Methods
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__init__
apply_gen_to_atoms
calculate_coords
process_all_anelated_rings
process_atom_neigbors
process_one_anelated_ring
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__init__
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__init__ ( self, bond_length=1 )
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apply_gen_to_atoms
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apply_gen_to_atoms (
self,
gen,
atoms,
start,
bond_length=None,
)
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calculate_coords
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calculate_coords (
self,
mol,
bond_length=0,
force=0,
)
the bond_length (when given) sets the self.bond_length,
if bond_length == -1 we suppose that there is already part of the molecule containing
coords and we calculate the bond_length from it;
force says if we should recalc all coords
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process_all_anelated_rings
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process_all_anelated_rings ( self, base )
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process_atom_neigbors
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process_atom_neigbors ( self, v )
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process_one_anelated_ring
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process_one_anelated_ring ( self, base )
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