biotite 0.39.0__cp312-cp312-win_amd64.whl → 0.41.0__cp312-cp312-win_amd64.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/mol/__init__.py

@@ -14,5 +14,7 @@ around MOL, is also supported.
 __name__ = "biotite.structure.io.mol"
 __author__ = "Patrick Kunzmann"
 
-from .file import *
-from .convert import *
+from .convert import *
+from .header import *
+from .mol import *
+from .sdf import *

biotite/structure/io/mol/convert.py

@@ -6,10 +6,12 @@ __name__ = "biotite.structure.io.mol"
 __author__ = "Patrick Kunzmann"
 __all__ = ["get_structure", "set_structure"]
 
+from .mol import MOLFile
+from .sdf import SDFile, SDRecord
 from ...bonds import BondType
 
 
-def get_structure(mol_file):
+def get_structure(mol_file, record_name=None):
     """
     Get an :class:`AtomArray` from the MOL file.
 
@@ -18,8 +20,12 @@ def get_structure(mol_file):
 
     Parameters
     ----------
-    mol_file : MOLFile
-        The MOL file.
+    mol_file : MOLFile or SDFile or SDRecord
+        The file.
+    record_name : str, optional
+        Has only an effect when `mol_file` is a :class:`SDFile`.
+        The name of the record in the SD file.
+        By default, the first record is used.
 
     Returns
     -------
@@ -29,10 +35,12 @@ def get_structure(mol_file):
         All other annotation categories, except ``element`` are
         empty.
     """
-    return mol_file.get_structure()
+    record = _get_record(mol_file, record_name)
+    return record.get_structure()
 
 
-def set_structure(mol_file, atoms, default_bond_type=BondType.ANY):
+def set_structure(mol_file, atoms, default_bond_type=BondType.ANY,
+                  version=None, record_name=None):
     """
     Set the :class:`AtomArray` for the MOL file.
 
@@ -46,6 +54,62 @@ def set_structure(mol_file, atoms, default_bond_type=BondType.ANY):
     array : AtomArray
         The array to be saved into this file.
         Must have an associated :class:`BondList`.
-
+        Bond type fallback for the *Bond block*, if a
+        :class:`BondType` has no CTAB counterpart.
+        By default, each such bond is treated as
+        :attr:`BondType.ANY`.
+    default_bond_type : BondType, optional
+        Bond type fallback for the *Bond block*, if a :class:`BondType`
+        has no CTAB counterpart.
+        By default, each such bond is treated as :attr:`BondType.ANY`.
+    version : {"V2000", "V3000"}, optional
+        The version of the CTAB format.
+        ``"V2000"`` uses the *Atom* and *Bond* block, while ``"V3000"``
+        uses the *Properties* block.
+        By default, ``"V2000"`` is used, unless the number of atoms or
+        bonds exceeds 999, in which case ``"V3000"`` is used.
+    record_name : str, optional
+        Has only an effect when `mol_file` is a :class:`SDFile`.
+        The name of the record.
+        Default is the first record of the file.
+        If the file is empty, a new record will be created.
     """
-    mol_file.set_structure(atoms, default_bond_type)
+    record = _get_or_create_record(mol_file, record_name)
+    record.set_structure(atoms, default_bond_type, version)
+
+
+def _get_record(file, record_name):
+    if isinstance(file, (MOLFile, SDRecord)):
+        return file
+    elif isinstance(file, SDFile):
+        # Determine record
+        if record_name is None:
+            return file.record
+        else:
+            return file[record_name]
+    else:
+        raise TypeError(
+            f"Unsupported file type '{type(file).__name__}'"
+        )
+
+
+def _get_or_create_record(file, record_name):
+    if isinstance(file, (MOLFile, SDRecord)):
+        return file
+    elif isinstance(file, SDFile):
+        if record_name is None:
+            if len(file) > 0:
+                # Choose first record by default
+                record_name = next(iter(file.keys()))
+            else:
+                # File is empty -> invent a new record name
+                record_name = "Molecule"
+
+        if record_name not in file:
+            record = SDRecord()
+            file[record_name] = record
+        return file[record_name]
+    else:
+        raise TypeError(
+            f"Unsupported file type '{type(file).__name__}'"
+        )