| Methods |  | 
        
        |  | 
            |  | __init__ | 
        
        | 
__init__ ( self,  structure=None )
 | 
            |  | cleanup | 
        
        | 
cleanup ( self )
 | 
            |  | 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 | 
            |  | put_it_all_together | 
        
        | 
put_it_all_together ( self )
 | 
            |  | read_charge_layer | 
        
        | 
read_charge_layer ( self )
 | 
            |  | read_connectivity_layer | 
        
        | 
read_connectivity_layer ( self )
 | 
            |  | read_hydrogen_layer | 
        
        | 
read_hydrogen_layer ( self,  run=0 )
 | 
            |  | read_inchi | 
        
        | 
read_inchi ( self,  text )
 
        
            | Exceptions |  |  
        | ValueError, "this version of INChI is not supported - %s" % self.layers [ 0 ] 
 |  | 
            |  | read_protonation_layer | 
        
        | 
read_protonation_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
 
 |  |