def testGetType(self):
cmd.fragment('gly', 'm1')
self.assertEqual(cmd.get_type('m1'), 'object:molecule')
cmd.ramp_new('ramp1', 'none')
self.assertEqual(cmd.get_type('ramp1'), 'object:ramp')
cmd.select('s1', 'elem C')
self.assertEqual(cmd.get_type('s1'), 'selection')
def Refresh_DDL(widget, var, exc, fun):
try:
cmd.unpick()
list = cmd.get_names('all')
# Delete all entries in DDL
widget['menu'].delete(0, END)
if len(list) > 0:
list = [ str(item) for item in list if not re.match(RESERVED_NAMES, item) ]
for item in sorted(list, key=str.lower):
type = cmd.get_type(str(item))
if (type == 'object:molecule' or type == 'selection') and exc.count(str(item)) == 0:
if fun != None:
widget['menu'].add_command(label=item, command=lambda temp = item: fun(temp))
else:
widget['menu'].add_command(label=item, command=lambda temp = item: widget.setvar(widget.cget('textvariable'), value = temp))
var.set(item)
else:
# Dummy value
widget['menu'].add_command(label='', command=lambda temp = '': widget.setvar(widget.cget('textvariable'), value = ''))
var.set('')
except:
pass
def fill_map_list(self):
self.objects_list = cmd.get_names('objects')
self.maps_list = [
e for e in self.objects_list if cmd.get_type(e) == 'object:map'
]
self.form.mapselector.clear()
self.form.mapselector.addItems(self.maps_list)
def update_object_list(self):
"""
update the internal state list
"""
# purge list of removed objects
pubObj = self.cmd.get_names("public_objects")
object_list_copy = self.object_list.copy()
for x in object_list_copy:
if x not in pubObj:
del self.object_list[x]
# for all VOLUME type objects not known to the list
for x in self.cmd.get_names("public_objects"):
if "object:volume"==cmd.get_type(x):
if x not in self.object_list.keys():
if self.cmd.get_volume_is_updated(x) == 0:
continue
# make a default pair for this volume object
tmpMap = VolumeHist(self.cmd.get_volume_histogram(x,self.cmd),nBins=64)
tmpRamp = ColorRamp(360,name=x)
self.object_list[x] = (tmpRamp,tmpMap)
if self.ramp_update.has_key(x) and self.ramp_update[x]:
tmpRamp.addColor(0, (0,0,1,0))
tmpRamp.addColor(359, (0,0,1,0))
for data, alpha, col, kind in self.ramp_update[x]:
self.addWithoutGUINow(x, data, alpha, col, kind=kind)
self.ramp_update[x] = []
tmpRamp.updateRamp()
self.cmd.volume_color(x, tmpRamp.getRamp())
self.cmd.set_volume_ramp(x, tmpRamp.getRampList())
else:
ramp_list = self.cmd.get_volume_ramp(x, self.cmd)
if ramp_list:
while ramp_list:
tmpRamp.addColor(ramp_list[0],
(ramp_list[1], ramp_list[2], ramp_list[3], ramp_list[4]))
ramp_list = ramp_list[5:]
else:
tmpRamp.addColor(0, (0,0,1,0))
tmpRamp.addColor(359, (0,0,1,0))
tmpRamp.addColor(200, (0.0, 0.0, 1.0, 0.0))
tmpRamp.addColor(210, (0.0, 0.8, 1.0, 0.2))
tmpRamp.addColor(220, (0.0, 0.0, 1.0, 0.0))
else:
# need to regenerate the histogram
(tmpRamp,tmpMap) = self.object_list[x]
tmpMap = VolumeHist(self.cmd.get_volume_histogram(x,self.cmd),nBins=64)
self.object_list[x] = (tmpRamp,tmpMap)
if len(self.object_list.keys())!=0:
# guaranteed to exist
k = self.object_list.keys()[0]
self.active_ramp, self.active_map = self.object_list[k]
self.active = k
self.update_transferframe()
def unmask_Objects(lstexc):
lstobj = cmd.get_names('objects')
for obj in lstobj:
if lstexc.count(str(obj)) == 0:
try:
type = cmd.get_type(str(obj))
if type == 'object:molecule' or type == 'selection':
cmd.unmask(str(obj))
except:
continue
def get_isoobjects(state=1, quiet=1):
'''
Get a list of (name, isolevel) tuples for all isomesh and isosurface
objects.
'''
state, quiet = int(state), int(quiet)
r = []
for name in cmd.get_names():
t = cmd.get_type(name)
if t in ('object:mesh', 'object:surface'):
level = cmd.isolevel(name, 0, state, 1)
if not quiet:
print '%-20s %5.2f' % (name, level)
r.append((name, level))
return r
def testFetch(self):
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', 'pdb pdbe')
cmd.fetch('1avy', '1avy1', type='pdb1')
names += ['1avy1']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.count_states('1avy1'), 3)
cmd.fetch('1avy', type='2fofc')
names += ['1avy_2fofc']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_type('1avy_2fofc'), 'object:map')
def get_isoobjects(state=1, quiet=1):
'''
Get a list of (name, isolevel) tuples for all isomesh and isosurface
objects.
'''
state, quiet = int(state), int(quiet)
r = []
for name in cmd.get_names():
t = cmd.get_type(name)
if t in ('object:mesh', 'object:surface'):
level = cmd.isolevel(name, 0, state, 1)
if not quiet:
print '%-20s %5.2f' % (name, level)
r.append((name, level))
return r
def testFetch(self):
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', 'pdb pdbe')
cmd.fetch('1avy', '1avy1', type='pdb1')
names += ['1avy1']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.count_states('1avy1'), 3)
cmd.fetch('1avy', type='2fofc')
names += ['1avy_2fofc']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_type('1avy_2fofc'), 'object:map')
def click(self):
residueName = self.createSelectionMacro("(sele)")
# transfer the click selection to a named selection
cmd.select(residueName, "(sele)")
# find the name of the object which contains the selection
new_name = None
obj_list = cmd.get_names("objects")
for object in obj_list:
if cmd.get_type(object) == "object:molecule":
if cmd.count_atoms("(%s and %s)" % (object, residueName)):
pickedObject = object
break
if pickedObject == None:
print "MtsslWizard: object not found."
self.cmd.refresh_wizard()
return residueName, pickedObject
def update_object_menu(self):
# find objects with > 1 state
self.avail_objects = []
for a in cmd.get_names('objects'):
if cmd.get_type(a)=='object:molecule':
if cmd.count_states(a)>1:
self.avail_objects.append(a)
# now create the object menu
self.menu['object'] = [[2,'Select Object','']]
for a in self.avail_objects:
self.menu['object'].append([ 1,a,'cmd.get_wizard().set_object("%s")'%(a) ])
self.menu['object'].append([ 1,'None','cmd.get_wizard().set_object(None)'])
def __init__(self, mobile, target, match):
self.autodelete = True
self.temporary = []
if match == 'none':
self.mobile = mobile
self.target = target
elif match in ['in', 'like']:
self.mobile = '(%s) %s (%s)' % (mobile, match, target)
self.target = '(%s) %s (%s)' % (target, match, mobile)
elif match in ['align', 'super']:
self.align(mobile, target, match)
elif match in cmd.get_names('all') and cmd.get_type(match) in ('object:', 'object:alignment'):
self.from_alignment(mobile, target, match)
else:
print(' Error: unkown match method', match)
raise CmdException
def update_object_menu(self):
# find objects with > 1 state
self.avail_objects = []
for a in cmd.get_names('objects'):
if cmd.get_type(a)=='object:molecule':
if cmd.count_states(a)>1:
self.avail_objects.append(a)
# now create the object menu
self.menu['object'] = [[2,'Select Object','']]
for a in self.avail_objects:
self.menu['object'].append([ 1,a,'cmd.get_wizard().set_object("%s")'%(a) ])
self.menu['object'].append([ 1,'None','cmd.get_wizard().set_object(None)'])
def update_object_menu(self):
# find objects with > 1 state
self.avail_objects = []
for a in cmd.get_names("objects"):
if cmd.get_type(a) == "object:molecule":
if cmd.count_states(a) > 1:
self.avail_objects.append(a)
# now create the object menu
self.menu["object"] = [[2, "Select Object", ""]]
for a in self.avail_objects:
self.menu["object"].append([1, a, 'cmd.get_wizard().set_object("%s")' % (a)])
self.menu["object"].append([1, "None", "cmd.get_wizard().set_object(None)"])
def createSelectionMacro(self, selection):
obj_list = cmd.get_names('objects')
selectedObject = ""
for object in obj_list:
if cmd.get_type(object) == "object:molecule":
if cmd.count_atoms("(%s and (sele))" % (object)):
selectedObject = object
break
my_dict = {"my_list": []}
cmd.iterate(selection,
"my_list.append((segi,chain,resi,resn))",
space=my_dict)
my_list = my_dict['my_list']
macro = "%s-%s-%s-%s-%s" % (selectedObject, my_list[0][0],
my_list[0][1], my_list[0][2],
my_list[0][3])
return macro
def __init__(self, mobile, target, match):
self.autodelete = True
self.temporary = []
if match == 'none':
self.mobile = mobile
self.target = target
elif match in ['in', 'like']:
self.mobile = '(%s) %s (%s)' % (mobile, match, target)
self.target = '(%s) %s (%s)' % (target, match, mobile)
elif match in ['align', 'super']:
self.align(mobile, target, match)
elif match in cmd.get_names('all') and cmd.get_type(match) in ('object:', 'object:alignment'):
self.from_alignment(mobile, target, match)
else:
print(' Error: unkown match method', match)
raise CmdException
def update_is_needed(self):
# check removed objects
pubObj = self.cmd.get_names("public_objects")
if not pubObj:
# if ModalDraw is set (e.g., a movie is running)
# then API cannot be accessed and get_names() returns
# None. In this case, the volume panel info does not
# need to be updated
return False
for x in self.object_list:
if x not in pubObj:
return True
# check new objects
for x in self.cmd.get_names("public_objects"):
if "object:volume" == cmd.get_type(x):
if x not in self.object_list.keys():
return True
return False
def update_is_needed(self):
# check removed objects
pubObj = self.cmd.get_names("public_objects")
if not pubObj:
# if ModalDraw is set (e.g., a movie is running)
# then API cannot be accessed and get_names() returns
# None. In this case, the volume panel info does not
# need to be updated
return False
for x in self.object_list:
if x not in pubObj:
return True
# check new objects
for x in self.cmd.get_names("public_objects"):
if "object:volume"==cmd.get_type(x):
if x not in self.object_list.keys():
return True
return False
def __init__(self, _self=cmd):
# initialize parent class
Wizard.__init__(self, _self)
# restore previous state from global storage
self.dict = static_dict
self.object = default_object
self.browse = default_browse
self.avail_objects = []
self.state_dict = {}
# if we don't have a current object, choose the first multi-state object
if self.object == None:
for a in cmd.get_names("objects"):
if cmd.get_type(a) == "object:molecule":
if cmd.count_states(a) > 1:
self.object = a
break
# menu for
self.menu["browse"] = [
[2, "Browse Mode", ""],
[1, "Browse All", "cmd.get_wizard().set_browse(1)"],
[1, "Browse Accepted", "cmd.get_wizard().set_browse(2)"],
[1, "Browse Rejected", "cmd.get_wizard().set_browse(3)"],
[1, "Browse Deferred", "cmd.get_wizard().set_browse(4)"],
[1, "Browse Remaining", "cmd.get_wizard().set_browse(5)"],
]
self.count_object()
self.load_state_dict()
self.update_object_menu()
cmd.set_key("F1", lambda s=self: s.accept())
cmd.set_key("F2", lambda s=self: s.reject())
cmd.set_key("F3", lambda s=self: s.defer())
cmd.set_key("right", lambda s=self: s.forward())
cmd.set_key("left", lambda s=self: s.backward())
def __init__(self, _self=cmd):
# initialize parent class
Wizard.__init__(self, _self)
# restore previous state from global storage
self.dict = static_dict
self.object = default_object
self.browse = default_browse
self.avail_objects = []
self.state_dict = {}
# if we don't have a current object, choose the first multi-state object
if self.object == None:
for a in cmd.get_names('objects'):
if cmd.get_type(a) == 'object:molecule':
if cmd.count_states(a) > 1:
self.object = a
break
# menu for
self.menu['browse'] = [
[2, 'Browse Mode', ''],
[1, 'Browse All', 'cmd.get_wizard().set_browse(1)'],
[1, 'Browse Accepted', 'cmd.get_wizard().set_browse(2)'],
[1, 'Browse Rejected', 'cmd.get_wizard().set_browse(3)'],
[1, 'Browse Deferred', 'cmd.get_wizard().set_browse(4)'],
[1, 'Browse Remaining', 'cmd.get_wizard().set_browse(5)'],
]
self.count_object()
self.load_state_dict()
self.update_object_menu()
cmd.set_key('F1', lambda s=self: s.accept())
cmd.set_key('F2', lambda s=self: s.reject())
cmd.set_key('F3', lambda s=self: s.defer())
cmd.set_key('right', lambda s=self: s.forward())
cmd.set_key('left', lambda s=self: s.backward())
def import_pymol_selections_from_main_menu(self):
"""
Method for importing PyMOL Selections into PyMod. It saves PyMOL objects selected by users
to file, and loads it into PyMOL using 'open_structure_file()'.
"""
# Find all structures already loaded into PyMod: items in struct_list are excluded from
# importable PyMOL object list.
struct_list = [
member.get_pymol_selector()
for member in self.get_pymod_elements_list()
if member.has_structure()
]
# Importable PyMOL objects.
scrolledlist_items = [
str(obj) for obj in cmd.get_names("objects") if
not obj in struct_list and cmd.get_type(obj) == "object:molecule"
]
if not scrolledlist_items:
if struct_list:
self.main_window.show_error_message(
"No Importable Object",
"All PyMOL objects are already imported into PyMod.")
else:
self.main_window.show_error_message(
"No Importable Object", "No PyMOL object to import.")
return
# Builds a new window.
self.import_from_pymol_window = Import_from_pymol_window_qt(
self.main_window,
title="Import from PyMOL",
upper_frame_title="Load PyMOL Objects into PyMod",
submit_command=self.import_selected_pymol_object,
selections_list=scrolledlist_items)
self.import_from_pymol_window.show()
def testLoadVaspCHGCAR(self):
cmd.load(self.datafile("vasp.CHGCAR"), 'vasp.CHGCAR')
self.assertEqual(cmd.get_type('vasp.CHGCAR'), 'object:map')
extend = cmd.get_extent('vasp.CHGCAR')
self.assertArrayEqual(extend, [[0.0, 0.0, 0.0], [6.5, 6.5, 7.7]],
delta=1e-2)
def apply(self):
cmd = self.cmd
pymol = cmd._pymol
if self.status == 1:
# find the name of the object which contains the selection
new_name = None
obj_list = cmd.get_names("objects")
for a in obj_list:
if cmd.get_type(a) == "object:molecule":
if cmd.count_atoms("(%s and %s)" % (a, src_sele)):
new_name = a
break
src_frame = cmd.get_state()
if new_name == None:
print " Mutagenesis: object not found."
else:
auto_zoom = cmd.get_setting_text("auto_zoom")
cmd.set("auto_zoom", "0", quiet=1)
if self.lib_mode != "current":
# create copy w/o residue
cmd.create(tmp_obj1, "(%s and not %s)" % (new_name, src_sele))
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)" % (tmp_obj1, src_sele))
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)" % (tmp_obj1, src_sele))
# save copy for bonded atom reference
cmd.create(tmp_obj3, new_name)
# transfer the selection to copy
cmd.select(src_sele, "(%s in %s)" % (tmp_obj3, src_sele))
# create copy with mutant in correct frame
cmd.create(tmp_obj2, obj_name, src_frame, 1)
cmd.set_title(tmp_obj2, 1, "")
cmd.delete(new_name)
# create the merged molecule
cmd.create(new_name, "(%s or %s)" % (tmp_obj1, tmp_obj2), 1) # only one state in merged object...
# now connect them
cmd.select(mut_sele, "(byres (%s like %s))" % (new_name, src_sele))
# bond N+0 to C-1
if (cmd.select(tmp_sele1, "(name C and (%s in (neighbor %s)))" % (new_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "((%s in %s) and n;N)" % (mut_sele, tmp_obj2)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.set_geometry(tmp_sele1, 3, 3) # make amide planer
cmd.set_geometry(tmp_sele2, 3, 3) # make amide planer
# bond C+0 to N+1
if (cmd.select(tmp_sele1, "(name N and (%s in (neighbor %s)))" % (new_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "((%s in %s) and n;C)" % (mut_sele, tmp_obj2)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.set_geometry(tmp_sele1, 3, 3) # make amide planer
cmd.set_geometry(tmp_sele2, 3, 3) # make amide planer
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
# fix N-H hydrogen position (if any exists)
cmd.h_fix("(name N and bound_to (%s in %s and n;H))" % (new_name, tmp_obj2))
# now transfer selection back to the modified object
cmd.delete(tmp_obj1)
cmd.delete(tmp_obj2)
cmd.delete(tmp_obj3)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2, obj_name, src_frame, 1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)" % (new_name, src_sele))
cmd.remove("(%s) and name OXT" % src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)" % (new_name, src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("(" + src_sele + ")")
# modify the conformation
cmd.update(new_name, tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set("auto_zoom", auto_zoom, quiet=1)
def contactsDialog(root):
"""Create GUI"""
PADDING=5
win = Toplevel(root, width=400, height=600, padx=PADDING, pady=PADDING)
win.resizable(0,0)
win.title("Visualize CASP RR contacts")
#### MAIN CONTROLS ####
frmMain = Frame(win)
frmMain.pack(fill=BOTH, expand=1)
frmMain.columnconfigure(0, weight=2, pad=PADDING)
frmMain.columnconfigure(1, weight=5, pad=PADDING)
frmMain.columnconfigure(2, weight=1, pad=PADDING)
Label(frmMain, text="RR file:").grid(row=0,column=0,sticky=N+E)
vTarget = StringVar(win)
txtTarget = Entry(frmMain, textvariable=vTarget)
txtTarget.grid(row=0, column=1, sticky=W+E)
def browseTarget():
cf = tkFileDialog.askopenfilename(parent=win, filetypes=[("CASP RR files", ".CASPRR")])
if cf:
vTarget.set(cf)
cmdTarget = Button(frmMain, text="...", command=browseTarget)
cmdTarget.grid(row=0, column=2, sticky=W+E)
Label(frmMain, text="Target:").grid(row=1,column=0,sticky=N+E)
lstObject = Listbox(frmMain, selectmode=SINGLE, exportselection=0, height=6)
objects = []
molecules = ( n for n in cmd.get_names() if cmd.get_type(n) == "object:molecule")
for n in molecules:
for ch in cmd.get_chains(n):
objects.append((n, ch))
lstObject.insert(END, "{0}/{1}".format(n,ch))
if objects: lstObject.selection_set(0)
lstObject.grid(row=1, column=1, columnspan=2, sticky=N+E+S+W)
Label(frmMain, text="Min. separation:").grid(row=2,column=0,sticky=E)
vSeparation = IntVar(win)
vSeparation.set(23)
sclSeparation = Scale(frmMain, from_=0, to=100, orient=HORIZONTAL, variable=vSeparation)
sclSeparation.grid(row=2, column=1, columnspan=2, sticky=W+E)
Label(frmMain, text="Num. contacts:").grid(row=3,column=0,sticky=E)
vContacts = IntVar(win)
vContacts.set(25)
sclContacts = Scale(frmMain, from_=1, to=500, orient=HORIZONTAL, variable=vContacts)
sclContacts.grid(row=3, column=1, columnspan=2, sticky=W+E)
Label(frmMain, text="Use atoms:").grid(row=4,column=0,sticky=E)
catms = sorted(contact_atoms.keys())
lstAtomMappings = Listbox(frmMain, selectmode=MULTIPLE, exportselection=0, height=4)
for n in catms:
lstAtomMappings.insert(END, n)
lstAtomMappings.selection_set(1)
lstAtomMappings.grid(row=4, column=1, columnspan=2, sticky=N+E+S+W)
#### BUTTONS ROW ####
frmButtons = Frame(win)
frmButtons.pack(fill=X, expand=1)
btnCancel = Button(frmButtons, text="Close", command=lambda: win.destroy())
btnCancel.pack(side=RIGHT, pady=PADDING)
def validate():
if not vTarget.get():
tkMessageBox.showwarning("No CASP RR file", "Please specify a valid CASP RR file to visualize!")
return False
if not lstObject.curselection():
tkMessageBox.showwarning("No Mapping Target", "Please specify a molecule to map contacts on!")
return False
if not lstAtomMappings.curselection():
tkMessageBox.showwarning("No Atom Selection", "Please specify at least one set of atoms to map contacts on!")
return False
return True
def confirm():
if not validate(): return
contactFile = vTarget.get()
target, chain = objects[int(lstObject.curselection()[0])]
num_contacts = vContacts.get()
min_separation = vSeparation.get()
#atom_mapping = contact_atoms[ vAtomMappings.get() ]
atom_mapping = [ contact_atoms[catms[int(k)]] for k in lstAtomMappings.curselection() ]
print atom_mapping
show_contacts(contactFile, target, chain, num_contacts, min_separation, atom_mapping)
btnOK = Button(frmButtons, text="Show", command=confirm)
btnOK.pack(side=RIGHT)
browseTarget()
def testLoadVaspCHGCAR(self):
cmd.load(self.datafile("vasp.CHGCAR"), 'vasp.CHGCAR')
self.assertEqual(cmd.get_type('vasp.CHGCAR'), 'object:map')
extend = cmd.get_extent('vasp.CHGCAR')
self.assertArrayEqual(extend, [[0.0, 0.0, 0.0], [6.5, 6.5, 7.7]], delta=1e-2)
def update_object_list(self):
"""
update the internal state list
"""
# purge list of removed objects
pubObj = self.cmd.get_names("public_objects")
object_list_copy = self.object_list.copy()
for x in object_list_copy:
if x not in pubObj:
del self.object_list[x]
# for all VOLUME type objects not known to the list
for x in self.cmd.get_names("public_objects"):
if "object:volume" == cmd.get_type(x):
if x not in self.object_list.keys():
if self.cmd.get_volume_is_updated(x) == 0:
continue
# make a default pair for this volume object
tmpMap = VolumeHist(self.cmd.get_volume_histogram(
x, self.cmd),
nBins=64)
tmpRamp = ColorRamp(360, name=x)
self.object_list[x] = (tmpRamp, tmpMap)
if self.ramp_update.has_key(x) and self.ramp_update[x]:
tmpRamp.addColor(0, (0, 0, 1, 0))
tmpRamp.addColor(359, (0, 0, 1, 0))
for data, alpha, col, kind in self.ramp_update[x]:
self.addWithoutGUINow(x,
data,
alpha,
col,
kind=kind)
self.ramp_update[x] = []
tmpRamp.updateRamp()
self.cmd.volume_color(x, tmpRamp.getRamp())
self.cmd.set_volume_ramp(x, tmpRamp.getRampList())
else:
ramp_list = self.cmd.get_volume_ramp(x, self.cmd)
if ramp_list:
while ramp_list:
tmpRamp.addColor(ramp_list[0],
(ramp_list[1], ramp_list[2],
ramp_list[3], ramp_list[4]))
ramp_list = ramp_list[5:]
else:
tmpRamp.addColor(0, (0, 0, 1, 0))
tmpRamp.addColor(359, (0, 0, 1, 0))
tmpRamp.addColor(200, (0.0, 0.0, 1.0, 0.0))
tmpRamp.addColor(210, (0.0, 0.8, 1.0, 0.2))
tmpRamp.addColor(220, (0.0, 0.0, 1.0, 0.0))
else:
# need to regenerate the histogram
(tmpRamp, tmpMap) = self.object_list[x]
tmpMap = VolumeHist(self.cmd.get_volume_histogram(
x, self.cmd),
nBins=64)
self.object_list[x] = (tmpRamp, tmpMap)
if len(self.object_list.keys()) != 0:
# guaranteed to exist
k = self.object_list.keys()[0]
self.active_ramp, self.active_map = self.object_list[k]
self.active = k
self.update_transferframe()
def apply(self):
cmd=self.cmd
pymol=cmd._pymol
if self.status==1:
# find the name of the object which contains the selection
new_name = None
obj_list = cmd.get_names('objects')
for a in obj_list:
if cmd.get_type(a)=="object:molecule":
if cmd.count_atoms("(%s and %s)"%(a,src_sele)):
new_name = a
break
src_frame = cmd.get_state()
if new_name==None:
print " Mutagenesis: object not found."
else:
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
if self.lib_mode!="current":
# create copy w/o residue
cmd.create(tmp_obj1,"(%s and not %s)"%(new_name,src_sele))
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)"%
(tmp_obj1,src_sele))
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)"%
(tmp_obj1,src_sele))
# save copy for bonded atom reference
cmd.create(tmp_obj3,new_name)
# transfer the selection to copy
cmd.select(src_sele,"(%s in %s)"%(tmp_obj3,src_sele))
# create copy with mutant in correct frame
cmd.create(tmp_obj2,obj_name,src_frame,1)
cmd.set_title(tmp_obj2,1,'')
cmd.delete(new_name)
# create the merged molecule
cmd.create(new_name,"(%s or %s)"%(tmp_obj1,tmp_obj2),1) # only one state in merged object...
# now connect them
cmd.select(mut_sele,"(byres (%s like %s))"%(new_name,src_sele))
# bond N+0 to C-1
if ((cmd.select(tmp_sele1, "(name C and (%s in (neighbor %s)))"%
(new_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "((%s in %s) and n;N)"%
(mut_sele,tmp_obj2)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.set_geometry(tmp_sele1,3,3) # make amide planer
cmd.set_geometry(tmp_sele2,3,3) # make amide planer
# bond C+0 to N+1
if ((cmd.select(tmp_sele1, "(name N and (%s in (neighbor %s)))"%
(new_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"((%s in %s) and n;C)"%
(mut_sele,tmp_obj2)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.set_geometry(tmp_sele1,3,3) # make amide planer
cmd.set_geometry(tmp_sele2,3,3) # make amide planer
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
# fix N-H hydrogen position (if any exists)
cmd.h_fix("(name N and bound_to (%s in %s and n;H))"%(new_name,tmp_obj2))
# now transfer selection back to the modified object
cmd.delete(tmp_obj1)
cmd.delete(tmp_obj2)
cmd.delete(tmp_obj3)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2,obj_name,src_frame,1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)"%
(new_name,src_sele))
cmd.remove("(%s) and name OXT"%src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)"%
(new_name,src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("("+src_sele+")")
# modify the conformation
cmd.update(new_name,tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set('auto_zoom',auto_zoom,quiet=1)