Refactor 3Di functionality

src/biotite/structure/alphabet/__init__.py

@@ -3,37 +3,10 @@
 # information.
 
 """
-NumPy port of the ``foldseek`` code for encoding structures to 3di.
+A subpackage for converting structures to structural alphabet sequences.
 """
 
 __name__ = "biotite.structure.alphabet"
-__author__ = "Martin Larralde"
-__all__ = ["Encoder", "StructureSequence", "to_3di"]
+__author__ = "Martin Larralde, Patrick Kunzmann"
 
-from .encoder import Encoder
-from .sequence import StructureSequence
-
-def to_3di(array):
-    r"""
-    Encode the atoms to the 3di structure alphabet.
-
-    Parameters
-    ----------
-    atoms : AtomArray
-        The atom array to encode to 3di. All atoms must be part of
-        a single chain.
-
-    Returns
-    -------
-    sequence : StructureSequence
-        The encoded structure sequence.
-
-    Note
-    ----
-    To encode atoms in different chains, use :func:`apply_chain_wise` to
-    return a list with one sequence per chain.
-    """
-    encoder = Encoder()
-    sequence = StructureSequence()
-    sequence.code = encoder.encode_atoms(array).filled()
-    return sequence
+from .i3d import *