Methods
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__init__
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__init__ ( self, vertices=[] )
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__str__
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__str__ ( self )
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_get_atom_distance_matrix
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_get_atom_distance_matrix ( self, a )
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_get_atoms_possible_aromatic_electrons
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_get_atoms_possible_aromatic_electrons (
self,
at,
ring,
)
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_read_file
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_read_file ( self, name="/home/beda/oasa/oasa/mol.graph" )
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add_missing_bond_orders
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add_missing_bond_orders ( self )
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add_missing_hydrogens
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add_missing_hydrogens ( self )
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create_graph
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create_graph ( self )
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find_longest_mostly_carbon_chain
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find_longest_mostly_carbon_chain ( self )
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get_symmetry_unique_atoms
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get_symmetry_unique_atoms ( self )
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localize_aromatic_bonds
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localize_aromatic_bonds ( self )
localizes aromatic bonds (does not relocalize already localized ones),
for those that are not aromatic but marked so
(it is for instance possible to misuse cccc in smiles to create butadiene)
they will be properly localized but marked as non-aromatic
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localize_fake_aromatic_bonds
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localize_fake_aromatic_bonds ( self )
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mark_aromatic_bonds
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mark_aromatic_bonds ( self )
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number_atoms_uniquely
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number_atoms_uniquely ( self )
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remove_all_hydrogens
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remove_all_hydrogens ( self )
removes all H atoms
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