| Methods |  | 
        
        |  | 
            |  | __init__ | 
        
        | 
__init__ (
        self,
        standard=None,
        xy=(),
        package=None,
        molecule=None,
        )
 | 
            |  | __str__ | 
        
        | 
__str__ ( self )
 | 
            |  | after_undo | 
        
        | 
after_undo ( self )
 this is run after undo | 
            |  | bbox | 
        
        | 
bbox ( self )
 returns the bounding box of the object as a list of [x1,y1,x2,y2] | 
            |  | decide_pos | 
        
        | 
decide_pos ( self )
 | 
            |  | draw | 
        
        | 
draw ( self,  redraw=False )
 draws atom with respect to its properties | 
            |  | focus | 
        
        | 
focus ( self )
 | 
            |  | generate_marks_from_cheminfo | 
        
        | 
generate_marks_from_cheminfo ( self )
 | 
            |  | get_charge_from_marks | 
        
        | 
get_charge_from_marks ( self )
 | 
            |  | get_formula_dict | 
        
        | 
get_formula_dict ( self )
 returns formula as dictionary that can
    be passed to functions in periodic_table | 
            |  | get_package | 
        
        | 
get_package ( self,  doc )
 returns a DOM element describing the object in CDML,
    doc is the parent document which is used for element creation
    (the returned element is not inserted into the document) | 
            |  | read_package | 
        
        | 
read_package ( self,  package )
 reads the dom element package and sets internal state according to it | 
            |  | select | 
        
        | 
select ( self )
 | 
            |  | set_name | 
        
        | 
set_name (
        self,
        name,
        interpret=1,
        check_valency=1,
        occupied_valency=None,
        )
 | 
            |  | set_valency_from_name | 
        
        | 
set_valency_from_name ( self )
 | 
            |  | split_element_and_charge | 
        
        | 
split_element_and_charge ( self,  txt )
 returns tuple of (element, charge) or None if the text does not match this pattern | 
            |  | unfocus | 
        
        | 
unfocus ( self )
 | 
            |  | unselect | 
        
        | 
unselect ( self )
 | 
            |  | update_after_valency_change | 
        
        | 
update_after_valency_change ( self )
 |