biotite 0.41.2__cp310-cp310-macosx_11_0_arm64.whl → 1.0.0__cp310-cp310-macosx_11_0_arm64.whl

{biotite-0.41.2.dist-info → biotite-1.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biotite
-Version: 0.41.2
+Version: 1.0.0
 Summary: A comprehensive library for computational molecular biology
 Project-URL: homepage, https://www.biotite-python.org
 Project-URL: repository, https://github.com/biotite-dev/biotite
@@ -37,7 +37,7 @@ License: BSD 3-Clause License
         (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
         SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 License-File: LICENSE.rst
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
@@ -49,9 +49,10 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.10
+Requires-Dist: biotraj<2.0,>=1.0
 Requires-Dist: msgpack>=0.5.6
 Requires-Dist: networkx>=2.0
-Requires-Dist: numpy<2.0,>=1.14.5
+Requires-Dist: numpy>=1.25
 Requires-Dist: requests>=2.12
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
@@ -80,7 +81,7 @@ This package bundles popular tasks in computational molecular biology
 into a uniform *Python* library.
 It can handle a major part of the typical workflow
 for sequence and biomolecular structure data:
-   
+
    - Searching and fetching data from biological databases
    - Reading and writing popular sequence/structure file formats
    - Analyzing and editing sequence/structure data
@@ -116,7 +117,6 @@ Installation
 
 Some functions require some extra packages:
 
-   - **mdtraj** - Required for trajetory file I/O operations.
    - **matplotlib** - Required for plotting purposes.
 
 *Biotite* can be installed via *Conda*...

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biotite/structure/io/ctab.py

@@ -1,72 +0,0 @@
-# This source code is part of the Biotite package and is distributed
-# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
-# information.
-
-__name__ = "biotite.structure.io"
-__author__ = "Patrick Kunzmann"
-__all__ = ["read_structure_from_ctab", "write_structure_to_ctab"]
-
-import warnings
-from ..bonds import BondType
-
-
-def read_structure_from_ctab(ctab_lines):
-    """
-    Parse a *MDL* connection table (Ctab) to obtain an
-    :class:`AtomArray`. :footcite:`Dalby1992`.
-
-    DEPRECATED: Moved to :mod:`biotite.structure.io.mol.ctab`.
-
-    Parameters
-    ----------
-    ctab_lines : lines of str
-        The lines containing the *ctab*.
-        Must begin with the *counts* line and end with the `M END` line
-
-    Returns
-    -------
-    atoms : AtomArray
-        This :class:`AtomArray` contains the optional ``charge``
-        annotation and has an associated :class:`BondList`.
-
-    References
-    ----------
-
-    .. footbibliography::
-    """
-    warnings.warn("Moved to biotite.structure.io.mol.ctab", DeprecationWarning)
-    from biotite.structure.io.mol.ctab import read_structure_from_ctab
-    return read_structure_from_ctab(ctab_lines)
-
-
-def write_structure_to_ctab(atoms, default_bond_type=BondType.ANY):
-    """
-    Convert an :class:`AtomArray` into a
-    *MDL* connection table (Ctab). :footcite:`Dalby1992`
-
-    DEPRECATED: Moved to :mod:`biotite.structure.io.mol.ctab`.
-
-    Parameters
-    ----------
-    atoms : AtomArray
-        The array must have an associated :class:`BondList`.
-
-    Returns
-    -------
-    ctab_lines : lines of str
-        The lines containing the *ctab*.
-        The lines begin with the *counts* line and end with the `M END`
-        .line
-    default_bond_type : BondType
-        Bond type fallback in the *Bond block* if a bond has no bond_type
-        defined in *atoms* array. By default, each bond is treated as
-        :attr:`BondType.ANY`.
-
-    References
-    ----------
-
-    .. footbibliography::
-    """
-    warnings.warn("Moved to biotite.structure.io.mol.ctab", DeprecationWarning)
-    from biotite.structure.io.mol.ctab import write_structure_to_ctab
-    return write_structure_to_ctab(atoms, default_bond_type)

biotite/structure/io/mmtf/__init__.py

@@ -1,21 +0,0 @@
-# This source code is part of the Biotite package and is distributed
-# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
-# information.
-
-"""
-This subpackage is used for reading and writing an :class:`AtomArray` or
-:class:`AtomArrayStack` using the binary MMTF format. This format
-features a smaller file size and a highly increased I/O operation
-performance, than the text based file formats.
-
-DEPRECATED: Use :class:`biotite.structure.io.pdbx.BinaryCIFFile`
-instead.
-"""
-
-__name__ = "biotite.structure.io.mmtf"
-__author__ = "Patrick Kunzmann"
-
-from .assembly import *
-from .file import *
-from .convertfile import *
-from .convertarray import *