def mini(total_steps=500,
gradient=0.001,
interval=100,
object='rt',
fix_flag=None,
rest_flag=None,
solvation=None,
finish=None):
global state
if not state:
print " realtime.mini: please run setup first..."
else:
model = state.model
print " realtime.mini: %d atoms total\n" % model.nAtom
try:
while total_steps>0:
total_steps = total_steps - interval
state.minimize(max_iter=interval,
fix_flag=fix_flag,
rest_flag=rest_flag,
solvation=solvation)
cmd.delete(object)
cmd.load_model(state.model,object,1)
cmd.refresh()
if finish!=None:
apply(finish[0],finish[1],finish[2])
except:
cmd.load_model(state.model,'ref')
traceback.print_exc()
print " realtime.mini: complete."
def load():
r = 0
rep = [ "simple", "technical", "ligands", "ligand_sites","ligand_sites_trans","ligand_sites_mesh","pretty", "publication" ]
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
print file
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.orient('pdb')
cur_rep = rep.pop(0)
rep = rep + [cur_rep]
getattr(pymol.preset,cur_rep)('pdb')
cmd.refresh()
# give PyMOL a chance
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
cmd.refresh()
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
while(pymol.run==0):
time.sleep(0.1)
def load():
try:
r = 0
list = glob(ent_dir)
list.sort()
# list = [ "pdb/vq" ]
for dir in list:
sys.__stdout__.write("\n"+dir)
sys.__stdout__.flush()
for file in glob(dir+"/pdb*"):
name = os.path.split(file)[-1]
name = string.split(name,'.')[0]
cmd.disable()
cmd.load(file,name)
cmd.show_as("cartoon",name)
cmd.refresh()
cmd.dss(name)
cmd.refresh()
time.sleep(0.1)
sys.__stdout__.write(".")
sys.__stdout__.flush()
sys.__stdout__.write("("+str(cmd.count_atoms())+")")
sys.__stdout__.flush()
cmd.dss()
cmd.delete('all')
except:
traceback.print_exc()
def Update(self):
try:
# Copy the initial protein (Frame 1) into the working state
cmd.create(self.TargetObj, self.TargetName, 1, self.State)
cmd.refresh()
# Display the last frame
cmd.frame(self.State)
#print "Switched to frame " + str(self.State)
except:
self.CriticalError("Object " + str(self.TargetName) + " no longer exists")
if not self.UpdateLigandAnchorPoint() and not self.UpdateLigandFlexibility():
self.selSideChains = self.UpdateSideChainConformations()
if self.WriteOutLigand() or self.EditView() or \
self.top.UpdateDataList(self.Line, self.TOP, self.top.Reference, self.dictCoord):
self.Delete_Object()
self.Delete_Object()
return
def RefreshDisplay(self):
try:
# Display the atoms spheres
cmd.show('spheres', self.LigDisplay)
cmd.refresh()
cmd.alter(self.LigDisplay,'vdw=0.25')
cmd.rebuild(self.LigDisplay)
cmd.refresh()
util.cbag(self.LigDisplay)
cmd.refresh()
if self.AnchorAtom != -1:
AtomSel = self.LigDisplay + ' & id ' + str(self.AnchorAtom)
cmd.color('white',AtomSel)
cmd.refresh()
cmd.alter(AtomSel ,'vdw=0.30')
cmd.rebuild(AtomSel)
cmd.refresh()
except:
self.ErrorCode = 1
return self.ErrorCode
def simulation():
import traceback
try:
while 1:
for part in particle:
# simplistic Euler intergration
# p = p + v
part[1] = (half_box + part[1] + part[5]) % box_size - half_box
part[2] = (half_box + part[2] + part[6]) % box_size - half_box
part[3] = (half_box + part[3] + part[7]) % box_size - half_box
# v = v + pseudo-gravitational acceleration
factor = max(0.1 * box_size, 0.1 * (part[1] ** 2 + part[2] ** 2 + part[3] ** 2) ** 1.5)
part[5] = part[5] - part[1] / factor
part[6] = part[6] - part[2] / factor
part[7] = part[7] - part[3] / factor
cmd.alter_state(1, "cloud", "(x,y,z) = particle[int(resi)][1:4]", space=globals())
cmd.refresh()
except:
traceback.print_exc()
def DisplaySphere(self):
try:
# Display the Sphere
cmd.delete(self.SphereDisplay)
cmd.refresh()
except:
pass
try:
cmd.pseudoatom(self.SphereDisplay,
pos=self.SphereView.Center,
vdw=self.SphereView.Radius,
state=self.State)
cmd.refresh()
cmd.color('oxygen', self.SphereDisplay)
cmd.refresh()
cmd.hide('everything', self.SphereDisplay)
cmd.refresh()
cmd.show('spheres', self.SphereDisplay)
cmd.refresh()
except:
self.ErrorCode = 1
return self.ErrorCode
def Quit_Wizard(self):
try:
# Delete Sphere object
General_cmd.unmask_Objects(self.exc)
cmd.config_mouse(self.config_mouse)
cmd.delete(self.SphereDisplay)
cmd.refresh()
except:
pass
# Catch error in App
if self.ErrorCode > 0:
self.App.WizardError = True
# Re-enable controls
self.App.ActiveWizard = None
cmd.set_wizard()
cmd.set_view(self.View)
cmd.refresh()
self.queue.put(lambda: self.top.SphereRunning(False))
self.queue.put(lambda: self.top.top.root.deiconify())
self.queue.put(lambda: self.top.top.root.update())
def displayPartition(self):
auto_zoom = cmd.get("auto_zoom")
try:
cmd.delete(self.PartitionDisplay)
cmd.refresh()
except:
pass
try:
cmd.set("auto_zoom", 0)
cmd.load(self.TempPartition, self.PartitionDisplay, format='pdb')
cmd.refresh()
cmd.hide('everything', self.PartitionDisplay)
cmd.refresh()
cmd.show('surface', self.PartitionDisplay)
cmd.refresh()
cmd.color('grey60', self.PartitionDisplay)
cmd.refresh()
General_cmd.Oscillate(self.Cleft.CleftName, 0.0)
except:
self.top.DisplayMessage(" ERROR: An error occured while displaying the partitionned cleft", 1)
cmd.set("auto_zoom", auto_zoom)
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
cmd.set("label_size",-1.0)
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.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 SphereRunning(self, boolRun):
if boolRun:
self.Start_Update()
try:
cmd.delete(self.SphereDisplay)
cmd.refresh()
except:
pass
self.Disable_Frame(self.ResizeSphere,self.lblRadius)
self.ResizeSphere.config(from_=0.5,to=self.Sphere.MaxRadius)
self.SphereSize.set(self.Sphere.Radius)
else:
self.End_Update()
self.Enable_Frame()
if not self.top.WizardError and self.top.WizardResult == 2:
self.dictSpheres[self.SphereID] = self.Sphere.Copy()
self.update_Spheres()
self.Vertex = self.write_Partition()
self.displayPartition()
self.Step2Selection.set('')
def Quit_Wizard(self, rv):
try:
cmd.delete(self.LigDisplay)
cmd.delete(self.AtomDisplay)
cmd.deselect()
if rv != 1:
General.unmask_Objects(self.exc)
cmd.set('mouse_selection_mode', self.selection_mode)
#cmd.config_mouse('three_button_editing', 1)
if rv > 0:
self.FlexAID.WizardError = True
self.FlexAID.ActiveWizard = None
cmd.set_wizard()
cmd.set_view(self.View)
cmd.refresh()
self.top.SATRunning(False)
self.queue.put(lambda: self.top.AnchorRunning(False))
self.queue.put(lambda: self.FlexAID.root.deiconify())
self.queue.put(lambda: self.FlexAID.root.update())
except:
pass
def Quit_Wizard(self):
try:
General_cmd.unmask_Objects(self.exc)
cmd.set('mouse_selection_mode', self.selection_mode)
cmd.delete(self.LigDisplay)
cmd.refresh()
cmd.deselect()
except:
pass
if self.ErrorCode > 0:
self.FlexAID.WizardError = True
self.FlexAID.WizardResult = self.AnchorAtom
self.FlexAID.ActiveWizard = None
self.queue.put(lambda: self.top.AnchorRunning(False))
self.queue.put(lambda: self.FlexAID.root.deiconify())
self.queue.put(lambda: self.FlexAID.root.update())
cmd.set_wizard()
cmd.set_view(self.View)
cmd.refresh()
def Btn_Anchor_Clicked(self):
if self.LigandPath.get():
self.AnchorRunning(True)
self.top.ActiveWizard = Anchor.anchor(self, self.queue, self.LigandPath.get(), self.Anchor.get())
cmd.set_wizard(self.top.ActiveWizard)
cmd.refresh()
self.top.ActiveWizard.Start()
def update(self, configuration=None):
try:
cmd.set("suspend_updates","1")
self._setCoordinates(configuration)
cmd.load_model(self.model, self.name, 1)
except:
cmd.set("suspend_updates","0")
traceback.print_exc()
cmd.set("suspend_updates","0")
cmd.refresh()
def wait_for(name, state=0, quiet=1):
'''
DESCRIPTION
Wait for "name" to be available as selectable object.
'''
if cmd.count_atoms('?' + name, 1, state) == 0:
s = cmd.get_setting_boolean('suspend_updates')
if s: cmd.set('suspend_updates', 0)
cmd.refresh()
if s: cmd.set('suspend_updates')
def Delete_Object(self):
try:
# delete temporary protein PDB file
cmd.delete(self.TargetObj)
cmd.refresh()
cmd.delete(self.LigandObj)
cmd.refresh()
except:
self.CriticalError("Object " + str(self.TargetObj) + " no longer exists")
def AddEditDel_Constraint(self):
if not self.PyMOL:
return
self.ConsRunning(True)
self.top.ActiveWizard = Constraint.constraint(self, self.queue)
cmd.set_wizard(self.top.ActiveWizard)
cmd.refresh()
self.top.ActiveWizard.Start()
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 Btn_DownloadPDB_Clicked(self):
PdbCode = self.FetchPDB.get()
try:
if self.PyMOL:
cmd.fetch(PdbCode, **{'async': 0})
cmd.refresh()
except:
self.DisplayMessage(' You entered an invalid PDB code.', 1)
self.FetchPDB.set('')
def ResizeSphere(self):
self.SphereView.Set_Radius(self.SphereSize.get())
try:
cmd.alter(self.SphereDisplay,'vdw=' + str(self.SphereView.Radius))
cmd.rebuild(self.SphereDisplay)
cmd.refresh()
except:
self.queue.put(lambda: self.App.DisplayMessage(" ERROR: Could not resize the Sphere", 1))
self.queue.put(lambda: self.App.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
def Btn_SaveObject_Clicked(self, objtype):
# Get the Drop Down List Selection Name
ddlSelection = self.defaultOption.get()
state = cmd.get_state()
self.Set_Object_Variables(objtype)
if ddlSelection == '' or self.Validate_ObjectSelection(ddlSelection, objtype, state):
return
Path = tkFileDialog.asksaveasfilename(filetypes=[('PDB File','*.pdb')],
initialdir=self.savepath, title='Save the PDB File',
initialfile=ddlSelection, defaultextension='.pdb')
if len(Path) > 0:
Path = os.path.normpath(Path)
if General.validate_String(Path, '.pdb', True, False, True):
self.DisplayMessage(" ERROR: Could not save the file because you entered an invalid name.", 2)
return
if self.top.ValidateSaveProject(Path, objtype):
self.DisplayMessage(" ERROR: The file can only be saved at its default location", 2)
return
try:
cmd.save(Path, ddlSelection, state)
Name = os.path.basename(os.path.splitext(Path)[0])
cmd.load(Path, Name, state=1)
cmd.refresh()
if ddlSelection != Name:
# as if the object was renamed, delete the object
cmd.delete(ddlSelection)
except:
self.DisplayMessage(" ERROR: An error occured while saving the object.", 1)
return
self.VarPath.set(os.path.normpath(Path))
self.VarName.set(Name)
self.VarProc.set('')
self.top.SaveSessionFile = ''
#self.VarMD5.set(General.hashfile(self.VarPath.get()))
if objtype == 'Ligand':
self.Reset_Ligand()
self.DisplayMessage(' Successfully saved and loaded the object: ' + self.VarName.get() + "'", 0)
def SmilesRunning(self, boolRun, Convert):
if boolRun:
self.Disable_Frame()
else:
# When a user inputs a SMILES string, need to first write to a .smi file
self.Enable_Frame()
if Convert and self.SmilesString.get():
Filebase = self.SmilesLigand
if self.SmilesName.get():
Filebase = self.SmilesName.get()
if not self.Write_Smiles(Filebase) and not self.Convert_Smiles() and \
not self.Move_TempLigand(Filebase):
LigandFile = os.path.join(self.top.FlexAIDTempProject_Dir, Filebase + '.mol2')
try:
cmd.delete(Filebase)
cmd.refresh()
except:
pass
self.LigandPath.set(LigandFile)
if not self.Load_ProcConvLigand(LigandFile, Filebase, True) and \
not self.Validate_ObjectSelection(Filebase, 'Ligand', 1):
self.LigandName.set(Filebase)
self.Reset_Ligand()
if self.ForceSaveObject(LigandFile, Filebase, 'Ligand'):
self.LigandPath.set('')
self.LigandName.set('')
#self.ProcessOnly = True
else:
self.LigandPath.set('')
self.LigandName.set('')
else:
self.LigandPath.set('')
self.LigandName.set('')
self.ProcessedLigandPath.set('')
self.ProcessedLigandINPPath.set('')
self.ProcessedLigandICPath.set('')
self.top.ChildWindow = None
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 Btn_AddRemove_FlexBonds(self):
if not self.PyMOL:
return
self.FlexStatus.set('')
self.FlexBondsRunning(True)
self.top.ActiveWizard = FlexBonds.flexbond(self, self.queue, self.top.IOFile.ResSeq.get(),self.top.IOFile.ProcessedLigandPath.get())
cmd.set_wizard(self.top.ActiveWizard)
cmd.refresh()
self.top.ActiveWizard.Start()
def Btn_Edit_AtomTypes(self):
if not self.PyMOL:
return
self.SATStatus.set('')
self.SATRunning(True)
self.top.ActiveWizard = AtomTypes.setType(self, self.queue, self.top.IOFile.OldTypes.get())
cmd.set_wizard(self.top.ActiveWizard)
cmd.refresh()
self.top.ActiveWizard.Start()
def Btn_LoadObject_Clicked(self, objtype):
self.Set_Object_Variables(objtype)
SupportedFormats = self.Get_SupportedFormats(objtype)
Path = tkFileDialog.askopenfilename(filetypes=SupportedFormats,
initialdir=self.savepath, title='Select a file to Load')
# Path = self.top.root.master.splitlist(Path)
if len(Path) > 0:
Path = os.path.normpath(Path)
if General.validate_String(Path, '', True, False, True):
self.DisplayMessage(" ERROR: Could not load the file because it has an invalid name.", 2)
return
if Path == self.VarPath.get():
self.DisplayMessage(" Loading skipped. File is the same as the one already loaded.", 2)
return
try:
Name = os.path.basename(os.path.splitext(Path)[0])
cmd.load(Path, Name, state=1)
cmd.refresh()
if self.Validate_ObjectSelection(Name, objtype, 1):
return
except:
self.DisplayMessage(" ERROR: An error occured while loading the file.", 1)
return
self.VarPath.set(Path)
self.VarName.set(Name)
self.VarProc.set('')
self.top.SaveSessionFile = ''
if objtype == 'Ligand':
self.Reset_Ligand()
if self.ForceSaveObject(Path,Name,objtype):
self.VarPath.set('')
self.VarName.set('')
#self.VarMD5.set(General.hashfile(self.VarPath.get()))
self.DisplayMessage(" Successfully loaded the object: '" + self.VarName.get() + "'", 0)
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 Step2_Prev(self):
if self.top.ActiveWizard is None:
self.activate_Step(1)
self.highlight_Step(1)
self.Step = 1
cmd.delete(self.PartitionDisplay)
cmd.refresh()
cmd.delete(self.SphereDisplay)
cmd.refresh()
else:
self.top.DisplayMessage("Could not execute task: A Wizard is active")
def load():
cmd.set("valence")
cmd.unset("auto_zoom")
cmd.zoom("center",100)
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.refresh()
except:
traceback.print_exc()
def edot1(event):
delcrea()
try:
cmd.isodot('map1', 'map', contour1.get(), 'sele')
except:
try:
cmd.set("suspend_updates", 1, quiet=1)
cmd.remove("hydro")
cmd.enable('all')
cmd.map_new('map', "gaussian", "0.75", 'all')
cmd.isodot("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates", 0, quiet=1)
cmd.refresh()
cmd.isodot('map1', 'map', contour1.get(), 'sele')
cmd.get_names('all')
except:
cmd.orient('all')
showinfo(
"Error", 'No PDB is present\nOr there is no selection ('
"sele"
')')
interior.mainloop()
def Step2_Add(self):
if self.top.ActiveWizard is None:
self.SphereID = self.Get_SphereID()
self.Sphere = SphereObj.SphereObj(self.Width / 1.5, self.Width,
self.Center)
self.SphereRunning(True)
self.top.ActiveWizard = Sphere.Sphere(
self, self.queue, self.Sphere, self.SphereID, self.SphereSize,
"The grayed volume of the cleft is the volume that will be conserved."
)
cmd.set_wizard(self.top.ActiveWizard)
cmd.refresh()
self.top.ActiveWizard.Start()
else:
self.top.DisplayMessage(
"Could not execute task: A Wizard is active")
def Modify_Display(self, var, display):
if var.get():
try:
cmd.show(display, 'TOP_*__ & ! resn LIG')
cmd.refresh()
#cmd.show(display, 'RESULT_*__ & ! resn LIG')
#cmd.refresh()
except:
pass
else:
try:
cmd.hide(display, 'TOP_*__ & ! resn LIG')
cmd.refresh()
#cmd.hide(display, 'RESULT_*__ & ! resn LIG')
#cmd.refresh()
except:
pass
def color_shift(start="Apo2",end="cterm2",divide=100):
stored.start_colors=[]
cmd.iterate("%s and name ca and chain A" % start,"stored.start_colors.append(color)")
stored.end_colors=[]
cmd.iterate("%s and name ca and chain A" % end,"stored.end_colors.append(color)")
print stored.start_colors[0],stored.end_colors[0]
print cmd.get_color_tuple(stored.start_colors[0]),cmd.get_color_tuple(stored.end_colors[0])
start_color_indice=cmd.get_color_tuple(stored.start_colors[0])
end_color_indice=cmd.get_color_tuple(stored.end_colors[0])
print "start ,end"
print start_color_indice,end_color_indice
print np.array(end_color_indice)-np.array(start_color_indice)
#print (np.array(end_color_indice)-np.array(start_color_indice))/float(divide)
graduate_color_indice=(np.array(end_color_indice)-np.array(start_color_indice))/float(divide)
i=1
while i<divide:
i+=1
#print list(np.array(start_color_indice)+graduate_color_indice*i)
time.sleep(0.1)
cmd.refresh()
cmd.recolor()
cmd.set_color("temp%s" %i,list(np.array(start_color_indice)+graduate_color_indice*i))
cmd.color("temp%s" % i,"%s and name ca and chain A" % start)
def Load_Clefts(self):
auto_zoom = cmd.get("auto_zoom")
cmd.set("auto_zoom", 0)
# for Cleft in self.TempBindingSite.listClefts:
for CleftName in self.TempBindingSite.Get_SortedCleftNames():
Cleft = self.TempBindingSite.Get_CleftName(CleftName)
try:
cmd.load(Cleft.CleftFile, Cleft.CleftName, state=1)
cmd.refresh()
if Cleft.Partition and Cleft.PartitionParent != None and \
General_cmd.object_Exists(Cleft.PartitionParent.CleftName):
General_cmd.Oscillate(Cleft.PartitionParent.CleftName, 0.0)
except:
self.top.DisplayMessage(
" ERROR: Failed to load cleft object '" +
Cleft.CleftName + "'", 2)
continue
cmd.set("auto_zoom", auto_zoom)
def highlight_FlexibleSC(self, selString):
Error = 0
try:
cmd.delete(self.FlexSCDisplay)
cmd.refresh()
except:
pass
try:
cmd.set("auto_zoom", 0)
# Create new object from selection
cmd.create(self.FlexSCDisplay, selString, target_state=self.State)
cmd.refresh()
# Visual appearance
cmd.hide('lines', self.FlexSCDisplay)
cmd.refresh()
cmd.show('sticks', self.FlexSCDisplay)
cmd.refresh()
cmd.color('white', self.FlexSCDisplay)
cmd.refresh()
cmd.label(self.FlexSCDisplay + " & name CA", "resn+resi")
cmd.mask(self.FlexSCDisplay)
except:
Error = 1
cmd.set("auto_zoom", self.auto_zoom)
return Error
def do_key(self, k, x, y, m):
if k in [8, 127]:
self.new_name = self.new_name[:-1]
elif k == 27:
cmd.set_wizard()
cmd.refresh()
elif k == 32:
self.new_name = self.new_name + "_"
elif k > 32:
self.new_name = self.new_name + chr(k)
elif k == 10 or k == 13:
self.new_name = string.strip(self.new_name)
if self.mode == 'object':
cmd.do("set_name %s,%s" % (self.old_name, self.new_name),
log=0)
elif self.mode == 'scene':
cmd.do("scene %s,rename,new_key=%s" %
(self.old_name, self.new_name),
log=0)
cmd.set_wizard()
cmd.refresh()
return 1
cmd.refresh_wizard()
return 1
def is_ATOM(Residue, Prot):
resn = Residue[0:3]
resi = Residue[3:len(Residue) - 1]
try:
cmd.select("rtmp1__",
"resi " + resi + " & resn " + resn + " & " + Prot)
cmd.select(
"rtmp2__", "resi " + resi + " & resn " + resn + " & " + Prot +
" & not hetatm")
if cmd.count_atoms("rtmp1__") == cmd.count_atoms("rtmp2__"):
cmd.delete("rtmp*__")
cmd.refresh()
return 1
cmd.delete("rtmp*__")
cmd.refresh()
except:
return -1
return 0
def Step2_Edit(self):
if self.top.ActiveWizard is None and self.Sphere is not None:
if not self.dictSpheres.get(self.Step2Selection.get()):
return
self.SphereID = self.Step2Selection.get()
self.SphereRunning(True)
self.top.ActiveWizard = Sphere.Sphere(
self, self.queue, self.Sphere, self.Step2Selection.get(),
self.SphereSize,
"The grayed volume of the cleft is the volume that will be conserved."
)
cmd.set_wizard(self.top.ActiveWizard)
cmd.refresh()
self.top.ActiveWizard.Start()
else:
self.top.DisplayMessage(
"Could not execute task: A Wizard is active")
def images_morph(images):
global imagecount
global ray
global filename
global ximage
global yimage
print "... Images %s - %s:" % (imagecount, imagecount + images - 1)
print "Writing %s images morphing froms state %s to state %s" % \
(images, 1, images)
#cycle over images
for i in range(0, images):
#change state
cmd.set("state", i + 1)
#print image
cmd.png("images/%s_%04d" % (filename, imagecount), ray=ray)
#increment imagecounter
imagecount = imagecount + 1
cmd.refresh()
def roving_density():
delcrea()
try:
cmd.set("suspend_updates", 1, quiet=1)
cmd.remove("hydro")
cmd.disable()
cmd.enable('all')
cmd.map_new('map', "gaussian", "0.75", 'all')
cmd.set('roving_isomesh', rovingradius1.get())
cmd.set("roving_detail", 1)
cmd.set("stick_radius", 0.5)
cmd.set("roving_sticks", 0)
cmd.set('roving_lines', rovingradius1.get())
cmd.set("roving_polar_contacts", 0)
cmd.set("line_width", "3")
cmd.set("roving_map1_name", 'map')
cmd.isomesh("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates", 0, quiet=1)
cmd.refresh()
cmd.delete('rov_s1')
cmd.set('roving_isosurface', 0)
except:
showinfo("Error", 'No PDB is present')
interior.mainloop()
def dyna(steps, iter=1):
global state
if not state:
print(" realtime.dyna: please run setup first.")
else:
state.echo = 0
model = state.model
print(" realtime.dyna: %d atoms total\n" % model.nAtom)
xtra_kw = []
xtra_kw.extend(keyword.get_inactive(model, 3))
xtra_kw.extend(keyword.get_restrain_positions(model, 2, 0, 10))
xtra_kw.extend(keyword.get_restrain_positions(model, 5, 0.5, 1))
xtra_kw.extend(keyword.get_inactive(model, 6))
state.keywords['chg-cutoff'] = 10.0
state.keywords['vdw-cutoff'] = 7.00
state.keywords['lights'] = ''
state.keywords['restrainterm'] = ''
for x in range(0, iter):
state.dynamics(steps=steps, timestep=1, kw=xtra_kw)
if not len(state.summary):
break
for a in state.summary:
print(a)
cmd.load_model(model, 'dyna')
cmd.ending()
cmd.refresh()
io.pkl.toFile("realtime.pkl")
print(" realtime.dyna: terminated after %d steps." % state.counter)
def roving(self, cleanup=0):
if not cleanup:
cmd.load("$PYMOL_DATA/demo/il2.pdb")
cmd.remove("hydro")
cmd.disable()
cmd.enable("il2")
cmd.set("ribbon_color", "blue", "il2")
cmd.set("roving_detail", 1)
cmd.set("roving_origin", 1)
cmd.set("stick_radius", 0.12, "il2")
# cmd.zoom("/il2///16/O")
# cmd.zoom("center",12)
cmd.set_view ((\
0.132852688, -0.729740858, 0.670686543,\
-0.228543565, 0.635894477, 0.737154961,\
-0.964425683, -0.251212329, -0.082298420,\
0.000062190, 0.000183226, -58.861488342,\
13.349151611, -1.565427899, 22.383148193,\
55.259441376, 63.259449005, 0.000000000 ))
else:
cmd.delete("il2")
cmd.set("roving_detail", 0)
cmd.refresh()
cmd.delete("rov_*")
def images_slide(images, distance, 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 per image" % \
(images, axis, distance/images)
#cycle for number of images
for i in range(0, images):
# transformations
cmd.move(axis, distance / images)
#print image
cmd.png("images/%s_%04d" % (filename, imagecount), ray=ray)
#increment imagecounter
imagecount = imagecount + 1
cmd.refresh()
def run(self):
print("FlexAID parsing thread has begun.")
# Set the auto_zoom to off
cmd.set("auto_zoom", 0)
cmd.delete("TOP_*__")
cmd.delete("RESULT_*")
cmd.refresh()
cmd.frame(1)
self.queue.put(lambda: self.top.InitStatus())
self.queue.put(lambda: self.top.progressBarHandler(0, self.NbTotalGen))
# send ready to simulate signal
print(' Signal sent to start simulation')
self.FlexAID.ParseState = 0
print(' Waiting for FlexAID to start')
# wait for FlexAID to start, to crash or to finish (if simulation is very short and quickly done)
while self.FlexAID.SimulateState < 0:
time.sleep(self.top.INTERVAL)
print(' Parsing the logfile of FlexAID')
while self.FlexAID.Run is not None: # and self.FlexAID.Run.poll() is None:
time.sleep(self.top.INTERVAL)
if self.ParseLines():
break
if not self.FlexAID.ParseState > 0:
self.ParseLines()
# Put back the auto_zoom to on
cmd.set("auto_zoom", self.auto_zoom)
# error in simulation or parsing?
if self.FlexAID.SimulateState > 0 or self.FlexAID.ParseState > 0:
self.queue.put(lambda: self.top.ErrorStatus(self.ErrorMsg))
else:
self.queue.put(lambda: self.top.SuccessStatus())
if self.top.Results:
cmd.enable("RESULT_*")
cmd.refresh()
cmd.disable("TOP_*__")
cmd.refresh()
cmd.frame(1)
self.FlexAID.ParseState = 10
print("FlexAID parsing thread has ended.")
def Oscillate(sel, interval):
# Determine if selection is enabled/disabled
Visible = 0
if cmd.count_atoms('v. & ' + sel) > 0:
Visible = 1
if Visible:
cmd.disable(sel)
cmd.refresh()
time.sleep(interval)
cmd.enable(sel)
cmd.refresh()
time.sleep(interval)
else:
cmd.enable(sel)
cmd.refresh()
time.sleep(interval)
cmd.disable(sel)
cmd.refresh()
time.sleep(interval)
def displaySphere(self):
try:
cmd.delete(self.SphereDisplay)
cmd.refresh()
except:
pass
if self.Sphere != None:
# Only display sphere in current state
cmd.pseudoatom(self.SphereDisplay, pos=self.Sphere.Center, vdw=self.Sphere.Radius,
color='purpleblue', state=cmd.get_state())
cmd.refresh()
cmd.hide('nonbonded',self.SphereDisplay)
cmd.refresh()
cmd.show('spheres', self.SphereDisplay)
cmd.refresh()
cmd.set('sphere_transparency', 0.7, self.SphereDisplay)
cmd.rebuild(self.SphereDisplay)
def highlight_Atom(self, atom):
try:
cmd.pseudoatom(self.AtomDisplay, pos=atom[5:], vdw=0.30, color='white')
cmd.refresh()
cmd.hide('nonbonded', self.AtomDisplay)
cmd.refresh()
cmd.show('spheres', self.AtomDisplay)
cmd.refresh()
cmd.mask(self.AtomDisplay)
except:
self.queue.put(lambda: self.top.DisplayMessage(" ERROR: Failed to highlight atom upon selecting atom", 1))
return
def DisplayLigand(self):
try:
cmd.set("auto_zoom", 0)
cmd.load(self.LigandPath, self.LigDisplay, state=self.State)
cmd.refresh()
cmd.translate(self.Translation, self.LigDisplay)
cmd.refresh()
cmd.zoom(self.LigDisplay)
cmd.refresh()
except:
self.ErrorCode = 1
cmd.set("auto_zoom", self.auto_zoom)
return self.ErrorCode
def Nice_Display(self, Result, ResultName):
cmd.hide('everything', ResultName)
cmd.refresh()
cmd.show('cartoon', ResultName)
cmd.refresh()
for opt in Result.Optimizable:
if opt.rnc[:3] == 'LIG':
cmd.show('lines', 'byres(resn LIG around 5.0) & ' + ResultName)
res = opt.rnc[:3].replace('-', '')
num = opt.rnc[3:len(opt.rnc) - 1].replace('-', '')
chn = opt.rnc[-1:].replace('-', '')
sele = 'resn ' + res + ' & resi ' + num + ' & chain \'' + chn + '\' & ' + ResultName
cmd.show('sticks', sele)
cmd.color('white', sele)
util.cnc(ResultName)
cmd.refresh()
def Quit_Wizard(self):
try:
#Delete the Residue objects
cmd.delete(self.FlexSCDisplay)
cmd.refresh()
cmd.delete(self.ResidueDisplay)
cmd.refresh()
#cmd.delete(self.BackboneDisplay)
#cmd.refresh()
except:
pass
if self.ErrorCode != 1:
General_cmd.unmask_Objects(self.exc)
cmd.set('mouse_selection_mode', self.selection_mode)
#cmd.config_mouse('three_button_editing', 1)
if self.ErrorCode > 0:
self.FlexAID.WizardError = True
self.FlexAID.WizardResult = self.TargetFlex.Count_SideChain()
self.queue.put(lambda: self.top.FlexSCRunning(False))
self.FlexAID.ActiveWizard = None
self.queue.put(lambda: self.FlexAID.root.deiconify())
self.queue.put(lambda: self.FlexAID.root.update())
cmd.set_wizard()
cmd.set_view(self.View)
cmd.refresh()
def Show_Clefts(self):
i = 0
for CleftName in self.TempBindingSite.Get_SortedCleftNames():
Cleft = self.TempBindingSite.Get_CleftName(CleftName)
try:
cmd.hide('everything', Cleft.CleftName)
cmd.refresh()
cmd.color(self.ColorList[i], Cleft.CleftName)
cmd.refresh()
cmd.show('surface', Cleft.CleftName)
cmd.refresh()
Cleft.Color = self.ColorHex[i]
i += 1
except:
self.DisplayMessage(
" ERROR: Could not display cleft object '" +
Cleft.CleftName + "'", 2)
continue
def ColorByDisplacementAll(objSel1, objSel2, super1='all', super2='all', doColor="True", doAlign="True", AlignedWhite='yes'):
# First create backup copies; names starting with __ (underscores) are normally hidden by PyMOL
tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
if strTrue(doAlign):
# Create temp objects
cmd.create(tObj1, objSel1)
cmd.create(tObj2, objSel2)
# Align and make create an object aln which indicates which atoms were paired between the two structures
# Super is must faster than align http://www.pymolwiki.org/index.php/Super
cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln)
# Modify the original matrix of object1 from the alignment
cmd.matrix_copy(tObj1, objSel1)
else:
# Create temp objects
cmd.create(tObj1, objSel1)
cmd.create(tObj2, objSel2)
# Align and make create an object aln which indicates which atoms were paired between the two structures
# Super is must faster than align http://www.pymolwiki.org/index.php/Super
cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln)
# Modify the B-factor columns of the original objects,
# in order to identify the residues NOT used for alignment, later on
cmd.alter(objSel1 + " or " + objSel2, "b=-0.2")
cmd.alter(tObj1 + " or " + tObj2, "chain='A'")
cmd.alter(tObj1 + " or " + tObj2, "segi='A'")
# Update pymol internal representations; one of these should do the trick
cmd.refresh()
cmd.rebuild()
cmd.sort(tObj1)
cmd.sort(tObj2)
# Create lists for storage
stored.alnAres, stored.alnBres = [], []
# Iterate over objects and get resi
if AlignedWhite == 'yes':
cmd.iterate(tObj1 + " and not " + aln, "stored.alnAres.append((resi, name))")
cmd.iterate(tObj2 + " and not " + aln, "stored.alnBres.append((resi, name))")
else:
cmd.iterate(tObj1, "stored.alnAres.append((resi, name))")
cmd.iterate(tObj2, "stored.alnBres.append((resi, name))")
# Change the B-factors for EACH object
displacementUpdateBAll(tObj1, stored.alnAres, tObj2, stored.alnBres)
# Store the NEW B-factors
stored.alnAnb, stored.alnBnb = [], []
# Iterate over objects and get b
if AlignedWhite == 'yes':
# Iterate over objects which is not aligned
cmd.iterate(tObj1 + " and not " + aln, "stored.alnAnb.append(b)")
cmd.iterate(tObj2 + " and not " + aln, "stored.alnBnb.append(b)")
else:
# Or Iterate over all objects with CA
cmd.iterate(tObj1, "stored.alnAnb.append(b)")
cmd.iterate(tObj2, "stored.alnBnb.append(b)")
# Get rid of all intermediate objects and clean up
cmd.delete(tObj1)
cmd.delete(tObj2)
cmd.delete(aln)
# Assign the just stored NEW B-factors to the original objects
print "Sooon ready. 1 more minute"
for x in range(len(stored.alnAres)):
cmd.alter(objSel1 + " and resi " + str(stored.alnAres[x][0]) + " and name " + str(stored.alnAres[x][1]), "b = " + str(stored.alnAnb[x]))
for x in range(len(stored.alnBres)):
cmd.alter(objSel2 + " and resi " + str(stored.alnBres[x][0]) + " and name " + str(stored.alnBres[x][1]), "b = " + str(stored.alnBnb[x]))
cmd.rebuild()
cmd.refresh()
cmd.sort(objSel1)
cmd.sort(objSel2)
# Provide some useful information
stored.allRMSDval = []
stored.allRMSDval = stored.alnAnb + stored.alnBnb
print "\nColorByDisplacementAll completed successfully."
print "The MAXIMUM Displacement is: " + str(max(stored.allRMSDval)) + " residue " + str(stored.alnAres[int(stored.allRMSDval.index(max(stored.allRMSDval)))])
if strTrue(doColor):
# Showcase what we did
# cmd.orient()
# cmd.hide("all")
cmd.show("sticks", objSel1 + " or " + objSel2)
# Select the residues not used for alignment; they still have their B-factors as "-0.2"
cmd.select("notUsedForAln", "b = -0.2")
# White-wash the residues not used for alignment
cmd.color("white", "notUsedForAln")
# Select the residues not in both pdb files; they have their B-factors as "-0.01"
cmd.select("ResNotInBothPDB", "b = -0.01")
# White-wash the residues not used for alignment
cmd.color("black", "ResNotInBothPDB")
# Color the residues used for alignment according to their B-factors (Displacement values)
#cmd.spectrum("b", 'rainbow', "((" + objSel1 + ") or (" + objSel2 +" )) and not notUsedForAln+ResNotInBothPDB")
cmd.spectrum("b", 'rainbow', "((" + objSel1 + ") or (" + objSel2 + " )) and not (notUsedForAln or ResNotInBothPDB)")
# Delete the selection of atoms not used for alignment
# If you would like to keep this selection intact,
# just comment "cmd.delete" line and
# uncomment the "cmd.disable" line abowe.
cmd.disable("notUsedForAln")
cmd.delete("notUsedForAln")
cmd.disable("ResNotInBothPDB")
cmd.delete("ResNotInBothPDB")
print "\nObjects are now colored by C-alpha displacement deviation."
print "Blue is minimum and red is maximum..."
print "White is those residues used in the alignment algorithm. Can be turned off in top of algorithm."
print "Black is residues that does not exist in both files..."
def volume_esp(name,
map,
stops=[0.1, 1.0],
neg='red',
pos='blue',
opacity=0.2,
quiet=1):
'''
DESCRIPTION
Create a volume object from a map object with default coloring
for electrostatic potential (similar to positive and negative
isosurface).
ARGUMENTS
name = string: name for the new volume object
map = string: name of the map object to use
stops = list of floats: 2 or 3 values in standard deviations for creating
the volume ramp {default: [0.1, 1.0]}
neg = string: color for negative volume {default: red}
pos = string: color for positive volume {default: blue}
opacity = float: maximum opacity in volume ramp {default: 0.2}
SEE ALSO
volume
'''
from .setting import set_temporary
opacity, quiet = float(opacity), int(quiet)
if isinstance(stops, str):
stops = cmd.safe_list_eval(stops)
try:
from pymol.colorramping import ColorRamp
except ImportError:
print(' Warning: volume_esp is deprecated')
stdevD = cmd.get_volume_histogram(map, 0)[3]
stops = [s * stdevD for s in stops]
ramp = [
-stops[1],
neg,
opacity,
-stops[0],
neg,
0.0,
stops[0],
pos,
0.0,
stops[1],
pos,
opacity,
]
if len(stops) == 3:
ramp = [-stops[2], neg, opacity] + ramp + [stops[2], pos, opacity]
cmd.volume(name, map, ramp, quiet=quiet)
return
c_neg = cmd.get_color_tuple(neg)
c_pos = cmd.get_color_tuple(pos)
c_pos_0 = c_pos + (0.0, )
c_pos_1 = c_pos + (opacity, )
c_neg_0 = c_neg + (0.0, )
c_neg_1 = c_neg + (opacity, )
if len(stops) == 2:
cstops = [(c_neg_1, -999), (c_neg_1, -stops[1]), (c_neg_0, -stops[0]),
(c_pos_0, stops[0]), (c_pos_1, stops[1]), (c_pos_1, 999)]
elif len(stops) == 3:
cstops = [(c_neg_0, -999), (c_neg_0, -stops[2]), (c_neg_1, -stops[1]),
(c_neg_0, -stops[0]), (c_pos_0, stops[0]),
(c_pos_1, stops[1]), (c_pos_0, stops[2]), (c_pos_0, 999)]
else:
print(' Error: need 2 or 3 stops')
raise CmdException
cmd.volume(name, map, quiet=quiet)
# get_volume_histogram returns zeros without refresh
with set_temporary(suspend_updates='off'):
cmd.refresh()
minD, maxD, meanD, stdevD = cmd.get_volume_histogram(name)[:4]
v_ramp = []
c_ramp = ColorRamp(360)
for c, s in cstops:
i = int(360 * ((s * stdevD) - minD) / (maxD - minD))
i = min(max(i, 0), 359)
v_ramp.append(i)
v_ramp.extend(c)
c_ramp.addColor(i, c)
cmd.set_volume_ramp(name, v_ramp)
cmd.volume_color(name, c_ramp.getRamp())
cmd.recolor(name)
def reps(self, cleanup=0):
rep_list = [
"lines", "sticks", "spheres", "surface", "mesh", "dots", "ribbon",
"cartoon"
]
try:
if not cleanup:
cmd.disable()
cmd.set("suspend_updates", 1, quiet=1)
cmd.load("$PYMOL_DATA/demo/pept.pdb", "rep1")
cmd.alter("rep1///1-5+8-13/", "ss='S'")
cmd.cartoon("auto")
cmd.hide("everything", "rep1")
for a in range(2, 9):
cmd.create("rep%d" % a, "rep1")
for x, y in enumerate(rep_list, 1):
cmd.show(x, "rep%d" % y)
cmd.reset()
cmd.zoom("rep1", 24)
util.cbay("rep2")
util.cbac("rep3")
util.cbas("rep4")
util.cbab("rep5")
util.cbaw("rep6")
util.cbay("rep8")
cmd.set("suspend_updates", 0, quiet=1)
scale = 0.5
for b in range(1, 20):
cmd.set("suspend_updates", 0, quiet=1)
cmd.refresh()
cmd.set("suspend_updates", 1, quiet=1)
xt = -3.2
yt = 1.6
for a in range(1, 5):
cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
yt = -yt
xt = -3.2
for a in range(5, 9):
cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
for a in range(1, 9):
cmd.origin("rep%d" % a, object="rep%d" % a)
cmd.mset("1")
st = ' '.join(
map(
lambda x, y: "rotate angle=-3,object=rep%d,axis=%s;" %
(x, y), list(range(1, 9)),
['x', 'y', 'x', 'y', 'x', 'y', 'x', 'y']))
cmd.mdo(1, st)
cmd.set("suspend_updates", 0, quiet=1)
cmd.mplay()
cgo = []
axes = [[4.5, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]]
c = 1
for a in rep_list:
ext = cmd.get_extent("rep%d" % c)
pos = [(ext[0][0] + ext[1][0]) / 2,
(ext[0][1] + ext[1][1]) / 2 + 14,
(ext[0][2] + ext[1][2]) / 2]
c = c + 1
pos[0] = pos[0] - (measure_text(plain, a, axes) / 2)
wire_text(cgo, plain, pos, a, axes)
cmd.set("cgo_line_width", 1.5)
cmd.set("auto_zoom", 0)
cmd.load_cgo(cgo, 'reps')
cmd.set("auto_zoom", 1)
else:
cmd.delete("rep*")
cmd.mset()
cmd.mstop()
except:
traceback.print_exc()
def colorbyrmsd(mobile,
target,
doAlign=1,
doPretty=1,
guide=1,
method='super',
quiet=1):
'''
DESCRIPTION
Align two structures and show the structural deviations in color to more
easily see variable regions.
Colors each mobile/target atom-pair by distance (the name is a bit
misleading).
Modifies the B-factor columns in your original structures.
ARGUMENTS
mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
doAlign = 0 or 1: Superpose selections before calculating distances
{default: 1}
doPretty = 0 or 1: Show nice representation and colors {default: 1}
EXAMPLE
fetch 1ake 4ake, async=0
remove chain B
colorbyrmsd 1ake, 4ake
'''
from chempy import cpv
doAlign, doPretty = int(doAlign), int(doPretty)
guide, quiet = int(guide), int(quiet)
aln, seleboth = '_aln', '_objSelBoth'
try:
align = cmd.keyword[method][0]
except:
print(' Error: no such method: ' + str(method))
raise CmdException
if guide:
mobile = '(%s) and guide' % mobile
target = '(%s) and guide' % target
try:
if doAlign:
# superpose
align(mobile, target)
# get alignment without superposing
align(mobile, target, cycles=0, transform=0, object=aln)
except:
print(' Error: Alignment with method %s failed' % (method))
raise CmdException
cmd.select(seleboth, '(%s) or (%s)' % (mobile, target))
idx2coords = dict()
cmd.iterate_state(-1,
seleboth,
'idx2coords[model,index] = (x,y,z)',
space=locals())
if cmd.count_atoms('?' + aln, 1, 1) == 0:
# this should ensure that "aln" will be available as selectable object
cmd.refresh()
b_dict = dict()
for col in cmd.get_raw_alignment(aln):
assert len(col) == 2
b = cpv.distance(idx2coords[col[0]], idx2coords[col[1]])
for idx in col:
b_dict[idx] = b
cmd.alter(seleboth, 'b = b_dict.get((model, index), -1)', space=locals())
if doPretty:
cmd.orient(seleboth)
cmd.show_as('cartoon', 'byobj ' + seleboth)
cmd.color('gray', seleboth)
cmd.spectrum('b', 'blue_red', seleboth + ' and b > -0.5')
if not quiet:
print(" ColorByRMSD: Minimum Distance: %.2f" % (min(b_dict.values())))
print(" ColorByRMSD: Maximum Distance: %.2f" % (max(b_dict.values())))
print(" ColorByRMSD: Average Distance: %.2f" %
(sum(b_dict.values()) / len(b_dict)))
cmd.delete(aln)
cmd.delete(seleboth)
def Btn_CreatePartition(self):
DestFile = ''
Output = self.Step3Output.get()
if General.validate_String(Output, '', False, False, True):
self.DisplayMessage(" ERROR: Could not save the partition file because you entered an invalid name.", 2)
return
auto_zoom = cmd.get("auto_zoom")
if Output != '':
if not self.Vertex:
self.top.DisplayMessage(" ERROR: Cannot save an empty cleft. Add spheres that include volume of the parent.", 1)
return
if General_cmd.object_Exists(Output):
answer = tkMessageBox.askquestion("Question",
message="An object with that name already exists. Would you like to overwrite it?",
icon='warning')
if str(answer) == 'no':
return
try:
cmd.set("auto_zoom", 0)
DestFile = os.path.join(self.top.GetCleftTempProject_Dir, Output + '.pdb')
self.top.Manage.copy_TempPartition(self.TempPartition, DestFile)
cmd.load(DestFile, Output, state=1)
cmd.refresh()
cmd.hide('everything', Output)
cmd.refresh()
cmd.show('surface', Output)
cmd.refresh()
partition_rgb = self.top.Default.SetPartitionColor(self.Cleft.CleftName)
if len(partition_rgb):
cmd.color('partition', Output)
cmd.refresh()
cmd.delete(self.PartitionDisplay)
cmd.refresh()
Cleft = CleftObj.CleftObj()
Cleft.CleftFile = DestFile
Cleft.CleftName = self.Step3Output.get()
Cleft.PartitionParent = self.Cleft
Cleft.Partition = True
Cleft.UTarget = self.Cleft.UTarget
Cleft.Set_CleftMD5()
Cleft.Color = General.rgb_to_hex(partition_rgb)
self.top.Default.TempBindingSite.Add_Cleft(Cleft)
self.top.CopySession = False
# Put the partition cleft over its parent
General_cmd.Oscillate(self.Cleft.CleftName, 0.0)
self.Reset_Step1()
else:
self.top.DisplayMessage(" ERROR: Cleft '" + self.Cleft.CleftName + "' could not be found to set partition color", 1)
except:
self.top.DisplayMessage(" ERROR: Could not create partition object: File not found.", 1)
else:
self.top.DisplayMessage(" ERROR: Could not create partition object: Output is null.", 1)
cmd.set("auto_zoom", auto_zoom)
def hide_Labels(self):
cmd.hide('labels', self.LigDisplay)
cmd.refresh()
def show_AtomsName(self):
cmd.label(self.LigDisplay, "\"%s\" % name")
cmd.refresh()
def show_AtomsNumber(self):
cmd.label(self.LigDisplay, "\"%d\" % ID")
cmd.refresh()