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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add_missing_bond_orders
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add_missing_bond_orders ( self, retry=False )
retry means to try a different approach because the last one was not successful
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add_missing_hydrogens
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add_missing_hydrogens ( self )
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clean_after_search
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clean_after_search ( self, other )
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create_edge
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create_edge ( self )
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create_graph
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create_graph ( self )
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create_vertex
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create_vertex ( self, vertex_class=None )
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find_longest_mostly_carbon_chain
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find_longest_mostly_carbon_chain ( self )
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get_mean_bond_length
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get_mean_bond_length ( self )
returns the mean bond length of bonds in the molecule
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get_mol_weight
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get_mol_weight ( 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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mark_morgan
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mark_morgan ( self )
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normalize_bond_length
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normalize_bond_length ( self, bond_length=30 )
make the average bond-length be bond_length by scaling the structure up
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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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select_matching_substructures
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select_matching_substructures (
self,
other,
implicit_freesites=False,
auto_cleanup=True,
)
select fragments that match the complete molecule other and yield them
as lists of atoms in the order of other.vertices; however when other has
explicit hydrogens that match implicit hydrogens on self the length of the
returned fragment might be shorter of the matched implicit hydrogens; IF YOU DON'T LET THE GENERATOR RUN TO THE END OR SET THE auto_cleanup TO FALSE, YOU HAVE TO
RUN clean_after_search MANUALLY NOT TO CLUTTER THE STRUCTURE
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