257 lines
9.7 KiB
Python
257 lines
9.7 KiB
Python
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from pymol.wizard import Wizard
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from pymol import cmd
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import pymol
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import copy
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default_map = [ '', '', '']
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default_level = [ 1.0, 3.0, -3.0]
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default_radius = 8.0
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default_track = 0
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class Density(Wizard):
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def __init__(self,_self=cmd):
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self.cmd = _self
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self.cmd.unpick()
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Wizard.__init__(self,_self)
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# mode selection subsystem
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self.radius = default_radius
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self.map = copy.deepcopy(default_map)
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self.level = copy.deepcopy(default_level)
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self.track = copy.deepcopy(default_track)
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self.avail_maps = []
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self.menu['radius'] = [
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[1, '4.0 A Radius','cmd.get_wizard().set_radius(4)'],
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[1, '5.0 A Radius','cmd.get_wizard().set_radius(5)'],
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[1, '6.0 A Radius','cmd.get_wizard().set_radius(6)'],
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[1, '8.0 A Radius','cmd.get_wizard().set_radius(8)'],
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[1, '10.0 A Radius','cmd.get_wizard().set_radius(10)'],
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[1, '15.0 A Radius','cmd.get_wizard().set_radius(15)'],
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[1, '20.0 A Radius','cmd.get_wizard().set_radius(20)'],
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[1, '50.0 A Radius','cmd.get_wizard().set_radius(50)'],
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]
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self.menu['map0'] = []
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self.menu['map1'] = []
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self.menu['map2'] = []
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level_menu = lambda x:[ [1, '1.0 sigma','cmd.get_wizard().set_level(%d,1.0)'%x],
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[1, '1.5 sigma','cmd.get_wizard().set_level(%d,1.5)'%x],
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[1, '2.0 sigma','cmd.get_wizard().set_level(%d,2.0)'%x],
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[1, '3.0 sigma','cmd.get_wizard().set_level(%d,3.0)'%x],
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[1, '5.0 sigma','cmd.get_wizard().set_level(%d,5.0)'%x],
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[1, '-3.0 sigma','cmd.get_wizard().set_level(%d,-3.0)'%x]]
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self.menu['level0'] = level_menu(0)
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self.menu['level1'] = level_menu(1)
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self.menu['level2'] = level_menu(2)
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self.menu['track'] = [
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[ 1, "Track & Zoom", 'cmd.get_wizard().set_track(0)'],
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[ 1, "Track & Center", 'cmd.get_wizard().set_track(1)'],
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[ 1, "Track & Set Origin", 'cmd.get_wizard().set_track(2)'],
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[ 1, "Track Off", 'cmd.get_wizard().set_track(3)'],
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]
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if (self.map[0] == '') and (self.map[1] == '') and (self.map[2]==''):
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for a in self.cmd.get_names(): # automatically load first map we find
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if self.cmd.get_type(a)=='object:map':
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self.map[0]=a
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break
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self.update_map_menus()
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self.cmd.set_key('pgup',lambda c=cmd:c.get_wizard().next_res(d=-1))
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self.cmd.set_key('pgdn',lambda c=cmd:c.get_wizard().next_res())
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def update_map_menus(self):
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self.avail_maps = []
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for a in self.cmd.get_names('objects'):
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if self.cmd.get_type(a)=='object:map':
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self.avail_maps.append(a)
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c = 0
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for a in self.map:
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map_kee = 'map'+str(c)
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level_kee = 'level'+str(c)
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self.menu[map_kee] = [[2,'Select Map','']]
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for a in self.avail_maps:
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self.menu[map_kee].append([ 1,a,'cmd.get_wizard().set_map(%d,"%s")'%(c,a) ])
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self.menu[map_kee].append([1,'(none)','cmd.get_wizard().set_map(%d,"")'%c])
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c = c + 1
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def set_track(self,track):
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self.track = track
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self.cmd.refresh_wizard()
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def set_level(self,map,level):
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self.level[map] = level
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self.update_maps()
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self.cmd.refresh_wizard()
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def set_map(self,map,map_name):
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self.map[map] = map_name
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self.cmd.refresh_wizard()
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def set_radius(self,radius):
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self.radius = radius
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self.update_maps()
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self.cmd.refresh_wizard()
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def update_maps(self,zoom=1):
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sele_name = "_dw"
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if sele_name not in cmd.get_names('selections'):
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sele_name = "center"
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if 1:
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save = self.cmd.get_setting_text('auto_zoom')
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self.cmd.set('auto_zoom',0,quiet=1)
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c = 0
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for a in self.map:
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oname = 'w'+str(c+1)+'_'+a
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if oname not in self.cmd.get_names():
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color = 1
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else:
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color = 0
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if len(a) and (a in self.cmd.get_names('objects')):
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if self.cmd.get_type(a)=='object:map':
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self.cmd.isomesh(oname,a,self.level[c],
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sele_name,self.radius,state=1)
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if color:
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if c == 0:
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self.cmd.color('blue',oname)
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elif c == 1:
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self.cmd.color('white',oname)
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else:
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self.cmd.color('magenta',oname)
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c = c + 1
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save = self.cmd.set('auto_zoom',save,quiet=1)
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if self.track==0:
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if zoom:
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self.cmd.zoom(sele_name,self.radius,animate=0.67)
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elif self.track==1:
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if zoom:
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self.cmd.center(sele_name,animate=0.67)
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elif self.track==2:
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if zoom:
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self.cmd.origin(sele_name)
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self.cmd.refresh_wizard()
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# generic set routines
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def zoom(self):
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if '_dw' in self.cmd.get_names('selections'):
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self.cmd.zoom("(_dw)",self.radius,animate=0.67)
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else:
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c = 0
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for a in self.map:
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oname = 'w'+str(c+1)+'_'+a
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if len(a):
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if a in self.cmd.get_names('objects'):
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self.cmd.zoom(oname,animate=0.67)
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c = c + 1
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def get_panel(self):
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self.update_map_menus()
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return [
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[ 1, 'Density Map Wizard',''],
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[ 2, 'Update Maps' , 'cmd.get_wizard().update_maps()'],
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[ 2, 'Zoom' , 'cmd.get_wizard().zoom()'],
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[ 2, 'Next Res. (PgDown)' , 'cmd.get_wizard().next_res()'],
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[ 2, 'Previous Res. (PgUp)' , 'cmd.get_wizard().next_res(d=-1)'],
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[ 3, "Radius: %3.1f A"%self.radius,'radius'],
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[ 3, "Map 1: "+self.map[0],'map0'],
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[ 3, " @ "+str(self.level[0])+" sigma",'level0'],
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[ 3, "Map 2: "+self.map[1],'map1'],
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[ 3, " @ "+str(self.level[1])+" sigma",'level1'],
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[ 3, "Map 3: "+self.map[2],'map2'],
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[ 3, " @ "+str(self.level[2])+" sigma",'level2'],
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[ 3, self.menu['track'][self.track][1], 'track' ],
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[ 2, 'Done','cmd.set_wizard()'],
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]
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def cleanup(self):
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global default_radius,default_map,default_level
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default_radius = self.radius
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default_map = self.map
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default_level = self.level
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default_track = self.track
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self.clear()
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self.cmd.set_key('pgup',None)
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self.cmd.set_key('pgdn',None)
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def clear(self):
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pass
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def do_select(self,name):
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if self.track!=2:
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self.cmd.select("_dw",name,quiet=1)
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self.update_maps()
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self.cmd.deselect()
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def do_pick(self,bondFlag):
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global dist_count
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if not bondFlag:
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if self.track!=2:
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self.cmd.select("_dw","pk1",quiet=1)
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self.update_maps()
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self.cmd.unpick()
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def get_event_mask(self):
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return Wizard.event_mask_pick + Wizard.event_mask_select + Wizard.event_mask_position
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def do_position(self):
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if '_dw' not in cmd.get_names("selections"):
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self.update_maps(zoom=0)
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def next_res(self, d=1):
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# Donated by Tom Lee
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if not self.cmd.count_atoms('?_dw'):
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if self.cmd.count_atoms("?pk1"):
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self.cmd.select("_dw","pk1")
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if not ('_dw' in self.cmd.get_names('selections')):
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print(" Density-Wizard: Please pick an atom first.")
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else:
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obj = self.cmd.index('_dw')[0][0]
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a0 = self.cmd.get_model('_dw').atom[0]
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self.cmd.select("_res0", "byres (_dw)")
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res0 = self.cmd.get_model("_res0")
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atn = a0.name
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for a in res0.atom:
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if (a.name == 'CA'):
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atn = 'CA'
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break
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elif (a.name == 'C1*'):
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atn = 'C1*'
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break
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elif (a.name == 'C1\''):
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atn = 'C1\''
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break
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n = self.cmd.select('_dw2', ''+obj+'/'+a0.segi+'/'+a0.chain+'/'+str(a0.resi_number+d)+'/'+atn)
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if (n == 0): # deal with gaps in sequence:
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self.cmd.select('_chain', ''+obj+'/'+a0.segi+'/'+a0.chain+'//'+atn)
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chain = self.cmd.get_model('_chain')
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resids = []
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for a in chain.atom:
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resids.append(a.resi)
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if (a.resi_number == a0.resi_number):
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i = len(resids) - 1
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next_i = i + d
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if ((next_i < 0) or (next_i >= len(resids))):
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print("Current residue is the end of a chain.")
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else:
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n = self.cmd.select('_dw2', ''+obj+'/'+a0.segi+'/'+a0.chain+'/'+resids[next_i]+'/'+atn)
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if (n > 0):
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self.cmd.hide("labels", "?_dw")
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self.cmd.select('dw_resi', 'byres _dw2')
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self.cmd.disable('dw_resi')
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self.cmd.label('(_dw2)', '" %s %s/%s/" % (resn,chain,resi)')
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self.cmd.select('_dw','_dw2')
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self.cmd.delete('_dw2')
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self.update_maps()
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