Python Wizard.__init__方法代码示例

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
    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 = ''

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
 def __init__(self,old_name,mode='object',_self=cmd):
     Wizard.__init__(self,_self)
     
     self.prefix = 'Renaming \\999%s\\--- to: \\999'%old_name
     self.old_name = old_name
     self.new_name = old_name
     self.mode = mode

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
    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 )

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
 def __init__(self,mode='label',pos='[0.0,0.0,0.0]',_self=cmd):
     Wizard.__init__(self,_self)
     self.mode = mode
     if mode == 'label':
         self.prefix = 'Label text: \888'
     self.text = ''
     self.pos = pos

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
    def __init__(self,_self=cmd):
        Wizard.__init__(self,_self)
        
        self.editing_name = 0
        self.copying = 0
        
        self.points_name = ''
        self.set_name(default_name)
    
        self.mode = default_mode
        self.modes = [
            'box',
            'walls', 
            'plane',
	    'quad',
            ]

        self.mode_name = {
            'box':'Box',
            'walls':'Walls',
            'plane':'Plane',
	    'quad':'Quad',
            }

        smm = []
        smm.append([ 2, 'Box Mode', '' ])
        for a in self.modes:
            smm.append([ 1, self.mode_name[a], 'cmd.get_wizard().set_mode("'+a+'")'])
        self.menu['mode']=smm

        self.update_box()

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
    def __init__(self, app, _self=cmd):
        Wizard.__init__(self, _self)

        # Clean the slate
        self.cmd.unpick()
        self.app = app

        # Default values
        self.rmsd_cutoff = 1.0
        self.number_of_structures = 25
        self.full_match = False
        self.url = URL
        self.LOGOurl = LOGOURL

        self.ref = Wizard

        # default values for sequence logo UI
        self.operations = []
        self.searches = []
        self.database = DATABASE_FULL
        self.database_name = "Full"
        self.search = None # current search action
        self.operation = None # current operation

        self.dictionary = {}

        self.searchThread = None
        self.logoThread = None

        self.status = 'waiting for selection'
        self.searchProgress = 0.0
        self.errorMessage = ''
        self.makeLogo = 0
        self.update()

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
    def __init__(self,_self=cmd):
        Wizard.__init__(self,_self)

        self.cmd.unpick()
        
        self.status = 0 # 0 no atoms selections, 1 atom selected, 2 atoms selected, 3 atoms selected
        self.error = None
        self.object_name = None

        # mode selection subsystem

        self.mode = self.session.get('default_mode','pairs')
        self.modes = [
            'pairs',
            'angle',
            'dihed', 
            'polar',
            'heavy',
            'neigh',
            ]
        
        self.mode_name = {
            'polar':'Polar Neighbors',
            'heavy':'Heavy Neighbors',
            'neigh':'Neighbors',
            'pairs':'Distances',
            'angle':'Angles',
            'dihed':'Dihedrals',
            }

        smm = []
        smm.append([ 2, 'Measurement Mode', '' ])
        for a in self.modes:
            smm.append([ 1, self.mode_name[a], 'cmd.get_wizard().set_mode("'+a+'")'])
        self.menu['mode']=smm

        # overwrite mode selection subsystem
        
        self.object_mode = self.session.get('default_object_mode','append')
        self.object_modes = [
            'merge', 
            'overwr',
            'append',
            ]
        self.object_mode_name = {
            'merge':'Merge With Previous',
            'overwr':'Replace Previous',
            'append':'Create New Object',         
            }

        smm = []
        smm.append([ 2, 'New Measurements?', '' ])
        for a in self.object_modes:
            smm.append([ 1, self.object_mode_name[a], 'cmd.get_wizard().set_object_mode("'+a+'")'])
        self.menu['object_mode']=smm
        self.selection_mode = self.cmd.get_setting_legacy("mouse_selection_mode")
        self.cmd.set("mouse_selection_mode",0) # set selection mode to atomic
        self.cmd.deselect() # disable the active selection (if any)

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
    def __init__(self,_self=cmd):

        self.cmd = _self
        self.cmd.unpick()
        
        Wizard.__init__(self,_self)
        
        # mode selection subsystem
        
        self.radius = default_radius
        self.map = copy.deepcopy(default_map)
        self.level = copy.deepcopy(default_level)
        self.track = copy.deepcopy(default_track)
        self.avail_maps = []
        
        self.menu['radius'] = [
                                      [1, '4.0 A Radius','cmd.get_wizard().set_radius(4)'],
                                      [1, '5.0 A Radius','cmd.get_wizard().set_radius(5)'],
                                      [1, '6.0 A Radius','cmd.get_wizard().set_radius(6)'],
                                      [1, '8.0 A Radius','cmd.get_wizard().set_radius(8)'],
                                      [1, '10.0 A Radius','cmd.get_wizard().set_radius(10)'],
                                      [1, '15.0 A Radius','cmd.get_wizard().set_radius(15)'],
                                      [1, '20.0 A Radius','cmd.get_wizard().set_radius(20)'],
                                      [1, '50.0 A Radius','cmd.get_wizard().set_radius(50)'],
                                      ]
                                        
        self.menu['map0'] = []
        self.menu['map1'] = []
        self.menu['map2'] = []

        level_menu = lambda x:[ [1, '1.0 sigma','cmd.get_wizard().set_level(%d,1.0)'%x],
                                        [1, '1.5 sigma','cmd.get_wizard().set_level(%d,1.5)'%x],
                                        [1, '2.0 sigma','cmd.get_wizard().set_level(%d,2.0)'%x],
                                        [1, '3.0 sigma','cmd.get_wizard().set_level(%d,3.0)'%x],
                                        [1, '5.0 sigma','cmd.get_wizard().set_level(%d,5.0)'%x],
                                        [1, '-3.0 sigma','cmd.get_wizard().set_level(%d,-3.0)'%x]]
        
        self.menu['level0'] = level_menu(0)
        self.menu['level1'] = level_menu(1)
        self.menu['level2'] = level_menu(2)
        
        self.menu['track'] = [
        [ 1, "Track & Zoom", 'cmd.get_wizard().set_track(0)'],
        [ 1, "Track & Center", 'cmd.get_wizard().set_track(1)'],
        [ 1, "Track & Set Origin", 'cmd.get_wizard().set_track(2)'],
        [ 1, "Track Off", 'cmd.get_wizard().set_track(3)'],
        ]

        if (self.map[0] == '') and (self.map[1] == '') and (self.map[2]==''):
            for a in self.cmd.get_names(): # automatically load first map we find
                if self.cmd.get_type(a)=='object:map':
                    self.map[0]=a
                    break
        self.update_map_menus()

        self.cmd.set_key('pgup',lambda c=cmd:c.get_wizard().next_res(d=-1))
        self.cmd.set_key('pgdn',lambda c=cmd:c.get_wizard().next_res())      

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
 def __init__(self,*arg,**kw):
     _self = kw.get('_self',cmd)
     Wizard.__init__(self,_self)
     self.message = []
     for a in arg:
         if not isinstance(a,list):
             self.message.append(a)
         else:
             self.message.extend(a)

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
 def __init__(self,*arg,**kw):
     _self = kw.get('_self',cmd)
     self.valid = 1
     Wizard.__init__(self,_self)
     if len(arg):
         self.old_button_mode = int(arg[0])
     self.check_valid()
     if self.valid:
         self.recount()

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
 def __init__(self,arg0=None,_self=cmd):
     Wizard.__init__(self,_self)        
     self.gl = 5.0
     self.short_cpu = 8.0
     self.long_cpu = 16.0
     self.message = []
     if arg0!=None:
         if hasattr(self,arg0):
             getattr(self,arg0)()

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
    def __init__(self,_self=cmd):

        Wizard.__init__(self,_self)
        
        self.memory = 0
        self.n_pair = 0
        self.status = 0 # 0 no atoms selections, 1 atom selected
        self.message = None

        self.selection_mode = cmd.get_setting_int("mouse_selection_mode")
        cmd.set("mouse_selection_mode",0) # set selection mode to atomic
        cmd.deselect() # disable the active selection (if any)

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
 def __init__(self,*arg,**kw):
     _self = kw.get('_self',cmd)
     Wizard.__init__(self,_self)        
     self.message = []
     for a in arg:
         if not isinstance(a,list):
             self.message.append(a)
         else:
             self.message.extend(a)
     for a in self.message:
         print(" " + _nuke_color_re.sub('',a))
     self.dismiss = int(kw.get("dismiss",1))

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
    def __init__(self,_self=cmd):

        cmd.unpick();
        Wizard.__init__(self,_self)
        
        self.status = 0 # 0 no atoms selections, 1 atom selected
        self.error = None
        self.object_name = None

        # mode selection subsystem
        
        self.mode = default_mode
        self.modes = [
            'polar',
            'heavy',
            'neigh',
            'pairs',
            ]
        
        self.mode_name = {
            'polar':'Polar Neighbors',
            'heavy':'Heavy Neighbors',
            'neigh':'Neighbors',
            'pairs':'Pairwise Distances',
            }

        smm = []
        smm.append([ 2, 'Measurement Mode', '' ])
        for a in self.modes:
            smm.append([ 1, self.mode_name[a], 'cmd.get_wizard().set_mode("'+a+'")'])
        self.menu['mode']=smm

        # overwrite mode selection subsystem
        
        self.object_mode=default_object_mode
        self.object_modes = [
            'overwr',
            'append',
            ]
        self.object_mode_name = {
            'overwr':'Replace Previous',
            'append':'Create New',         
            }

        smm = []
        smm.append([ 2, 'New Distances?', '' ])
        for a in self.object_modes:
            smm.append([ 1, self.object_mode_name[a], 'cmd.get_wizard().set_object_mode("'+a+'")'])
        self.menu['object_mode']=smm
        self.selection_mode = cmd.get_setting_int("mouse_selection_mode")
        cmd.set("mouse_selection_mode",0) # set selection mode to atomic
        cmd.deselect() # disable the active selection (if any)

# 需要导入模块: from pymol.wizard import Wizard [as 别名]
# 或者: from pymol.wizard.Wizard import __init__ [as 别名]
 def __init__(self,_self=cmd):
     Wizard.__init__(self,_self)
     
     self.ligand = ""
     for a in self.cmd.get_names("public_objects",1):
         if self.cmd.count_atoms(a) < 1000:
             self.ligand = a
             break
     self.target = "(none)"
     self.message = []
     self.menu = {}
     self.update_menus()
     self.cmd.edit_mode()