object.'''
o = main.get_object(mpobj.get())
flipkin = self.flipkin_radio.getvalue()
reduce_obj = o.pdb['reduce']
flipkin_obj = o.pdb[flipkin]
userflips_obj = o.pdb['userflips']
# Create a new userflips object even if it already exists in case
# previous selections have been changed.
v = cmd.get_view()
cmd.create(userflips_obj, reduce_obj)
cmd.set_view(v)
for i, v in enumerate(o.views[flipkin]):
# If reduce value and user value are different, copy the
# coordinates from the current flipkin molecule
if v['reduce_chk_val'].get() != v['user_chk_val'].get():
# Do it the hard way, by combining objects. This is plenty
# fast (we typically won't have too many flips to switch)
# and doesn't result in atom name mismatch errors for
# differently protonated HIS residues the way the
# load_coords method does.
flipped_sel = '({} and chain {} and resi {})'.format(
flipkin_obj, v['chain'], v['resi'])
userflips_sel = '({} and not (chain {} and resi {}))'.format(
userflips_obj, v['chain'], v['resi'])
combined_sel = '{} or {}'.format(
userflips_sel, flipped_sel)
v = cmd.get_view()
cmd.create(userflips_obj, combined_sel)
cmd.set_view(v)
msg = 'added flip for {} to {}'.format(flipped_sel,
userflips_obj)
logger.debug(msg)
o.solo_pdb('userflips')
def save_flip_selections():
'''Save the user-selected flips to a new PDB object.'''
o = main.get_object(mpobj.get())
flipkin = self.flipkin_radio.getvalue()
reduce_obj = o.pdb['reduce']
flipkin_obj = o.pdb[flipkin]
userflips_obj = o.pdb['userflips']
# Create a new userflips object even if it already exists in case
# previous selections have been changed.
v = cmd.get_view()
cmd.create(userflips_obj, reduce_obj)
cmd.set_view(v)
for i, v in enumerate(o.views[flipkin]):
# If reduce value and user value are different, copy the
# coordinates from the current flipkin molecule
if v['reduce_chk_val'].get() != v['user_chk_val'].get():
# Do it the hard way, by combining objects. This is plenty
# fast (we typically won't have too many flips to switch)
# and doesn't result in atom name mismatch errors for
# differently protonated HIS residues the way the
# load_coords method does.
flipped_sel = '({} and chain {} and resi {})'.format(
flipkin_obj, v['chain'], v['resi'])
userflips_sel = '({} and not (chain {} and resi {}))'.format(
userflips_obj, v['chain'], v['resi'])
combined_sel = '{} or {}'.format(userflips_sel,
flipped_sel)
v = cmd.get_view()
cmd.create(userflips_obj, combined_sel)
cmd.set_view(v)
msg = 'added flip for {} to {}'.format(
flipped_sel, userflips_obj)
logger.debug(msg)
o.solo_pdb('userflips')
def images_refocus(images, target):
global imagecount
global ray
global filename
global ximage
global yimage
print "... Images %s - %s:" % (imagecount, imagecount + images - 1)
print "Writing %s images zooming to selection:" % images
print " %s" % target
current_view = cmd.get_view() #get the starting view
temporary_view = current_view #make variabe to track interpolation
cmd.zoom(target) #zoom to the target selection
end_view = cmd.get_view() #get the ending view
#get the difference between the start and ending views, divide per step
views_difference = tuple(np.subtract(end_view, temporary_view))
diff_per_image = tuple(i / images for i in views_difference)
for i in range(0, images): #cycle for number of images
#update the interpolating view
temporary_view = tuple(np.add(temporary_view, diff_per_image))
cmd.set_view(temporary_view)
#print image
cmd.png("images/%s_%04d" % (filename, imagecount), ray=ray)
#increment imagecounter
imagecount = imagecount + 1
cmd.refresh()
def testScene(self):
cmd.fragment('ala', 'm1')
cmd.fragment('gly', 'm2')
cmd.create('m2', 'm2', 1, 2)
cmd.create('m2', 'm2', 1, 3)
cmd.create('m2', 'm2', 1, 4)
# store
cmd.show_as('sticks', 'm1')
cmd.show_as('spheres', 'm2')
cmd.color('blue', 'm1')
cmd.color('yellow', 'm2')
view_001 = cmd.get_view()
cmd.scene('new', 'store', 'hello world')
# store
cmd.frame(3)
cmd.show_as('lines')
cmd.color('red')
cmd.turn('x', 45)
view_002 = cmd.get_view()
cmd.scene('new', 'store')
# we actually don't know the auto naming counter
# self.assertEqual(cmd.get_scene_list(), ['001', '002'])
names = cmd.get_scene_list()
# recall
cmd.scene(names[0], 'recall', animate=0)
self.assertArrayEqual(view_001, cmd.get_view(), delta=1e-3)
self.assertEqual(cmd.count_atoms('m1'), cmd.count_atoms('color blue'))
self.assertEqual(cmd.count_atoms('m1'), cmd.count_atoms('rep sticks'))
self.assertEqual(cmd.count_atoms('m2'),
cmd.count_atoms('color yellow'))
self.assertEqual(cmd.count_atoms('m2'), cmd.count_atoms('rep spheres'))
self.assertNotEqual(cmd.get_wizard(), None)
self.assertEqual(cmd.get_state(), 1)
# recall
cmd.scene(names[1], 'recall', animate=0)
self.assertArrayEqual(view_002, cmd.get_view(), delta=1e-3)
self.assertEqual(0, cmd.count_atoms('color blue'))
self.assertEqual(0, cmd.count_atoms('rep sticks'))
self.assertEqual(cmd.count_atoms(), cmd.count_atoms('color red'))
self.assertEqual(cmd.count_atoms(), cmd.count_atoms('rep lines'))
self.assertEqual(cmd.get_wizard(), None)
self.assertEqual(cmd.get_state(), 3)
# with movie (not playing) it must not recall the state
cmd.mset('1-4')
cmd.frame(1)
cmd.scene(names[1], 'recall', animate=0)
self.assertEqual(cmd.get_state(), 1)
# rename and delete
cmd.scene('F2', 'store')
cmd.scene(names[0], 'rename', new_key='F1')
cmd.scene(names[1], 'delete')
self.assertEqual(cmd.get_scene_list(), ['F1', 'F2'])
def testView(self):
cmd.turn('x', 30)
a = cmd.get_view()
cmd.view('A', 'store')
cmd.turn('y', 30)
self.assertNotEqual(a, cmd.get_view())
cmd.view('A', 'recall', animate=0)
self.assertEqual(a, cmd.get_view())
def testView(self):
cmd.turn('x', 30)
a = cmd.get_view()
cmd.view('A', 'store')
cmd.turn('y', 30)
self.assertNotEqual(a, cmd.get_view())
cmd.view('A', 'recall', animate=0)
self.assertEqual(a, cmd.get_view())
def testScene(self):
cmd.fragment('ala', 'm1')
cmd.fragment('gly', 'm2')
cmd.create('m2', 'm2', 1, 2)
cmd.create('m2', 'm2', 1, 3)
cmd.create('m2', 'm2', 1, 4)
# store
cmd.show_as('sticks', 'm1')
cmd.show_as('spheres', 'm2')
cmd.color('blue', 'm1')
cmd.color('yellow', 'm2')
view_001 = cmd.get_view()
cmd.scene('new', 'store', 'hello world')
# store
cmd.frame(3)
cmd.show_as('lines')
cmd.color('red')
cmd.turn('x', 45)
view_002 = cmd.get_view()
cmd.scene('new', 'store')
# we actually don't know the auto naming counter
# self.assertEqual(cmd.get_scene_list(), ['001', '002'])
names = cmd.get_scene_list()
# recall
cmd.scene(names[0], 'recall', animate=0)
self.assertArrayEqual(view_001, cmd.get_view(), delta=1e-3)
self.assertEqual(cmd.count_atoms('m1'), cmd.count_atoms('color blue'))
self.assertEqual(cmd.count_atoms('m1'), cmd.count_atoms('rep sticks'))
self.assertEqual(cmd.count_atoms('m2'), cmd.count_atoms('color yellow'))
self.assertEqual(cmd.count_atoms('m2'), cmd.count_atoms('rep spheres'))
self.assertNotEqual(cmd.get_wizard(), None)
self.assertEqual(cmd.get_state(), 1)
# recall
cmd.scene(names[1], 'recall', animate=0)
self.assertArrayEqual(view_002, cmd.get_view(), delta=1e-3)
self.assertEqual(0, cmd.count_atoms('color blue'))
self.assertEqual(0, cmd.count_atoms('rep sticks'))
self.assertEqual(cmd.count_atoms(), cmd.count_atoms('color red'))
self.assertEqual(cmd.count_atoms(), cmd.count_atoms('rep lines'))
self.assertEqual(cmd.get_wizard(), None)
self.assertEqual(cmd.get_state(), 3)
# with movie (not playing) it must not recall the state
cmd.mset('1-4')
cmd.frame(1)
cmd.scene(names[1], 'recall', animate=0)
self.assertEqual(cmd.get_state(), 1)
# rename and delete
cmd.scene('F2', 'store')
cmd.scene(names[0], 'rename', new_key='F1')
cmd.scene(names[1], 'delete')
self.assertEqual(cmd.get_scene_list(), ['F1', 'F2'])
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 centeractive(self): if self.toggle['view']: cmd.set_view(self.toggle['view']) self.toggle['view'] = None else: self.toggle['view'] = cmd.get_view() cmd.center(self.m.rdes.sel())
def __init__(self, top, queue):
#print "New instance of FlexSC Wizard"
Wizard.__init__(self)
self.top = top
self.queue = queue
self.FlexAID = self.top.top
self.FlexAID.WizardError = False
self.TargetName = self.FlexAID.IOFile.Target
self.TargetFlex = self.top.Vars.TargetFlex
self.ResidueName = '...'
self.PanelResidue = ' Residue: '
# Initial view
self.View = cmd.get_view()
self.State = cmd.get_state()
self.auto_zoom = cmd.get("auto_zoom")
# for Quit_Wizard
self.ErrorCode = 1
self.ErrorStatus = [ "Side-chains shown in white are already set as flexible.",
"Side-chains shown in orange are 'active' and are ready to be added." ]
def check_file(self):
while (self.watch):
if (os.path.exists(self.file_name)):
print "checking..."
mtime = os.path.getmtime(self.file_name)
if (mtime > self.mtime):
self.mtime = mtime
print "Re-loading %s" % self.file_name
time.sleep(2)
cmd.load(self.file_name, state=1)
cmd.reset()
cmd.hide(representation="lines", selection="all")
cmd.show(representation="cartoon", selection="all")
view = cmd.get_view()
camera = list(view)
camera[0] = -1
camera[1] = 0
camera[2] = 0
camera[3] = 0
camera[4] = 0
camera[5] = 1
camera[6] = 0
camera[7] = 1
camera[8] = 0
cmd.set_view(camera)
time.sleep(self.time_wait)
def insert_current():
#insert the current view into the list after the view
#in views[cur_index]
#set frames to default
global cur_index
global cur_view
global views
global frames
global actions
global scenes
global settings
global models
global fades
cur_index += 1
cur_view = cmd.get_view()
views.insert(cur_index, [cv for cv in cur_view])
frames.insert(cur_index, 50)
#deal with actions dictionary
actions = incKeyAbove(actions, cur_index)
scenes = incKeyAbove(scenes, cur_index)
settings = incKeyAbove(settings, cur_index)
models = incKeyAbove(models, cur_index)
fades = incKeyAbove(fades, cur_index)
print "New view:"
print_view(cur_view)
print "Inserted view with index", cur_index, "and a 50 frame transition"
def revert(self):
v = cmd.get_view()
cmd.remove(self.rdes.obj+" and not chain A")
m = cmd.get_model(self.rdes.obj)
n = self.oldcrd
if not n:
cmd.create("tmp12345",self.rnat.sel())
cmd.align("tmp12345",self.rdes.sel())
n = cmd.get_model("tmp12345").atom
cmd.delete("tmp12345")
di,ni = 0,0
while m.atom[di].resi != str(self.rdes.resi): di += 1
dj = di
while m.atom[dj].resi == str(self.rdes.resi): dj += 1
if self.oldcrd: self.oldcrd = None
else: self.oldcrd = m.atom[di:dj]
m.atom = m.atom[:di] + n + m.atom[dj:]
for i in range(di,di+len(n)):
m.atom[i].resi = str(self.rdes.resi)
m.atom[i].chain = str(self.rdes.chain)
cmd.load_model(m,self.rdes.obj,1)
cmd.save("tmp.pdb",self.rdes.obj)
cmd.delete(self.rdes.obj)
cmd.load("tmp.pdb",self.rdes.obj,1)
cmd.show('car',self.rdes.obj)
cmd.show('lines')
redopent(self.rdes.obj)
cmd.set_view(v)
print "revert removing "+"".join(self.aas)+" from aas!"
self.aas = [getaa('A',self.rdes.resi,self.manager.d.obj)]
def showvecfrompoint(a, c, col=(1, 1, 1), lbl=''):
"""TODO: Summary
Args:
a (TYPE): Description
c (TYPE): Description
col (tuple, optional): Description
lbl (str, optional): Description
"""
if not lbl:
global numray
lbl = "ray%i" % numray
numray += 1
cmd.delete(lbl)
v = cmd.get_view()
OBJ = [
cgo.BEGIN, cgo.LINES, cgo.COLOR, col[0], col[1], col[2], cgo.VERTEX,
c[0], c[1], c[2], cgo.VERTEX, c[0] + a[0], c[1] + a[1], c[2] + a[2],
cgo.END
]
cmd.load_cgo(OBJ, lbl)
# cmd.load_cgo([cgo.COLOR, col[0],col[1],col[2],
# cgo.SPHERE, c[0], c[1], c[2], 0.08,
# cgo.CYLINDER, c[0], c[1], c[2],
# c[0] + a[0], c[1] + a[1], c[2] + a[2], 0.02,
# col[0],col[1],col[2],col[0],col[1],col[2],], lbl)
cmd.set_view(v)
def showline(a, c, col=(1, 1, 1), lbl=""):
"""TODO: Summary
Args:
a (TYPE): Description
c (TYPE): Description
col (tuple, optional): Description
lbl (str, optional): Description
"""
if not lbl:
global numline
lbl = "line%i" % numline
numline += 1
cmd.delete(lbl)
v = cmd.get_view()
OBJ = [
cgo.BEGIN,
cgo.LINES,
cgo.COLOR,
col[0],
col[1],
col[2],
cgo.VERTEX,
c[0] - a[0],
c[1] - a[1],
c[2] - a[2],
cgo.VERTEX,
c[0] + a[0],
c[1] + a[1],
c[2] + a[2],
cgo.END,
]
cmd.load_cgo(OBJ, lbl)
cmd.set_view(v)
def orient(self): if self.toggle['view']: cmd.set_view(self.toggle['view']) self.toggle['view'] = None else: self.toggle['view'] = cmd.get_view() cmd.orient(self.d.obj+" or pnt*")
def __init__(self, top, queue, UseOldTypes):
#print "New instance of Wizard SetAtomType"
Wizard.__init__(self)
self.top = top
self.FlexAID = self.top.top
self.queue = queue
# Save view
self.View = cmd.get_view()
self.State = cmd.get_state()
#self.pdbPath = self.FlexAID.SimPath + 'tmp.pdb'
self.pdbPath = self.FlexAID.IOFile.ProcessedLigandPath.get()
self.ErrorCode = 1
self.SelAtomName = '...'
self.SelAtomType = '...'
self.Set_DDL_Colors(UseOldTypes)
smm = []
smm.append([ 2, 'Type Selection', '' ])
for a in self.types:
smm.append([ 1, self.type_name[a], 'cmd.get_wizard().set_AtomType("' + a + '")'])
self.menu['type']=smm
self.atom = list()
self.ID = ''
def mysetview(look, up, pos=None, cen=None, ncp=None, fcp=None):
Xaxis = -look.cross(up).normalized()
Yaxis = projperp(look, up).normalized()
Zaxis = -look.normalized()
oldv = cmd.get_view()
v = list(oldv)
r = Mat(Xaxis, Yaxis, Zaxis)
v[0] = r.xx
v[1] = r.xy
v[2] = r.xz
v[3] = r.yx
v[4] = r.yy
v[5] = r.yz
v[6] = r.zx
v[7] = r.zy
v[8] = r.zz
if pos is not None:
v[9:12] = pos.x, pos.y, pos.z
if cen is not None:
v[12:15] = cen.x, cen.y, cen.z
if ncp is not None:
v[15] = ncp
if fcp is not None:
v[16] = fcp
cmd.set_view(v)
return Yaxis
def __call__(self):
if self.name not in cmd.get_names('objects'):
import threading
threading.Thread(None, cmd.delete, args=(self.cb_name,)).start()
return
v = cmd.get_view()
if v == self.prev_v:
return
self.prev_v = v
t = v[12:15]
if self.corner:
vp = cmd.get_viewport()
R_mc = [v[0:3], v[3:6], v[6:9]]
off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
if self.corner in [2,3]:
off_c[0] *= -1
if self.corner in [3,4]:
off_c[1] *= -1
off_m = cpv.transform(R_mc, off_c)
t = cpv.add(t, off_m)
z = -v[11] / 30.0
m = [z, 0, 0, 0, 0, z, 0, 0, 0, 0, z, 0, t[0] / z, t[1] / z, t[2] / z, 1]
cmd.set_object_ttt(self.name, m)
def get_coord(v):
if not isinstance(v, str):
try:
return v[:3]
except:
return False
if v.startswith('['):
return cmd.safe_list_eval(v)[:3]
try:
if cmd.count_atoms(v) == 1:
# atom coordinates
return cmd.get_atom_coords(v)
else:
# more than one atom --> use "center"
# alt check!
if cmd.count_atoms('(alt *) and not (alt "")') != 0:
print(
"distancetoatom: warning! alternative coordinates found for origin, using center!"
)
view_temp = cmd.get_view()
cmd.zoom(v)
v = cmd.get_position()
cmd.set_view(view_temp)
return v
except:
return False
def __init__(self, top, queue, Sphere, SphereDisplay, SphereSize,
ExtraPrompt):
#print "New instance of flexsphere Wizard"
Wizard.__init__(self)
self.top = top
self.queue = queue
self.App = self.top.top
self.App.WizardError = False
self.App.WizardResult = 0
self.Sphere = Sphere
self.SphereView = self.Sphere.Copy()
self.SphereSize = SphereSize
self.SphereDisplay = SphereDisplay
self.View = cmd.get_view()
self.ErrorCode = 0
self.Prompt = [
"Press Shift + Mouse3 (Wheel Click) to move the sphere.",
"Use the scaler in the " + self.App.Name +
" interface to edit its radius."
]
if ExtraPrompt:
self.Prompt.append(ExtraPrompt)
def make_pov(file, meta=True):
f1, f2 = file, file[:-4] + '.inc'
(header,data) = cmd.get_povray()
povfile = open(f1,'w')
if meta: povfile.write(header)
povview = cmd.get_view()
povfile.write("""\n
// Uncomment the following lines if you have the pymolmacro.inc include file and want to use it.
/*
#include \"pymolmacro.inc\"
PYMOL_VIEW( %10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f )
*/
""" % povview)
povfile.write('#include "%s"\n\n' % f2)
povfile.close()
povfile = open(f2,'w')
povfile.write(data)
povfile.close()
def show_points(points, color = [1.0, 0.0, 0.0], selection='all', name = 'samples', labels=[]):
view = cmd.get_view(quiet=not DEBUG)
# adjust radius to size of bounding box
bb = cmd.get_extent(selection, quiet=not DEBUG)
ll = vec3(bb[0])
tr = vec3(bb[1])
diag = tr - ll
r = diag.length() / 2.0
# origin of rotation in model space
#o = vec3(view[12:15])
c = com.COM(selection)
o = vec3(c)
#spheres = [BEGIN, TRIANGLE_STRIP]
spheres = [COLOR]
spheres.extend(color)
i = 0.0
j = 0
for p in points:
#spheres.extend([COLOR, 1.0, 1 - scaled_value, 1 - scaled_value])
spheres.extend([SPHERE, o[0]+r*p[0], o[1]+r*p[1], o[2]+r*p[2], 1.25])
#drawVector(o, o + r * vec3(p))
#spheres.extend([VERTEX, o[0]+r*p[0], o[1]+r*p[1], o[2]+r*p[2]])
#i += 1.0/len(values)
l = 1.1
if (len(labels) > j):
cmd.pseudoatom(labels[j] + "_label", pos = [o[0]+l * r*p[0], o[1]+l*r*p[1], o[2]+l*r*p[2], 1.25], label = labels[j])
j += 1
#spheres.extend([END])
cmd.load_cgo(spheres, name, 1)
def crisscross(x, y, z, d, name="ref_center"):
obj = [
LINEWIDTH, 3, COLOR,
float(1.05),
float(0.15),
float(1.5), BEGIN, LINE_STRIP, VERTEX,
float(x - d),
float(y),
float(z), VERTEX,
float(x + d),
float(y),
float(z), END, BEGIN, LINE_STRIP, VERTEX,
float(x),
float(y - d),
float(z), VERTEX,
float(x),
float(y + d),
float(z), END, BEGIN, LINE_STRIP, VERTEX,
float(x),
float(y),
float(z - d), VERTEX,
float(x),
float(y),
float(z + d), END
]
if name[0] == 'O':
obj[3:6] = [float(1.00), float(0.80), float(0.80)]
view = cmd.get_view()
cmd.load_cgo(obj, name)
cmd.set_view(view)
def __init__(self, top, queue, ResSeq, LigandPath):
#print "New instance of flexbond Class.\n"
Wizard.__init__(self)
self.top = top
self.queue = queue
self.FlexAID = self.top.top
self.FlexAID.WizardError = False
self.ResSeq = ResSeq
self.dictFlexBonds = self.FlexAID.IOFile.Vars.dictFlexBonds
self.dictNeighbours = self.FlexAID.IOFile.Vars.dictNeighbours
self.RefLigand = LigandPath
self.View = cmd.get_view()
self.State = cmd.get_state()
self.auto_zoom = cmd.get("auto_zoom")
self.pick_count = 0
self.panelForceBond = 'Adv.: Force bond OFF'
self.Force = False
self.point1 = list()
self.point2 = list()
self.atom1 = list()
self.atom2 = list()
self.ErrorStatus = [ "Flexible bonds of the ligand are shown in orange.",
"Selected flexible bonds of the ligand are shown in white." ]
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 __call__(self):
if self.name not in cmd.get_names('objects'):
import threading
threading.Thread(None, cmd.delete, args=(self.cb_name,)).start()
return
v = cmd.get_view()
if v == self.prev_v:
return
self.prev_v = v
t = v[12:15]
if self.corner:
vp = cmd.get_viewport()
R_mc = [v[0:3], v[3:6], v[6:9]]
off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
if self.corner in [2,3]:
off_c[0] *= -1
if self.corner in [3,4]:
off_c[1] *= -1
off_m = cpv.transform(R_mc, off_c)
t = cpv.add(t, off_m)
z = -v[11] / 30.0
m = [z, 0, 0, t[0] / z, 0, z, 0, t[1] / z, 0, 0, z, t[2] / z, 0, 0, 0, 1]
cmd.set_object_ttt(self.name, m, homogenous=1)
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 crisscross(self, x, y, z, d, name="crisscross"):
obj = [
LINEWIDTH, 3, BEGIN, LINE_STRIP, VERTEX,
float(x - d),
float(y),
float(z), VERTEX,
float(x + d),
flaot(y),
float(z), END, BEGIN, LINE_STRIP, VERTEX,
float(x),
float(y - d),
float(z), VERTEX,
float(x),
float(y + d),
float(z), END, BEGIN, LINE_STRIP, VERTEX,
float(x),
float(y),
float(z - d), VERTEX,
float(x),
float(y),
float(z + d), END
]
view = cmd.get_view()
cmd.load_cgo(obj, name)
cmd.set_view(view)
def make_pov(file, meta=True):
f1, f2 = file, file[:-4] + '.inc'
(header, data) = cmd.get_povray()
povfile = open(f1, 'w')
if meta: povfile.write(header)
povview = cmd.get_view()
povfile.write("""\n
// Uncomment the following lines if you have the pymolmacro.inc include file and want to use it.
/*
#include \"pymolmacro.inc\"
PYMOL_VIEW( %10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f )
*/
""" % povview)
povfile.write('#include "%s"\n\n' % f2)
povfile.close()
povfile = open(f2, 'w')
povfile.write(data)
povfile.close()
def storeview(viewname):
"""
Store the current view as a set view command under the given filename
"""
view = cmd.get_view()
of = open(viewname, "w")
oof = open(viewname + "a", "w")
oof.write( ` view ` + "\n")
oof.close()
#also echo to screen
print("set_view (\\")
of.write("set_view (\\\n")
for x in range(0, 6):
for y in range(0, 3):
index = x * 3 + y
print("%15.9f" % view[index]),
of.write("%15.9f" % view[index])
if x == 5 and y == 2:
print(" "),
of.write(" ")
else:
print(","),
of.write(",")
if x < 5:
print("\\")
of.write("\\\n")
else:
print(")")
of.write(")\n")
of.close()
def insert_current():
#insert the current view into the list after the view
#in views[cur_index]
#set frames to default
global cur_index
global cur_view
global views
global frames
global actions
global scenes
global settings
global models
global fades
cur_index += 1
cur_view = cmd.get_view()
views.insert( cur_index, [cv for cv in cur_view] )
frames.insert( cur_index, 50 )
#deal with actions dictionary
actions = incKeyAbove( actions, cur_index )
scenes = incKeyAbove( scenes, cur_index )
settings = incKeyAbove( settings, cur_index )
models = incKeyAbove( models, cur_index )
fades = incKeyAbove( fades, cur_index )
print "New view:"
print_view( cur_view )
print "Inserted view with index", cur_index, "and a 50 frame transition"
def __init__(self, top, queue, Sphere, SphereDisplay, SphereSize, ExtraPrompt):
#print "New instance of flexsphere Wizard"
Wizard.__init__(self)
self.top = top
self.queue = queue
self.App = self.top.top
self.App.WizardError = False
self.App.WizardResult = 0
self.Sphere = Sphere
self.SphereView = self.Sphere.Copy()
self.SphereSize = SphereSize
self.SphereDisplay = SphereDisplay
self.View = cmd.get_view()
self.ErrorCode = 0
self.Prompt = [ "Press Shift + Mouse3 (Wheel Click) to move the sphere.",
"Use the scaler in the " + self.App.Name + " interface to edit its radius." ]
if ExtraPrompt:
self.Prompt.append( ExtraPrompt )
def mkhelix(sel, t, r, n):
v = cmd.get_view()
for i in range(1, n):
cmd.delete("h%i" % i)
cmd.create("h%i" % i, sel)
rot("h%i" % i, Vec(0, 0, 1), i * r, Vec(0, 0, 0))
trans("h%i" % i, Vec(0, 0, i * t))
cmd.set_view(v)
def transform_by_camera_rotation():
view = list(cmd.get_view())
M = view[0:3] + [-view[12]] + \
view[3:6] + [-view[13]] + \
view[6:9] + [-view[14]] + \
view[12:15] + [1.]
cmd.transform_selection('(all)', M, transpose=1)
cmd.set_view([1,0,0,0,1,0,0,0,1] + view[9:])
def mkhelix(sel, t, r, n):
v = cmd.get_view()
for i in range(1, n):
cmd.delete("h%i" % i)
cmd.create("h%i" % i, sel)
rot("h%i" % i, Vec(0, 0, 1), i * r, Vec(0, 0, 0))
trans("h%i" % i, Vec(0, 0, i * t))
cmd.set_view(v)
def mki213(N, sel = 'all'):
v = cmd.get_view()
cmd.delete("i213_*")
cmd.delete('base80345769083457')
cmd.delete('tmp80345769083457')
c2 = com(sel)
c3 = Vec(0, 0, 0)
cmd.create( 'tmp80345769083457', sel)
a2 = c2axis('tmp80345769083457')
cmd.delete( 'tmp80345769083457')
a3 = Vec(0, 0, 1)
cmd.create('base80345769083457', sel+" and chain A and visible")
seenit = []
R2 = [rotation_matrix(a2, 0), rotation_matrix(a2, 180), ]
R3 = [rotation_matrix(a3, 0), rotation_matrix(a3, 120), rotation_matrix(a3, 240), ]
C = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
print a2, c2, a3, c3
for i21 in range(2):
for i32 in range(3 if N > 1 else 1):
for i22 in range(2 if N > 2 else 1):
for i33 in range(3 if N > 3 else 1):
for i23 in range(2 if N > 4 else 1):
for i34 in range(3 if N > 5 else 1):
for i24 in range(2 if N > 6 else 1):
for i35 in range(3 if N > 7 else 1):
for i25 in range(2 if N > 8 else 1):
test = Vec(0, 0, 0)
test = R2[i21]*(test-c2)+c2
test = R3[i32]*(test-c3)+c3
test = R2[i22]*(test-c2)+c2
test = R3[i33]*(test-c3)+c3
test = R2[i23]*(test-c2)+c2
test = R3[i34]*(test-c3)+c3
test = R2[i24]*(test-c2)+c2
test = R3[i35]*(test-c3)+c3
test = R2[i25]*(test-c2)+c2
#print test
seen = False
for xs in seenit:
if (xs-test).length() < 0.1:
seen = True
break
if seen: continue
else: seenit.append(test)
n = "i213_%i%i%i%i%i%i%i%i%i"%(i25, i35, i24, i34, i23, i33, i22, i32, i21)
cmd.create(n, 'base80345769083457 and name n+ca+c')
rot(n, a2, i21*180.0, c2)
rot(n, a3, i32*120.0, c3)
rot(n, a2, i22*180.0, c2)
rot(n, a3, i33*120.0, c3)
rot(n, a2, i23*180.0, c2)
rot(n, a3, i34*120.0, c3)
rot(n, a2, i24*180.0, c2)
rot(n, a3, i35*120.0, c3)
rot(n, a2, i25*180.0, c2)
print len(seenit)
cmd.delete('base80345769083457')
cmd.set_view(v)
def showsphere(c, r=1, col=(1, 1, 1), lbl=''):
v = cmd.get_view()
if not lbl:
global numvec
lbl = "sphere%i" % numvec
numvec += 1
mycgo = cgo_sphere(c=c, r=r, col=col)
cmd.load_cgo(mycgo, lbl)
cmd.set_view(v)
def showcyl(c1, c2, r, col=(1, 1, 1), col2=None, lbl=''):
if not lbl:
global numseg
lbl = "seg%i" % numseg
numseg += 1
cmd.delete(lbl)
v = cmd.get_view()
cmd.load_cgo(cgo_cyl(c1=c1, c2=c2, r=r, col=col, col2=col2), lbl)
cmd.set_view(v)
def get_views(points):
''' computes view matrices from points.
assumes that the current view defines the up vector '''
view = cmd.get_view(quiet=not DEBUG)
rot = get_rotation(view)
cam = rot.getRow(2).normalize()
model_up = rot.getRow(1).normalize()
model_right = rot.getRow(0).normalize()
# temporarily decrease epsilon used for comparisons of vectors in cgit
# to prevent math domain error when computing angles
epsilon = getEpsilon()
setEpsilon(9e-4)
e = []
for point in points:
# find rotation matrix R to the new point
spn = vec3(point).normalize()
q = rotation_to(spn, cam)
R = q.toMat3()
# add rotation to initial rotation
RR = rot * R
# new camera coordinate system aligns
# up vector with model_up vector
# new_cam = vec3(point).normalize()
new_cam = RR.getRow(2).normalize()
lookAt = -new_cam
up = model_right.cross(lookAt).normalize()
#print "up: " + str(up) + "model_up: " + str(model_up)
#print up == model_up
#print up.cross(model_up).length() < 9e-4
if up != model_up:
if up.cross(model_up).length() < 9e-4 or up.angle(model_up) > pi/2:
up = -(model_right).cross(lookAt).normalize()
right = lookAt.cross(up).normalize()
# compute the new view matrix
RRR = mat3()
RRR.setRow(0, right)
RRR.setRow(1, up)
RRR.setRow(2, new_cam)
new_view = []
new_view.extend(RRR.toList())
new_view.extend(view[9:18])
e.append((point, new_view))
setEpsilon(epsilon)
return e
def __call__(self):
# get view on screen
my_view = cmd.get_view()
delta_mv = 0.
for i in range(18):
delta_mv = max(delta_mv,abs(my_view[i] - self.my_view[i]))
self.my_view[i] = my_view[i]
#print my_view
# get orientation/position matrices for two molecules
# how does pymol define rotation center of molecule?
# apparnetly by geometric average
pdbmat1 = cmd.get_object_matrix(self.pdbobj1)
pdbmat2 = cmd.get_object_matrix(self.pdbobj2)
delta_mm = 0.
for i in range(12):
delta_mm = max(delta_mm,abs(pdbmat1[i] - self.objmat1[i]))
delta_mm = max(delta_mm,abs(pdbmat2[i] - self.objmat2[i]))
self.objmat1[i] = pdbmat1[i]
self.objmat2[i] = pdbmat2[i]
if(delta_mm > 0.01): # we only do expensive energy calc if pose changed
do_mm = True
else:
do_mm = False
if((delta_mv > 0.01) or do_mm): # we only update if pose or view changed
cgo_obj = pdb_interaction(pdbmat1,pdbmat2,self.pdb1,self.pdb2,self.gcen1,self.gcen2,
self.energy,do_mm,self.logscale,self.dielectric,self.eps,self.nbest,self.energy_min)
if(self.nbest[0] != self.nbest[1]):
# print('Switching models ',self.nbest)
self.nbest[1] = self.nbest[0]
#
# write new best pose to logfile
#
et = self.energy[0]
ee = self.energy[1]
ev = self.energy[2]
if(self.energy[0] < self.energy_min):
print(' NEW MIN ee: %12.3g ev: %12.3g et: %12.3g model %4d ' % (ee,ev,et,self.nbest[0]))
self.energy_min = et
self.dockeye_log.write('new min: %12.5g %12.5g %12.5g model %4d \n' % (ee,ev,et,self.nbest[0]))
for i in range(4):
for j in range(4):
indx = j + 4*i
self.dockeye_log.write('%12.5f ' % (pdbmat1[indx]))
self.dockeye_log.write('\n')
for i in range(4):
for j in range(4):
indx = j + 4*i
self.dockeye_log.write('%12.5f ' % (pdbmat2[indx]))
self.dockeye_log.write('\n')
#else:
# if(do_mm):
# #print('Current energy: ee: %12.3g ev: %12.3g et: %12.3g' % (ee,ev,et))
# continue
if(do_mm):
cmd.delete('dockeye_obj')
cmd.load_cgo(cgo_obj,'dockeye_obj')
draw_ligand(pdbmat2,self.pdb2,self.gcen2,self.nbest[0])
def display_box(name, max_coords, min_coords):
#
# From the original AutoDock plugin
#
box = [
[max_coords[0], min_coords[0]],
[max_coords[1], min_coords[1]],
[max_coords[2], min_coords[2]],
]
cylinder_size = 0.2
color = [1.0, 1.0, 1.0]
view = cmd.get_view()
obj = []
# box_color
for i in range(2):
for k in range(2):
for j in range(2):
if i != 1:
obj.append(CYLINDER)
obj.extend([box[0][i], box[1][j], box[2][k]])
obj.extend([box[0][i + 1], box[1][j], box[2][k]])
obj.append(cylinder_size)
obj.extend(color)
obj.extend(color)
obj.append(COLOR)
obj.extend(color)
obj.append(SPHERE)
obj.extend([box[0][i], box[1][j], box[2][k], cylinder_size])
if j != 1:
obj.append(CYLINDER)
obj.extend([box[0][i], box[1][j], box[2][k]])
obj.extend([box[0][i], box[1][j + 1], box[2][k]])
obj.append(cylinder_size)
obj.extend(color)
obj.extend(color)
obj.append(COLOR)
obj.extend(color)
obj.append(SPHERE)
obj.extend([box[0][i], box[1][j + 1], box[2][k], cylinder_size])
if k != 1:
obj.append(CYLINDER)
obj.extend([box[0][i], box[1][j], box[2][k]])
obj.extend([box[0][i], box[1][j], box[2][k + 1]])
obj.append(cylinder_size)
obj.extend(color)
obj.extend(color)
obj.append(COLOR)
obj.extend(color)
obj.append(SPHERE)
obj.extend([box[0][i], box[1][j], box[2][k + 1], cylinder_size])
axes = [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]
cmd.load_cgo(obj, name)
cmd.set_view(view)
def dump_rep(name):
if 'PYMOL_GIT_MOD' in os.environ:
import shutil
try:
shutil.copytree(
os.path.join(os.environ['PYMOL_GIT_MOD'], 'pymol2glmol', 'js'),
os.path.join(os.getcwd(), 'js'))
except OSError:
pass
names = cmd.get_session()['names']
cmd.set('pdb_retain_ids', 1)
ret = ''
for obj in names:
if (obj == None):
continue
if (obj[2] == 0): # not visible
continue
if (obj[1] == 0 and obj[4] == 1 and obj[0] == name):
ret += parseObjMol(obj)
if (obj[1] == 0
and obj[4] == 4): # currently all dist objects are exported
ret += parseDistObj(obj)
cmd.turn('z', 180)
view = cmd.get_view()
cmd.turn('z', 180)
cx = -view[12]
cy = -view[13]
cz = -view[14]
cameraZ = -view[11] - 150
fov = float(cmd.get("field_of_view"))
fogStart = float(cmd.get("fog_start"))
slabNear = view[15] + view[11]
slabFar = view[16] + view[11]
ret += "\nview:%.3f,%.3f,%.3f,%.3f,%.3f,%.3f,%.3f,%.3f" % \
(cx, cy, cz, cameraZ, slabNear, slabFar, fogStart, fov)
for i in range(9):
ret += ",%.3f" % view[i]
bgcolor = cmd.get_setting_tuple('bg_rgb')[1]
ret += "\nbgcolor:%02x%02x%02x" % (int(255 * float(bgcolor[0])), \
int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
if 'PYMOL_GIT_MOD' in os.environ:
template = open(os.path.join(os.environ['PYMOL_GIT_MOD'], 'pymol2glmol', 'imported.html')).read().\
replace("###INCLUDE_PDB_FILE_HERE###", cmd.get_pdbstr(name)).\
replace('###INCLUDE_REPRESENTATION_HERE###', ret)
else:
template = open('imported.html').read().\
replace("###INCLUDE_PDB_FILE_HERE###", cmd.get_pdbstr(name)).\
replace('###INCLUDE_REPRESENTATION_HERE###', ret)
f = open(name + '.html', 'w')
f.write(template)
f.close()
def orient_origin(selection):
shift_to_center(selection)
cmd.orient(selection)
cv = list(cmd.get_view(quiet=1))
#cmd.origin(selection, position=origin1)
cmd.transform_selection(selection,
cv[0:3] + [0.0] + cv[3:6] + [0.0] + cv[6:9] +
[0.0] + cv[12:15] + [1.0],
transpose=1)
cmd.reset()
def createAtomObj(self, number):
view = cmd.get_view()
cmd.create(self.indexes_list[number], self.object_prefix + str(number))
cmd.set_view(view)
cmd.set("sphere_scale", '0.3', self.indexes_list[number])
cmd.show_as('spheres', self.indexes_list[number])
if number < 3:
cmd.color("red", self.indexes_list[number])
else:
cmd.color("green", self.indexes_list[number])
def showlineabs(a, c, col=(1, 1, 1), lbl=''):
if not lbl:
global numline
lbl = "line%i" % numline
numline += 1
cmd.delete(lbl)
v = cmd.get_view()
cgo = cgo_lineabs(a, c, col)
cmd.load_cgo(cgo, lbl)
cmd.set_view(v)
def dump_mviews():
'''
DESCRIPTION
Dump the current movie as 'set_view' with 'mview store' commands.
'''
for frame in get_keyframes() or ():
cmd.frame(frame)
print(cmd.get_view(3).strip())
print('mview store, {}'.format(frame))
def get_PCA_views(selection):
old_view = cmd.get_view(quiet=1)
cmd.orient(selection)
view = cmd.get_view(quiet=1)
rot = get_rotation_from_view(view)
# now rot resembles view
pc3 = rot.getRow(2)
pc1 = rot.getRow(0)
pc2 = rot.getRow(1)
preferred1 = rot.getRow(2).normalize()
rot2 = rot.rotate(pi, pc1)
preferred2 = rot2.getRow(2).normalize()
return (preferred1, preferred2)
def probe_object(obj):
'''Run Probe on the "Reduce-d" coordinates of a loaded PyMOL object.
ARGUMENTS
obj (str)
Name of a loaded PyMOL object that has already been passed as an
argument to `reduce_object()` (or `reduce_obj` from the PyMOL
command line).
NOTE
Reduce_object() must be run prior to probe_object() in order to set up
an MPObject instance in the `objects` dictionary. Running
probe_object() on a plain PyMOL object will fail. Also, accordingly,
keep in mind that the coordinates probe_object() uses are those of the
Reduce-modified version. For an object `myobj`, this will typically
be `mp_myobj.myobj_reduce`.
'''
o = get_object(obj)
# Clear previous results
cmd.delete(o.pdb['probe']) # coords
cmd.delete(o.get_kin_cgo_group('probe')) # cgo
# Create the PDB to use with the 'probe' kinemage
if o.pdb['userflips'] in cmd.get_names():
which = 'userflips'
else:
which = 'reduce'
v = cmd.get_view()
cmd.create(o.pdb['probe'], o.pdb[which])
cmd.set_view(v)
pdbstr = o.get_pdbstr('probe')
output = generate_probe_output(pdbstr)
# Fail gracefully if probe call returns no output.
if not output:
msg = 'Failed to generate Probe output for {}.'.format(obj)
logger.error(msg)
return
logger.info("Generated Probe output for '{}'.".format(obj))
# Store list of dots and vectors
o.kin['probe'] = process_probe_output(output)
# Draw dots and vectors
o.draw('probe')
cmd.set_view(v)
def save(self,manual=False,savepse=False): sd = "mutalyze_MANUAL_SAVE/" if manual else savedir if not os.path.exists(sd): os.mkdir(sd) redopent(self.obj) sname = self.getsavename(sd) if savepse: cmd.save(sname+".pse") cmd.save (sname+".pdb",self.obj+" or pnt*") with open(sname+".resfile","w") as o: o.write(self.resfile()+"\n") #print "saved pse, pdb, and resfile with notes" self.remembermm = self.manager.m self.remembermv = cmd.get_view()
def frame_scaler():
previous_frame = None
while True:
frame = (yield)
if previous_frame and frame and frame.scale_probability(previous_frame) > 0.2:
scale_factor = frame.scale_factor(previous_frame)
if scale_factor != 1.0:
view = list(cmd.get_view())
delta_z = math.log(scale_factor) * 100.0
view[11] += delta_z
view[15] -= delta_z
view[16] -= delta_z
cmd.set_view(view)
previous_frame = frame
def insert_scene():
global views
global actions
global settings
global frames
global cur_index
global cur_view
global scenes
global scene_counter
global models
global fades
cur_index += 1
cur_view = cmd.get_view()
views.insert( cur_index, [cv for cv in cur_view] )
frames.insert( cur_index, 50 )
#deal with dictionaries
actions = incKeyAbove( actions, cur_index )
scenes = incKeyAbove( scenes, cur_index )
settings = incKeyAbove( settings, cur_index )
models = incKeyAbove( models, cur_index )
fades = incKeyAbove( fades, cur_index )
#this stuff has to be done after the above
#find a free scene name
i = 1
found = 1
while found == 1:
found = 0
for sname in scenes.values():
print "|"+sname+"|"
if sname == "slerpy_"+str(i):
found = 1
break
if found == 1:
i += 1
else:
break
newname = "slerpy_"+str(i)
scene_counter += 1
cmd.scene( newname, "store" )
scenes[ cur_index ] = newname
actions[ cur_index ] = "scene "+newname
print "New view:"
print_view( cur_view )
print "Inserted view with index", cur_index, "and a 50 frame transition"
print "Added scene",newname
def focus(self):
self.manager.m = self
if self.manager.prevm: cmd.hide('sticks',self.manager.prevm.rdes.sel())
if self.manager.prevm: cmd.color('green',self.manager.prevm.rdes.sel()+" and elem C")
fr = self.rnat.obj+" and name n+ca+c and resi %i-%i"%(self.rnat.resi-10,self.rnat.resi+10)
to = self.rdes.obj+" and name n+ca+c and resi %i-%i"%(self.rdes.resi-10,self.rdes.resi+10)
cmd.align(fr,to)
cmd.show('sticks',self.rdes.sel())
cmd.color('white',self.rdes.sel()+" and elem C")
cmd.center(self.rdes.sel())
v = list(cmd.get_view())
v[11] = -80.0
cmd.set_view(tuple(v))
cmd.clip('slab',50,self.rdes.sel())
def Rotate( angleX, angleY): #if not CheckMaster(controller): # return currtime = time.clock() global lastmovetime #Slowdown code vvv - don't use for right now if ((currtime - lastmovetime) < .01): #print "derp" return view = list(cmd.get_view()) view = rotateView(view, angleX/20, angleY/20, 0) cmd.set_view(view) #DamageGUI() cmd.refresh() lastmovetime = time.clock()
def append_view():
global views
global frames
global cur_index
global cur_view
cur_index = len(views)
cur_view = cmd.get_view()
views.append( [cv for cv in cur_view] )
frames.append( 50 )
print "New view: "
print_view( cur_view )
print "Appended view with index", cur_index, "and a 50 frame transition"
print "The current view is", cur_index
def getnative():
v = cmd.get_view()
nats = []
for obj in cmd.get_object_list():
if len(obj) == 4:
nats.append(obj)
continue
pid = obj[:4]
if pid in nats:
continue
print "fetching native", pid
cmd.fetch(pid)
cmd.remove(pid + " and not chain A")
cmd.remove(pid + " and resn HOH")
cmd.align(pid, obj)
cmd.set_view(v)
def hand_rotator():
previous_frame = None
while True:
hand = (yield)
if previous_frame and hand and hand.rotation_probability(previous_frame) > 0.1:
view = list(cmd.get_view())
matrix = hand.rotation_matrix(previous_frame)
matrix *= Leap.Matrix(Leap.Vector(*view[0:3]),
Leap.Vector(*view[3:6]),
Leap.Vector(*view[6:9]))
view[:9] = matrix.to_array_3x3()
cmd.set_view(view)
if hand:
previous_frame = hand.frame
else:
previous_frame = None
