biotite 0.38.0__cp311-cp311-macosx_11_0_arm64.whl → 0.40.0__cp311-cp311-macosx_11_0_arm64.whl

biotite/structure/io/mmtf/file.py

@@ -12,6 +12,7 @@ import struct
 import copy
 import numpy as np
 import msgpack
+import warnings
 from ....file import File, is_binary, is_open_compatible
 from ...error import BadStructureError
 from .decode import decode_array
@@ -21,7 +22,7 @@ from .encode import encode_array
 class MMTFFile(File, MutableMapping):
     """
     This class represents a MMTF file.
-    
+
     When reading a file, the *MessagePack* unpacker is used to create
     a dictionary of the file content.
     This dictionary is accessed by indexing the :class:`MMTFFile`
@@ -29,10 +30,13 @@ class MMTFFile(File, MutableMapping):
     If the dictionary value is an encoded array, the value automatically
     decoded.
     Decoded arrays are always returned as :class:`ndarray` instances.
-    
+
+    DEPRECATED: Use :class:`biotite.structure.io.pdbx.BinaryCIFFile`
+    instead.
+
     Examples
     --------
-    
+
     >>> import os.path
     >>> mmtf_file = MMTFFile.read(os.path.join(path_to_structures, "1l2y.mmtf"))
     >>> print(mmtf_file["title"])
@@ -42,24 +46,28 @@ class MMTFFile(File, MutableMapping):
      'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A'
      'A' 'A']
     """
-    
+
     def __init__(self):
+        warnings.warn(
+            "'MMTFFile' is deprecated, use 'BinaryCIFFile' instead",
+            DeprecationWarning
+        )
         super().__init__()
         self._content = {}
         self._content["mmtfVersion"] = "1.0.0"
         self._content["mmtfProducer"] = "UNKNOWN"
-    
+
     @classmethod
     def read(self, file):
         """
         Read a MMTF file.
-        
+
         Parameters
         ----------
         file : file-like object or str
             The file to be read.
             Alternatively a file path can be supplied.
-        
+
         Returns
         -------
         file_object : MMTFFile
@@ -80,11 +88,11 @@ class MMTFFile(File, MutableMapping):
                 file.read(), use_list=True, raw=False
             )
         return mmtf_file
-    
+
     def write(self, file):
         """
         Write contents into a MMTF file.
-        
+
         Parameters
         ----------
         file : file-like object or str
@@ -101,20 +109,20 @@ class MMTFFile(File, MutableMapping):
             if not is_binary(file):
                 raise TypeError("A file opened in 'binary' mode is required")
             file.write(packed_bytes)
-    
+
     def __copy_fill__(self, clone):
         super().__copy_fill__(clone)
         clone._content = copy.deepcopy(self._content)
-    
+
     def get_codec(self, key):
         """
         Obtain the codec ID of an MMTF encoded value.
-        
+
         Parameters
         ----------
         key : str
             The key for the potentially encoded value.
-        
+
         Returns
         -------
         codec : int or None
@@ -126,16 +134,16 @@ class MMTFFile(File, MutableMapping):
             return codec
         else:
             return None
-    
+
     def get_length(self, key):
         """
         Obtain the length of an MMTF encoded value.
-        
+
         Parameters
         ----------
         key : str
             The key for the potentially encoded value.
-        
+
         Returns
         -------
         codec : int or None
@@ -148,16 +156,16 @@ class MMTFFile(File, MutableMapping):
             return length
         else:
             return None
-    
+
     def get_param(self, key):
         """
         Obtain the parameter of an MMTF encoded value.
-        
+
         Parameters
         ----------
         key : str
             The key for the potentially encoded value.
-        
+
         Returns
         -------
         codec : int or None
@@ -170,7 +178,7 @@ class MMTFFile(File, MutableMapping):
             return param
         else:
             return None
-    
+
     def set_array(self, key, array, codec, param=0):
         length = len(array)
         raw_bytes = encode_array(array, codec, param)
@@ -179,7 +187,7 @@ class MMTFFile(File, MutableMapping):
              + struct.pack(">i", param) \
              + raw_bytes
         self._content[key] = data
-    
+
     def __getitem__(self, key):
         data = self._content[key]
         if isinstance(data, bytes) and data[0] == 0:
@@ -191,22 +199,22 @@ class MMTFFile(File, MutableMapping):
             return decode_array(codec, raw_bytes, param)
         else:
             return data
-    
+
     def __setitem__(self, key, item):
         if isinstance(item, np.ndarray):
             raise TypeError("Arrays that need to be encoded must be addeed "
                             "via 'set_array()'")
         self._content[key] = item
-    
+
     def __delitem__(self, key):
         del self._content[key]
-    
+
     def __iter__(self):
         return self._content.__iter__()
-    
+
     def __len__(self):
         return len(self._content)
-    
+
     def __contains__(self, item):
         return item in self._content
 

biotite/structure/io/npz/__init__.py

@@ -9,6 +9,9 @@ format is used to store `NumPy` arrays. Since atom arrays and stacks are
 completely built on `NumPy` arrays, this format is preferable for
 Biotite internal usage due to fast I/O operations and preservation
 of all atom annotation arrays.
+
+DEPRECATED: Pickle data directly or use
+:class:`biotite.structure.io.pdbx.BinaryCIFFile` instead.
 """
 
 __name__ = "biotite.structure.io.npz"

biotite/structure/io/npz/file.py

@@ -15,19 +15,22 @@ from ....file import File, is_binary
 class NpzFile(File):
     r"""
     This class represents a NPZ file, the preferable format for
-    Biotite internal structure storage. 
-    
+    Biotite internal structure storage.
+
     Internally the this class writes/reads all attribute arrays of an
     :class:`AtomArray` or :class:`AtomArrayStack` using the *NumPy*
     :func:`save()`/:func:`load()`
     method. This format offers the fastest I/O operations and completely
     preserves the content all atom annotation arrays.
-    
+
+    DEPRECATED: Pickle data directly or use
+    :class:`biotite.structure.io.pdbx.BinaryCIFFile` instead.
+
     Examples
     --------
     Load a \\*.npz file, modify the structure and save the new
     structure into a new file:
-    
+
     >>> import os.path
     >>> file = NpzFile.read(os.path.join(path_to_structures, "1l2y.npz"))
     >>> array_stack = file.get_structure()
@@ -35,30 +38,30 @@ class NpzFile(File):
     >>> file = NpzFile()
     >>> file.set_structure(array_stack_mod)
     >>> file.write(os.path.join(path_to_directory, "1l2y_mod.npz"))
-    
+
     """
-    
+
     def __init__(self):
         super().__init__()
         self._data_dict = None
-    
+
     def __copy_fill__(self, clone):
         super().__copy_fill__(clone)
         if self._data_dict is not None:
             for key, value in self._data_dict.items():
                 clone._data_dict[key] = np.copy(value)
-    
+
     @classmethod
     def read(cls, file):
         """
         Read a NPZ file.
-        
+
         Parameters
         ----------
         file : file-like object or str
             The file to be read.
             Alternatively a file path can be supplied.
-        
+
         Returns
         -------
         file_object : NPZFile
@@ -75,11 +78,11 @@ class NpzFile(File):
                 raise TypeError("A file opened in 'binary' mode is required")
             npz_file._data_dict = dict(np.load(file, allow_pickle=False))
         return npz_file
-                
+
     def write(self, file):
         """
         Write a NPZ file.
-        
+
         Parameters
         ----------
         file : file-like object or str
@@ -93,15 +96,15 @@ class NpzFile(File):
             if not is_binary(file):
                 raise TypeError("A file opened in 'binary' mode is required")
             np.savez(file, **self._data_dict)
-    
+
     def get_structure(self):
         """
         Get an :class:`AtomArray` or :class:`AtomArrayStack` from the
         file.
-        
+
         If this method returns an array or stack depends on which type
         of object was used when the file was written.
-        
+
         Returns
         -------
         array : AtomArray or AtomArrayStack
@@ -117,7 +120,7 @@ class NpzFile(File):
             array = AtomArrayStack(coord.shape[0], coord.shape[1])
         else:
             array = AtomArray(coord.shape[0])
-        
+
         for key, value in self._data_dict.items():
             if key == "coord":
                 array.coord = value
@@ -128,12 +131,12 @@ class NpzFile(File):
             else:
                 array.set_annotation(key, value)
         return array
-        
+
     def set_structure(self, array):
         """
         Set the :class:`AtomArray` or :class:`AtomArrayStack` for the
         file.
-        
+
         Parameters
         ----------
         array : AtomArray or AtomArrayStack

biotite/structure/io/pdb/__init__.py

@@ -6,11 +6,11 @@
 This subpackage is used for reading and writing an :class:`AtomArray` or
 :class:`AtomArrayStack` using the popular PDB format.
 Since this format has some limitations, it will be completely replaced
-someday by the modern PDBx/mmCIF format.
+someday by the modern PDBx format.
 Therefore this subpackage should only be used, if usage of the
-PDBx/mmCIF format is not suitable (e.g. when interfacing
+PDBx (CIF or BinaryCIF) format is not suitable (e.g. when interfacing
 other software).
-In all other cases, usage of the ``pdbx`` subpackage is encouraged.
+In all other cases, usage of the :mod:`pdbx` subpackage is encouraged.
 """
 
 __name__ = "biotite.structure.io.pdb"