| Methods |  | 
        
        |  | 
            |  | __init__ | 
        
        | 
__init__ ( self,  structure=None )
 | 
            |  | cleanup | 
        
        | 
cleanup ( self )
 | 
            |  | compensate_for_forced_charges | 
        
        | 
compensate_for_forced_charges ( self )
 if there were foced charges and they the molecule should not have any charge,
    we have to take care of it here | 
            |  | deal_with_da_bonds | 
        
        | 
deal_with_da_bonds ( self )
 deal with donor-acceptor bonds, this fixes mostly boron containing compounds | 
            |  | get_layer | 
        
        | 
get_layer ( self,  prefix )
 | 
            |  | get_number_of_hydrogens_in_hydrogen_layer | 
        
        | 
get_number_of_hydrogens_in_hydrogen_layer ( self )
 
        
            | Exceptions |  |  
        | oasa_not_implemented_error( "INChI", "multiple compound systems are not supported by the library" ) 
 |  | 
            |  | get_structure | 
        
        | 
get_structure ( self )
 | 
            |  | process_forced_charges | 
        
        | 
process_forced_charges ( self )
 this marks the charges that are forced by the connectivity and thus helps
    process zwitrions | 
            |  | read_charge_layer | 
        
        | 
read_charge_layer ( self )
 
        
            | Exceptions |  |  
        | oasa_exceptions.oasa_inchi_error( "The molecular charge could not be allocated to any atom (%d)." % charge ) 
 |  | 
            |  | read_connectivity_layer | 
        
        | 
read_connectivity_layer ( self )
 
        
            | Exceptions |  |  
        | ValueError, "unexpected character %s in the connectivity layer" % c 
 |  | 
            |  | read_hydrogen_layer | 
        
        | 
read_hydrogen_layer ( self,  run=0 )
 | 
            |  | read_inchi | 
        
        | 
read_inchi ( self,  text )
 
        
            | Exceptions |  |  
        | oasa_inchi_error( "Localization of bonds, charges or movable hydrogens failed" ) 
 |  | 
            |  | read_p_layer | 
        
        | 
read_p_layer ( self )
 | 
            |  | read_sum_layer | 
        
        | 
read_sum_layer ( self )
 
        
            | Exceptions |  |  
        | oasa_not_implemented_error( "INChI", "multiple compound systems are not supported by the library" ) 
 |  | 
            |  | set_structure | 
        
        | 
set_structure ( self,  structure )
 | 
            |  | split_layers | 
        
        | 
split_layers ( self,  text )
 
        
            | Exceptions |  |  
        | "no '%s' tag found in xml string" % name "no structures found in xml string %s" % text
 
 |  |