Exemple #1
0
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))
Exemple #2
0
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))
Exemple #3
0
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)
Exemple #4
0
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)