build.rna_tools.tools.PyMOL4RNA.libs.show_contacts.show_contacts()

Complexity

Conditions

30

Size

Total Lines	186
Code Lines	113

Duplication

Lines	0
Ratio	0 %

Importance

Changes

0

#!/usr/bin/python
def show_contacts(selection='*', selection2='*',
                  result="contacts",
                  cutoff=3.6,
                  bigcutoff = 4.0,
                  labels=False,
                  SC_DEBUG = DEBUG):
    """
    USAGE
    
    show_contacts selection, selection2, [result=contacts],[cutoff=3.6],[bigcutoff=4.0]
    
    Show various polar contacts, the good, the bad, and the ugly.
    
    Edit MPB 6-26-14: The distances are heavy atom distances, so I upped the default cutoff to 4.0
    
    Returns:
    True/False -  if False, something went wrong
    """
    if SC_DEBUG > 4:
        print('Starting show_contacts')
        print('selection = "' + selection + '"')
        print('selection2 = "' + selection2 + '"')
            
    result = cmd.get_legal_name(result)

    #if the group of contacts already exist, delete them
    cmd.delete(result)

    # ensure only N and O atoms are in the selection
    all_don_acc1 = selection + " and (donor or acceptor)"
    all_don_acc2 = selection2 + " and  (donor or acceptor)"
    
    if SC_DEBUG > 4:
        print('all_don_acc1 = "' + all_don_acc1 + '"')
        print('all_don_acc2 = "' + all_don_acc2 + '"')
    
    #if theses selections turn out not to have any atoms in them, pymol throws cryptic errors when calling the dist function like:
    #'Selector-Error: Invalid selection name'
    #So for each one, manually perform the selection and then pass the reference to the distance command and at the end, clean up the selections
    #the return values are the count of the number of atoms
    all1_sele_count = cmd.select('all_don_acc1_sele', all_don_acc1)
    all2_sele_count = cmd.select('all_don_acc2_sele', all_don_acc2)
    
    #print out some warnings
    if DEBUG > 3:
        if not all1_sele_count:
            print('Warning: all_don_acc1 selection empty!')
        if not all2_sele_count:
            print('Warning: all_don_acc2 selection empty!')
    
    ########################################
    allres = result + "_all"
    if all1_sele_count and all2_sele_count:
        #print(allres)
        #print(cmd.get_distance(allres, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 0))
        any = cmd.distance(allres, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 0)
        # if any is 0 it seems that there is no distance!
        if any:
            cmd.set("dash_radius", "0.05", allres)
            if not labels:
                cmd.hide("labels", allres)
        else:
            # just do nothing and clena up
            print('no contacts')
            cmd.delete('all_don_acc1_sele')
            cmd.delete('all_don_acc2_sele')
            cmd.delete(result + "_all")
            return None
    ########################################
    # compute good polar interactions according to pymol
    polres = result + "_polar"
    if all1_sele_count and all2_sele_count:
        cmd.distance(polres, 'all_don_acc1_sele', 'all_don_acc2_sele', cutoff, mode = 2) #hopefully this checks angles? Yes
        #cmd.set("dash_color", "marine", allres)
        #cmd.set('dash_gap', '0')
        cmd.set("dash_radius","0.2", polres) #"0.126"
        #cmd.set("dash_color", "marine", allres)
        if not labels:
            cmd.hide("labels", polres)
    
    ########################################
    # When running distance in mode=2, the cutoff parameter is ignored if set higher then the default of 3.6
    # so set it to the passed in cutoff and change it back when you are done.
    old_h_bond_cutoff_center = cmd.get('h_bond_cutoff_center') # ideal geometry
    old_h_bond_cutoff_edge = cmd.get('h_bond_cutoff_edge') # minimally acceptable geometry
    cmd.set('h_bond_cutoff_center', bigcutoff)
    cmd.set('h_bond_cutoff_edge', bigcutoff)
        
    # compute possibly suboptimal polar interactions using the user specified distance
    pol_ok_res = result + "_polar_ok"
    if all1_sele_count and all2_sele_count:
        cmd.distance(pol_ok_res, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 2) 
        cmd.set("dash_radius", "0.06", pol_ok_res)
        if not labels:
            cmd.hide("labels", pol_ok_res)

    #now reset the h_bond cutoffs
    cmd.set('h_bond_cutoff_center', old_h_bond_cutoff_center)
    cmd.set('h_bond_cutoff_edge', old_h_bond_cutoff_edge) 
    
    
    ########################################
    
    onlyacceptors1 = selection + " and (acceptor and !donor)"
    onlyacceptors2 = selection2 + " and (acceptor and !donor)"
    onlydonors1 = selection + " and (!acceptor and donor)"
    onlydonors2 = selection2 + " and (!acceptor and donor)"  
    
    #perform the selections
    onlyacceptors1_sele_count = cmd.select('onlyacceptors1_sele', onlyacceptors1)
    onlyacceptors2_sele_count = cmd.select('onlyacceptors2_sele', onlyacceptors2)
    onlydonors1_sele_count = cmd.select('onlydonors1_sele', onlydonors1)
    onlydonors2_sele_count = cmd.select('onlydonors2_sele', onlydonors2)    
    
    #print out some warnings
    if SC_DEBUG > 2:
        if not onlyacceptors1_sele_count:
            print('Warning: onlyacceptors1 selection empty!')
        if not onlyacceptors2_sele_count:
            print('Warning: onlyacceptors2 selection empty!')
        if not onlydonors1_sele_count:
            print('Warning: onlydonors1 selection empty!')
        if not onlydonors2_sele_count:
            print('Warning: onlydonors2 selection empty!')    
            
    # acceptors  acceptors
    accres = result+"_aa"
    if onlyacceptors1_sele_count and onlyacceptors2_sele_count:
        aa_dist_out = cmd.distance(accres, 'onlyacceptors1_sele', 'onlyacceptors2_sele', cutoff, 0)
        if aa_dist_out < 0:
            print('\n\nCaught a pymol selection error in acceptor-acceptor selection of show_contacts')
            print('accres:', accres)
            print('onlyacceptors1', onlyacceptors1)
            print('onlyacceptors2', onlyacceptors2)
            return False
        cmd.set("dash_color","red",accres)
        cmd.set("dash_radius","0.125",accres)
        if not labels:
            cmd.hide("labels", accres)
    
    ########################################
    # donors donors
    donres = result+"_dd"
    if onlydonors1_sele_count and onlydonors2_sele_count:
        dd_dist_out = cmd.distance(donres, 'onlydonors1_sele', 'onlydonors2_sele', cutoff, 0)
        
        #try to catch the error state 
        if dd_dist_out < 0:
            print('\n\nCaught a pymol selection error in dd selection of show_contacts')
            print('donres:', donres)
            print('onlydonors1', onlydonors1)
            print('onlydonors2', onlydonors2)
            print("cmd.distance('" + donres + "', '" + onlydonors1 + "', '" + onlydonors2 + "', " + str(cutoff) + ", 0)")  
            return False
        
        cmd.set("dash_color","red",donres)  
        cmd.set("dash_radius","0.125",donres)
        if not labels:
            cmd.hide("labels", donres)
    
    ##########################################################
    ##### find the buried unpaired atoms of the receptor #####
    ##########################################################
    
    #initialize the variable for when CALC_SASA is False
    unpaired_atoms = ''

    ## Group
    print(allres) # contacts_all
    cmd.group(result,"%s %s %s %s %s %s" % (polres, allres, accres, donres, pol_ok_res, unpaired_atoms))
    
    ## Clean up the selection objects
    #if the show_contacts debug level is high enough, don't delete them.
    if SC_DEBUG < 5:
        cmd.delete('all_don_acc1_sele')
        cmd.delete('all_don_acc2_sele')
        cmd.delete('onlyacceptors1_sele')
        cmd.delete('onlyacceptors2_sele')
        cmd.delete('onlydonors1_sele')
        cmd.delete('onlydonors2_sele')
    
    cmd.disable('contacts_all')
    cmd.disable('contacts_polar_ok')
    cmd.disable('contacts_aa')
    cmd.disable('contacts_dd')    
    return True