def pickAtoms(ignoreDensity=False):
"""Prompt the user to pick two atoms to rotamerize a stretch of nucleotides. Alternatively, if
we're already waiting for the user to pick atoms, then cancel the pending picks.
ARGUMENTS:
None
OPTIONAL ARGUMENTS:
ignoreDensity - ignore the density when performing the minimization
defaults to False
RETURNS:
None
"""
#create the citation pop-up if necessary
createCitationPopup()
global waitingForClicks
#make sure that we're not waiting on a pending extendChain call
extendChain.clearPendingExtendChain()
if waitingForClicks:
#if we're already in the middle of a rotamerize call, then cancel the pending rotamerize
print "Rotamerize cancelled"
add_status_bar_text("Rotamerize cancelled")
clear_pending_picks(
) #tell Coot to stop waiting for the user to click on atoms
__setMenuToRotamerize()
waitingForClicks = False
else:
#if we're not in the middle of a rotamerize call, then start one
#make sure that there is a refinement map set
if not ignoreDensity and imol_refinement_map() == -1:
print "No refinement map set for RCrane rotamerize"
selectMapDialog(pickAtoms)
return
print "Click on 2 atoms (in the same molecule)"
add_status_bar_text(
"Pick 2 atoms [Ctrl Left-mouse rotates the view]...")
__setMenuToCancel()
waitingForClicks = True
user_defined_click(
2, lambda atomSpec1, atomSpec2: rotamerizeFromAtomSpecs(
atomSpec1, atomSpec2, ignoreDensity))
def pickAtoms(ignoreDensity = False):
"""Prompt the user to pick two atoms to rotamerize a stretch of nucleotides. Alternatively, if
we're already waiting for the user to pick atoms, then cancel the pending picks.
ARGUMENTS:
None
OPTIONAL ARGUMENTS:
ignoreDensity - ignore the density when performing the minimization
defaults to False
RETURNS:
None
"""
#create the citation pop-up if necessary
createCitationPopup()
global waitingForClicks
#make sure that we're not waiting on a pending extendChain call
extendChain.clearPendingExtendChain()
if waitingForClicks:
#if we're already in the middle of a rotamerize call, then cancel the pending rotamerize
print "Rotamerize cancelled"
add_status_bar_text("Rotamerize cancelled")
clear_pending_picks() #tell Coot to stop waiting for the user to click on atoms
__setMenuToRotamerize()
waitingForClicks = False
else:
#if we're not in the middle of a rotamerize call, then start one
#make sure that there is a refinement map set
if not ignoreDensity and imol_refinement_map() == -1:
print "No refinement map set for RCrane rotamerize"
selectMapDialog(pickAtoms)
return
print "Click on 2 atoms (in the same molecule)"
add_status_bar_text("Pick 2 atoms [Ctrl Left-mouse rotates the view]...")
__setMenuToCancel()
waitingForClicks = True
user_defined_click(2, lambda atomSpec1, atomSpec2: rotamerizeFromAtomSpecs(atomSpec1, atomSpec2, ignoreDensity))
def pickAtoms():
"""Prompt the user to pick an atoms to extend a stretch of nucleotides. Alternatively, if
we're already waiting for the user to pick an atom, then cancel the pending pick.
ARGUMENTS:
None
RETURNS:
None
"""
#create the citation pop-up if necessary
createCitationPopup()
#make sure that we're not waiting on a pending rotamerize call
rotamerize.clearPendingRotamerize()
global waitingForClicks
if waitingForClicks:
#if we're already in the middle of an extend chain call, then cancel the pending call
print "Rotamerize cancelled"
add_status_bar_text("Extend chain cancelled")
clear_pending_picks(
) #tell Coot to stop waiting for the user to click on atoms
__setMenuToExtendChain()
waitingForClicks = False
else:
#if we're not in the middle of a extend chain call, then start one
#make sure that there is a refinement map set
if imol_refinement_map() == -1:
print "No refinement map set for RCrane extend chain"
selectMapDialog(pickAtoms)
return
print "Click on a nucleotide to extend"
add_status_bar_text(
"Pick a nucleotide [Ctrl Left-mouse rotates the view]...")
__setMenuToCancel()
waitingForClicks = True
user_defined_click(1, extendChainFromAtomSpec)
def pickAtoms():
"""Prompt the user to pick an atoms to extend a stretch of nucleotides. Alternatively, if
we're already waiting for the user to pick an atom, then cancel the pending pick.
ARGUMENTS:
None
RETURNS:
None
"""
#create the citation pop-up if necessary
createCitationPopup()
#make sure that we're not waiting on a pending rotamerize call
rotamerize.clearPendingRotamerize()
global waitingForClicks
if waitingForClicks:
#if we're already in the middle of an extend chain call, then cancel the pending call
print "Rotamerize cancelled"
add_status_bar_text("Extend chain cancelled")
clear_pending_picks() #tell Coot to stop waiting for the user to click on atoms
__setMenuToExtendChain()
waitingForClicks = False
else:
#if we're not in the middle of a extend chain call, then start one
#make sure that there is a refinement map set
if imol_refinement_map() == -1:
print "No refinement map set for RCrane extend chain"
selectMapDialog(pickAtoms)
return
print "Click on a nucleotide to extend"
add_status_bar_text("Pick a nucleotide [Ctrl Left-mouse rotates the view]...")
__setMenuToCancel()
waitingForClicks = True
user_defined_click(1, extendChainFromAtomSpec)
def selectMapDialog(callback=None):
"""Display a GUI for selecting the refinement map.
OPTIONAL ARGUMENTS:
callback - a function to call when the user clicks OK
RETURNS:
None
"""
# create a list of map molecules and their names
mapList = []
for imol in xrange(graphics_n_molecules()):
if is_valid_map_molecule(imol):
mapList.append(imol)
# if we have no maps, then display an error and don't invoke the callback
if len(mapList) == 0:
warningMessage = gtk.MessageDialog(
type=gtk.MESSAGE_ERROR, buttons=gtk.BUTTONS_OK, message_format="Please load a map before using RCrane."
)
warningMessage.set_title("RCrane Error")
warningMessage.run()
warningMessage.destroy()
else:
# if we have one or more maps
dialog = gtk.Dialog(title="Select Map for Fitting", buttons=(gtk.STOCK_OK, gtk.RESPONSE_OK))
# create a combo box that lists maps
mapListStore = gtk.ListStore(int, str)
for imol in mapList:
mapListStore.append([imol, str(imol) + " " + molecule_name(imol)])
mapCombo = gtk.ComboBox(mapListStore)
mapRender = gtk.CellRendererText()
mapCombo.pack_start(mapRender, True)
mapCombo.add_attribute(mapRender, "text", 1)
# select the current refinemnt map, or the first map if no map has been selected
currentMap = imol_refinement_map()
if currentMap == -1:
set_imol_refinement_map(mapListStore[0][0])
mapCombo.set_active(0)
else:
# figure out which combobox row corresponds to the currently selected map
comboIndex = [i[0] for i in mapListStore].index(currentMap)
mapCombo.set_active(comboIndex)
# connect the changed signal for the combobox
mapCombo.connect("changed", __changeMap)
# add the label and frame
chooseLabel = gtk.Label("Choose a Map:")
frame = gtk.Frame()
frameBox = gtk.VBox(False, 0)
frame.add(frameBox)
frameBox.pack_start(chooseLabel, False, False, 2)
frameBox.pack_start(mapCombo, False, False, 2)
# pack things into the top area of the dialog box
dialog.vbox.pack_start(frame, False, False, 2)
dialog.vbox.show_all()
# connect the callback function
if callback is not None:
# if there is a callback function and the user clicks OK, then call the callback
# if the user clicks the close button, then don't call the callback
def checkResponse(dialog, responseID, callback):
if responseID == gtk.RESPONSE_OK:
callback()
dialog.connect("response", checkResponse, callback)
# create the dialog box
dialog.run()
dialog.destroy()
def selectMapDialog(callback=None):
"""Display a GUI for selecting the refinement map.
OPTIONAL ARGUMENTS:
callback - a function to call when the user clicks OK
RETURNS:
None
"""
#create a list of map molecules and their names
mapList = []
for imol in xrange(graphics_n_molecules()):
if is_valid_map_molecule(imol):
mapList.append(imol)
#if we have no maps, then display an error and don't invoke the callback
if len(mapList) == 0:
warningMessage = gtk.MessageDialog(
type=gtk.MESSAGE_ERROR,
buttons=gtk.BUTTONS_OK,
message_format="Please load a map before using RCrane.")
warningMessage.set_title("RCrane Error")
warningMessage.run()
warningMessage.destroy()
else:
#if we have one or more maps
dialog = gtk.Dialog(title="Select Map for Fitting",
buttons=(gtk.STOCK_OK, gtk.RESPONSE_OK))
#create a combo box that lists maps
mapListStore = gtk.ListStore(int, str)
for imol in mapList:
mapListStore.append([imol, str(imol) + " " + molecule_name(imol)])
mapCombo = gtk.ComboBox(mapListStore)
mapRender = gtk.CellRendererText()
mapCombo.pack_start(mapRender, True)
mapCombo.add_attribute(mapRender, 'text', 1)
#select the current refinemnt map, or the first map if no map has been selected
currentMap = imol_refinement_map()
if currentMap == -1:
set_imol_refinement_map(mapListStore[0][0])
mapCombo.set_active(0)
else:
#figure out which combobox row corresponds to the currently selected map
comboIndex = [i[0] for i in mapListStore].index(currentMap)
mapCombo.set_active(comboIndex)
#connect the changed signal for the combobox
mapCombo.connect("changed", __changeMap)
#add the label and frame
chooseLabel = gtk.Label("Choose a Map:")
frame = gtk.Frame()
frameBox = gtk.VBox(False, 0)
frame.add(frameBox)
frameBox.pack_start(chooseLabel, False, False, 2)
frameBox.pack_start(mapCombo, False, False, 2)
#pack things into the top area of the dialog box
dialog.vbox.pack_start(frame, False, False, 2)
dialog.vbox.show_all()
#connect the callback function
if callback is not None:
#if there is a callback function and the user clicks OK, then call the callback
#if the user clicks the close button, then don't call the callback
def checkResponse(dialog, responseID, callback):
if responseID == gtk.RESPONSE_OK: callback()
dialog.connect("response", checkResponse, callback)
#create the dialog box
dialog.run()
dialog.destroy()
