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