biotite 0.41.2__tar.gz → 1.0.1__tar.gz

{biotite-0.41.2 → biotite-1.0.1}/.gitignore

@@ -39,7 +39,6 @@ htmlcov
 # Ignore all compiled python files (e.g. from running the unit tests)
 *.pyc
 *.pyo
-*.py{}
 *.py-e
 
 # Ignore potential directory created during install

{biotite-0.41.2 → biotite-1.0.1}/CONTRIB.rst

@@ -17,4 +17,5 @@ CONTRIBUTORS
 - Jincai Yang <https://github.com/0ut0fcontrol>
 - Tom Eulenfeld <https://github.com/trichter>
 - Benjamin E. Mayer <https://github.com/entropybit>
-- Natasha Jaffe <https://github.com/tcjaffe>
+- Natasha Jaffe <https://github.com/tcjaffe>
+- Tristen J. Mier  <https://github.com/tjmier>

{biotite-0.41.2 → biotite-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biotite
-Version: 0.41.2
+Version: 1.0.1
 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
@@ -49,12 +49,14 @@ 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'
+Requires-Dist: pytest-codspeed; extra == 'test'
 Description-Content-Type: text/x-rst
 
 .. image:: https://img.shields.io/pypi/v/biotite.svg
@@ -80,7 +82,7 @@ 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 +118,6 @@ 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*...

{biotite-0.41.2 → biotite-1.0.1}/README.rst

@@ -21,7 +21,7 @@ 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
@@ -57,7 +57,6 @@ 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*...

biotite-1.0.1/pyproject.toml

@@ -0,0 +1,135 @@
+[project]
+name = "biotite"
+requires-python = ">=3.10"
+description = "A comprehensive library for computational molecular biology"
+readme = "README.rst"
+authors = [{name = "The Biotite contributors"}]
+license = {"file" = "LICENSE.rst"}
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+  # Wheels compiled with NumPy 2.0 are backward compatible with NumPy 1.x
+  # https://numpy.org/devdocs/dev/depending_on_numpy.html#numpy-2-0-specific-advice
+  "numpy >= 1.25",
+  "biotraj >= 1.0, < 2.0",
+  "requests >= 2.12",
+  "msgpack >= 0.5.6",
+  "networkx >= 2.0",
+  "requests >= 2.12",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+test = [
+  "pytest",
+  "pytest-codspeed",
+]
+
+[project.urls]
+homepage = "https://www.biotite-python.org"
+repository = "https://github.com/biotite-dev/biotite"
+documentation = "https://www.biotite-python.org"
+
+[tool.ruff.lint]
+# pyflakes, pycodestyle isort and varibale naming
+select = ["F", "E", "W", "I", "TID", "N"]
+ignore = [
+    # In docstrings long lines are often intentional
+    # Most other ocassions are caught by the ruff formatter
+    "E501",
+    # Due to constants and class placeholders defined in functions
+    "N806",
+]
+
+[tool.ruff.lint.per-file-ignores]
+# Due to `* import` of BCIF encoding
+"setup_ccd.py" = ["F405", "F403"]
+# Due to imports after the PATH has been adjusted
+"doc/conf.py" = ["E402"]
+# Due to `from .module import *` imports in `__init__.py` modules
+"__init__.py" = ["F403", "TID252"]
+# Due to pymol scripts that are evaluated in other example scripts
+"doc/examples/**/*_pymol.py" = ["F821"]
+
+[tool.ruff.lint.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.lint.isort]
+# No separator lines between import sections
+no-lines-before = [
+    "future",
+    "standard-library",
+    "third-party",
+    "first-party",
+    "local-folder",
+]
+order-by-type = true
+known-first-party = ["biotite"]
+
+[tool.pytest.ini_options]
+testpaths = [
+  "tests",
+  "benchmarks"
+]
+python_files = [
+  "test_*.py",
+  "benchmark_*.py",
+]
+python_functions = [
+  "test_*",
+  "benchmark_*",
+]
+filterwarnings = [
+  # Appears in loading NetCDF trajectory files
+  "ignore:The 'netCDF4' Python package is not installed.",
+  "ignore:Input structure has no associated 'BondList'",
+]
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "tests",
+  "benchmarks",
+  "doc",
+  "environment.yml",
+  "setup_ccd.py",
+  # .github, .gitignore, .gitattributes
+  ".git*",
+]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/biotite/version.py"
+
+[tool.hatch.build.targets.wheel.hooks.cython]
+dependencies = ["hatch-cython"]
+
+[tool.hatch.build.targets.wheel.hooks.cython.options]
+include_numpy = true
+compile_py = false
+define_macros = [
+    ["NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"],
+]
+
+[build-system]
+requires = [
+    "hatchling",
+    "hatch-vcs == 0.4",
+    "hatch-cython == 0.5",
+    "numpy >= 2.0",
+    "cython >= 3.0",
+]
+build-backend = "hatchling.build"

{biotite-0.41.2 → biotite-1.0.1}/src/biotite/__init__.py

@@ -12,8 +12,7 @@ modules.
 __name__ = "biotite"
 __author__ = "Patrick Kunzmann"
 
-from .file import *
-from .temp import *
 from .copyable import *
+from .file import *
+from .version import __version__, __version_tuple__  # noqa: F401
 from .visualize import *
-from .version import __version__, __version_tuple__

{biotite-0.41.2 → biotite-1.0.1}/src/biotite/application/__init__.py

@@ -65,5 +65,5 @@ __author__ = "Patrick Kunzmann"
 
 from .application import *
 from .localapp import *
+from .msaapp import *
 from .webapp import *
-from .msaapp import *

{biotite-0.41.2 → biotite-1.0.1}/src/biotite/application/application.py

@@ -4,19 +4,26 @@
 
 __name__ = "biotite.application"
 __author__ = "Patrick Kunzmann"
-__all__ = ["Application", "AppStateError", "TimeoutError", "VersionError",
-           "AppState", "requires_state"]
+__all__ = [
+    "Application",
+    "AppStateError",
+    "TimeoutError",
+    "VersionError",
+    "AppState",
+    "requires_state",
+]
 
 import abc
 import time
-from functools import wraps
 from enum import Flag, auto
+from functools import wraps
 
 
 class AppState(Flag):
     """
     This enum type represents the app states of an application.
     """
+
     CREATED = auto()
     RUNNING = auto()
     FINISHED = auto()
@@ -45,6 +52,7 @@ def requires_state(app_state):
     ... def function(self):
     ...     pass
     """
+
     def decorator(func):
         @wraps(func)
         def wrapper(*args, **kwargs):
@@ -52,16 +60,16 @@ def requires_state(app_state):
             try:
                 instance = args[0]
             except IndexError:
-                raise TypeError(
-                    "This method must be called from a class instance"
-                )
+                raise TypeError("This method must be called from a class instance")
             if not instance._state & app_state:
                 raise AppStateError(
                     f"The application is in {instance.get_app_state()} state, "
                     f"but {app_state} state is required"
                 )
             return func(*args, **kwargs)
+
         return wrapper
+
     return decorator
 
 
@@ -146,11 +154,10 @@ class Application(metaclass=abc.ABCMeta):
         """
         time.sleep(self.wait_interval())
         while self.get_app_state() != AppState.FINISHED:
-            if timeout is not None and time.time()-self._start_time > timeout:
+            if timeout is not None and time.time() - self._start_time > timeout:
                 self.cancel()
                 raise TimeoutError(
-                    f"The application expired its timeout "
-                    f"({timeout:.1f} s)"
+                    f"The application expired its timeout " f"({timeout:.1f} s)"
                 )
             else:
                 time.sleep(self.wait_interval())
@@ -249,6 +256,7 @@ class AppStateError(Exception):
     """
     Indicate that the application lifecycle was violated.
     """
+
     pass
 
 
@@ -256,6 +264,7 @@ class TimeoutError(Exception):
     """
     Indicate that the application's timeout expired.
     """
+
     pass
 
 
@@ -263,4 +272,5 @@ class VersionError(Exception):
     """
     Indicate that the application's version is invalid.
     """
-    pass
+
+    pass

{biotite-0.41.2 → biotite-1.0.1}/src/biotite/application/autodock/__init__.py

@@ -9,4 +9,4 @@ A subpackage for static ligand docking with *Autodock*.
 __name__ = "biotite.application.autodock"
 __author__ = "Patrick Kunzmann"
 
-from .app import *
+from .app import *

{biotite-0.41.2 → biotite-1.0.1}/src/biotite/application/autodock/app.py

@@ -9,12 +9,12 @@ __all__ = ["VinaApp"]
 import copy
 from tempfile import NamedTemporaryFile
 import numpy as np
-from ..localapp import LocalApp, cleanup_tempfile
-from ..application import AppState, requires_state
-from ...structure.io.pdbqt import PDBQTFile
-from ...structure.residues import get_residue_starts_for, get_residue_masks
-from ...structure.bonds import find_connected
-from ...structure.error import BadStructureError
+from biotite.application.application import AppState, requires_state
+from biotite.application.localapp import LocalApp, cleanup_tempfile
+from biotite.structure.bonds import find_connected
+from biotite.structure.error import BadStructureError
+from biotite.structure.io.pdbqt import PDBQTFile
+from biotite.structure.residues import get_residue_masks, get_residue_starts_for
 
 
 class VinaApp(LocalApp):
@@ -62,8 +62,8 @@ class VinaApp(LocalApp):
     ...     flexible=(receptor.res_id == 2) | (receptor.res_id == 5)
     ... )
     """
-    def __init__(self, ligand, receptor, center, size, flexible=None,
-                 bin_path="vina"):
+
+    def __init__(self, ligand, receptor, center, size, flexible=None, bin_path="vina"):
         super().__init__(bin_path)
 
         if ligand.bonds is None:
@@ -83,23 +83,17 @@ class VinaApp(LocalApp):
 
         if self._is_flexible:
             flexible_indices = np.where(flexible)[0]
-            self._flex_res_starts = np.unique(get_residue_starts_for(
-                receptor, flexible_indices
-            ))
-        
-        self._ligand_file  = NamedTemporaryFile(
-            "w", suffix=".pdbqt", delete=False
-        )
-        self._receptor_file  = NamedTemporaryFile(
-            "w", suffix=".pdbqt", delete=False
-        )
-        self._receptor_flex_file  = NamedTemporaryFile(
+            self._flex_res_starts = np.unique(
+                get_residue_starts_for(receptor, flexible_indices)
+            )
+
+        self._ligand_file = NamedTemporaryFile("w", suffix=".pdbqt", delete=False)
+        self._receptor_file = NamedTemporaryFile("w", suffix=".pdbqt", delete=False)
+        self._receptor_flex_file = NamedTemporaryFile(
             "w", suffix=".pdbqt", delete=False
         )
-        self._out_file  = NamedTemporaryFile(
-            "r", suffix=".pdbqt", delete=False
-        )
-    
+        self._out_file = NamedTemporaryFile("r", suffix=".pdbqt", delete=False)
+
     @requires_state(AppState.CREATED)
     def set_seed(self, seed):
         """
@@ -114,7 +108,7 @@ class VinaApp(LocalApp):
             The seed for the random number generator.
         """
         self._seed = seed
-    
+
     @requires_state(AppState.CREATED)
     def set_exhaustiveness(self, exhaustiveness):
         """
@@ -131,7 +125,7 @@ class VinaApp(LocalApp):
             Must be greater than 0.
         """
         self._exhaustiveness = exhaustiveness
-    
+
     @requires_state(AppState.CREATED)
     def set_max_number_of_models(self, number):
         """
@@ -147,7 +141,7 @@ class VinaApp(LocalApp):
             The maximum number of generated modes/models.
         """
         self._number = number
-    
+
     @requires_state(AppState.CREATED)
     def set_energy_range(self, energy_range):
         """
@@ -168,34 +162,31 @@ class VinaApp(LocalApp):
         # Use different atom ID ranges for atoms in ligand and receptor
         # for unambiguous assignment, if the receptor contains flexible
         # residues
-        self._ligand.set_annotation("atom_id", np.arange(
-            1,
-            self._ligand.array_length() + 1
-        ))
-        self._receptor.set_annotation("atom_id", np.arange(
-            self._ligand.array_length() + 1,
-            self._ligand.array_length() + self._receptor.array_length() + 1
-        ))
+        self._ligand.set_annotation(
+            "atom_id", np.arange(1, self._ligand.array_length() + 1)
+        )
+        self._receptor.set_annotation(
+            "atom_id",
+            np.arange(
+                self._ligand.array_length() + 1,
+                self._ligand.array_length() + self._receptor.array_length() + 1,
+            ),
+        )
 
         ligand_file = PDBQTFile()
-        # Contains 'true' entries for all atoms that have not been 
+        # Contains 'true' entries for all atoms that have not been
         # removed from ligand
         self._ligand_mask = ligand_file.set_structure(
-            self._ligand,
-            rotatable_bonds="all"
+            self._ligand, rotatable_bonds="all"
         )
         ligand_file.write(self._ligand_file)
         self._ligand_file.flush()
-        
+
         if self._is_flexible:
-            self._rigid_mask = np.ones(
-                self._receptor.array_length(), dtype=bool
-            )
-            # Contains 'true' entries for all atoms that have not been 
+            self._rigid_mask = np.ones(self._receptor.array_length(), dtype=bool)
+            # Contains 'true' entries for all atoms that have not been
             # removed from receptor in flexible side chains
-            self._receptor_mask = np.zeros(
-                self._receptor.array_length(), dtype=bool
-            )
+            self._receptor_mask = np.zeros(self._receptor.array_length(), dtype=bool)
             for i, start in enumerate(self._flex_res_starts):
                 flex_mask, rigid_mask, root = self._get_flexible_residue(start)
                 self._rigid_mask &= rigid_mask
@@ -207,7 +198,7 @@ class VinaApp(LocalApp):
                     self._receptor[flex_mask],
                     rotatable_bonds="all",
                     root=root_in_flex_residue,
-                    include_torsdof=False
+                    include_torsdof=False,
                 )
                 # Enclose each flexible residue
                 # with BEGIN_RES and END_RES
@@ -220,7 +211,7 @@ class VinaApp(LocalApp):
             receptor_file.set_structure(
                 self._receptor[self._rigid_mask],
                 rotatable_bonds=None,
-                include_torsdof=False
+                include_torsdof=False,
             )
             receptor_file.write(self._receptor_file)
             self._receptor_file.flush()
@@ -228,23 +219,30 @@ class VinaApp(LocalApp):
         else:
             receptor_file = PDBQTFile()
             receptor_file.set_structure(
-                self._receptor,
-                rotatable_bonds=None,
-                include_torsdof=False
+                self._receptor, rotatable_bonds=None, include_torsdof=False
             )
             receptor_file.write(self._receptor_file)
             self._receptor_file.flush()
 
         arguments = [
-            "--ligand", self._ligand_file.name,
-            "--receptor", self._receptor_file.name,
-            "--out", self._out_file.name,
-            "--center_x", f"{self._center[0]:.3f}",
-            "--center_y", f"{self._center[1]:.3f}",
-            "--center_z", f"{self._center[2]:.3f}",
-            "--size_x", f"{self._size[0]:.3f}",
-            "--size_y", f"{self._size[1]:.3f}",
-            "--size_z", f"{self._size[2]:.3f}",
+            "--ligand",
+            self._ligand_file.name,
+            "--receptor",
+            self._receptor_file.name,
+            "--out",
+            self._out_file.name,
+            "--center_x",
+            f"{self._center[0]:.3f}",
+            "--center_y",
+            f"{self._center[1]:.3f}",
+            "--center_z",
+            f"{self._center[2]:.3f}",
+            "--size_x",
+            f"{self._size[0]:.3f}",
+            "--size_y",
+            f"{self._size[1]:.3f}",
+            "--size_z",
+            f"{self._size[2]:.3f}",
         ]
         if self._seed is not None:
             arguments.extend(["--seed", str(self._seed)])
@@ -259,32 +257,32 @@ class VinaApp(LocalApp):
 
         self.set_arguments(arguments)
         super().run()
-    
+
     def evaluate(self):
         super().evaluate()
         out_file = PDBQTFile.read(self._out_file)
-        
+
         models = out_file.get_structure()
 
         n_ligand_atoms = np.count_nonzero(self._ligand_mask)
         self._ligand_models = models[..., :n_ligand_atoms]
         self._flex_models = models[..., n_ligand_atoms:]
         self._n_models = models.stack_depth()
-        
+
         remarks = out_file.get_remarks()
         self._energies = np.array(
             # VINA RESULT:      -5.8      0.000      0.000
             #                     ^
             [float(remark[12:].split()[0]) for remark in remarks]
         )
-    
+
     def clean_up(self):
         super().clean_up()
         cleanup_tempfile(self._ligand_file)
         cleanup_tempfile(self._receptor_file)
         cleanup_tempfile(self._receptor_flex_file)
         cleanup_tempfile(self._out_file)
-    
+
     @requires_state(AppState.JOINED)
     def get_energies(self):
         """
@@ -302,7 +300,7 @@ class VinaApp(LocalApp):
     @requires_state(AppState.JOINED)
     def get_ligand_models(self):
         """
-        Get the ligand structure with the conformations for each 
+        Get the ligand structure with the conformations for each
         generated binding mode.
 
         Returns
@@ -312,7 +310,7 @@ class VinaApp(LocalApp):
             Each model corresponds to one binding mode.
             The models are sorted from best to worst predicted binding
             affinity.
-        
+
         Notes
         -----
         The returned structure may contain less atoms than the input
@@ -338,12 +336,11 @@ class VinaApp(LocalApp):
             atoms are set to *NaN*.
         """
         coord = np.full(
-            (self._n_models, self._ligand.array_length(), 3),
-            np.nan, dtype=np.float32
+            (self._n_models, self._ligand.array_length(), 3), np.nan, dtype=np.float32
         )
         coord[:, self._ligand_mask] = self._ligand_models.coord
         return coord
-    
+
     @requires_state(AppState.JOINED)
     def get_flexible_residue_models(self):
         """
@@ -360,7 +357,7 @@ class VinaApp(LocalApp):
             Each model corresponds to one binding mode.
             The models are sorted from best to worst predicted binding
             affinity.
-        
+
         Notes
         -----
         The returned structure may contain less atoms than the input
@@ -385,7 +382,7 @@ class VinaApp(LocalApp):
             affinity.
             Missing coordinates due to the removed nonpolar hydrogen
             atoms from flexible side chains are set to *NaN*.
-        
+
         Notes
         -----
         The output is only meaningful, if flexible side chains were
@@ -394,8 +391,7 @@ class VinaApp(LocalApp):
         of the input receptor coordinates.
         """
         coord = np.repeat(
-            self._receptor.coord[np.newaxis, ...],
-            repeats=self._n_models, axis=0
+            self._receptor.coord[np.newaxis, ...], repeats=self._n_models, axis=0
         )
         if self._is_flexible:
             # Replace original coordinates with modeled coordinates
@@ -424,16 +420,16 @@ class VinaApp(LocalApp):
         root_connect_indices, _ = self._receptor.bonds.get_bonds(root_index)
         connected_index = None
         try:
-            connected_index = root_connect_indices[np.isin(
-                self._receptor.atom_name[root_connect_indices], ("CB",)
-            )][0]
+            connected_index = root_connect_indices[
+                np.isin(self._receptor.atom_name[root_connect_indices], ("CB",))
+            ][0]
         except IndexError:
             # Residue has no appropriate connection (e.g. in glycine)
             # -> There is no atom in the flexible side chain
             flex_mask = np.zeros(self._receptor.array_length(), dtype=bool)
             rigid_mask = np.ones(self._receptor.array_length(), dtype=bool)
             return flex_mask, rigid_mask, root_index
-        
+
         # Remove the root bond from the bond list
         # to find the atoms involved in the flexible part
         bonds = self._receptor.bonds.copy()
@@ -442,7 +438,7 @@ class VinaApp(LocalApp):
         if root_index in flexible_indices:
             raise BadStructureError(
                 "There are multiple connections between the flexible and "
-                "rigid part, maybe a cyclic residue like proline was selected" 
+                "rigid part, maybe a cyclic residue like proline was selected"
             )
 
         flex_mask = np.zeros(self._receptor.array_length(), dtype=bool)
@@ -452,7 +448,6 @@ class VinaApp(LocalApp):
         flex_mask[root_index] = True
 
         return flex_mask, rigid_mask, root_index
-    
 
     @staticmethod
     def dock(ligand, receptor, center, size, flexible=None, bin_path="vina"):

{biotite-0.41.2 → biotite-1.0.1}/src/biotite/application/blast/__init__.py

@@ -10,5 +10,5 @@ using BLAST.
 __name__ = "biotite.application.blast"
 __author__ = "Patrick Kunzmann"
 
+from .alignment import *
 from .webapp import *
-from .alignment import *