def storeMenuItem(menuItem, resetLabel=False, ignoreDensity=False):
"""Store the "Rotamerize existing structure..." and "Rotamerize without density..." menu entries so that we can later change them to "Cancel current rotamerize..."
ARGUMENTS:
menuItem - the gtk MenuItem to store
OPTIONAL ARGUMENTS:
resetLabel - whether we should reset the menu label to "Rotamerize existing structure..."
(and also clear all pending atom picks in Coot)
This is intended for use when we're reloading RCrane
Defaults to False
ignoreDensity - whether this is the menu entry for "Rotamerize without density..."
RETURNS:
None
EFFECTS:
stores menuItem in the module-level variable __menuItem
"""
if ignoreDensity:
global __menuItemNoDensity
__menuItemNoDensity = menuItem
else:
global __menuItem
__menuItem = menuItem
#if we're being called during an RCrane reload, then reset everything back to the appropriate starting position
global waitingForClicks
if resetLabel:
waitingForClicks = False #this is redundant with module initialization, but can't hurt to do
#in case this function is called in an unexpected way
__setMenuToRotamerize()
clear_pending_picks()
def storeMenuItem(menuItem, resetLabel = False, ignoreDensity = False):
"""Store the "Rotamerize existing structure..." and "Rotamerize without density..." menu entries so that we can later change them to "Cancel current rotamerize..."
ARGUMENTS:
menuItem - the gtk MenuItem to store
OPTIONAL ARGUMENTS:
resetLabel - whether we should reset the menu label to "Rotamerize existing structure..."
(and also clear all pending atom picks in Coot)
This is intended for use when we're reloading RCrane
Defaults to False
ignoreDensity - whether this is the menu entry for "Rotamerize without density..."
RETURNS:
None
EFFECTS:
stores menuItem in the module-level variable __menuItem
"""
if ignoreDensity:
global __menuItemNoDensity
__menuItemNoDensity = menuItem
else:
global __menuItem
__menuItem = menuItem
#if we're being called during an RCrane reload, then reset everything back to the appropriate starting position
global waitingForClicks
if resetLabel:
waitingForClicks = False #this is redundant with module initialization, but can't hurt to do
#in case this function is called in an unexpected way
__setMenuToRotamerize()
clear_pending_picks()
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 clearPendingExtendChain():
"""Cancel any pending extend chain call (intended to be called by rotamerize)
ARGUMENTS:
None
RETURNS:
True if there was a pending extend chain call
False otherwise
"""
global waitingForClicks
if waitingForClicks:
#if we're already in the middle of a extend chain call, then cancel the pending extend chain
print "Extend chain cancelled"
clear_pending_picks() #tell Coot to stop waiting for the user to click on atoms
__setMenuToExtendChain()
waitingForClicks = False
return True
else:
return False
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 clearPendingRotamerize():
"""Cancel any pending rotamerize call (intended to be called by extendChain)
ARGUMENTS:
None
RETURNS:
True if there was a pending rotamerize call
False otherwise
"""
global waitingForClicks
if waitingForClicks:
#if we're already in the middle of a rotamerize call, then cancel the pending rotamerize
print "Rotamerize cancelled"
clear_pending_picks(
) #tell Coot to stop waiting for the user to click on atoms
__setMenuToRotamerize()
waitingForClicks = False
return True
else:
return False
def storeMenuItem(menuItem, resetLabel = False):
"""ARGUMENTS:
menuItem - the gtk MenuItem to store
OPTIONAL ARGUMENTS:
resetLabel - whether we should reset the menu label to "Extend chain..."
(and also clear all pending atom picks in Coot)
This is intended for use when we're reloading RCrane
Defaults to False
RETURNS:
None
EFFECTS:
stores menuItem in the module-level variable __menuItem
"""
global __menuItem
__menuItem = menuItem
#if we're being called during an RCrane reload, then reset everything back to the appropriate starting position
global waitingForClicks
if resetLabel:
waitingForClicks = False #this is redundant with module initialization, but can't hurt to do
#in case this function is called in an unexpected way
__setMenuToExtendChain()
clear_pending_picks()
def storeMenuItem(menuItem, resetLabel=False):
"""ARGUMENTS:
menuItem - the gtk MenuItem to store
OPTIONAL ARGUMENTS:
resetLabel - whether we should reset the menu label to "Extend chain..."
(and also clear all pending atom picks in Coot)
This is intended for use when we're reloading RCrane
Defaults to False
RETURNS:
None
EFFECTS:
stores menuItem in the module-level variable __menuItem
"""
global __menuItem
__menuItem = menuItem
#if we're being called during an RCrane reload, then reset everything back to the appropriate starting position
global waitingForClicks
if resetLabel:
waitingForClicks = False #this is redundant with module initialization, but can't hurt to do
#in case this function is called in an unexpected way
__setMenuToExtendChain()
clear_pending_picks()