CAT 0.8.8 (#114)

* Fixed a bug where ligands weren't properly rotated when using ``optional.ligand.optimize = False``.
* Added tests for ``CAT.utils.SetAttr``.

CAT/__version__.py

@@ -1 +1 @@
-__version__ = '0.8.7'
+__version__ = '0.8.8'

CAT/_setattr.py

@@ -1,4 +1,10 @@
-"""A module for containing the :class:`SetAttr` class."""
+"""A module for containing the :class:`SetAttr` class.
+
+Notes
+-----
+:class:`SetAttr` should be imported from :mod:`CAT.utils`.
+
+"""
 
 import reprlib
 from threading import RLock
@@ -87,6 +93,7 @@ def __init__(self, obj: T1, name: str, value: T2) -> None:
         self._value_old = self.attr
         self._lock = RLock()
 
+    @reprlib.recursive_repr()
     def __repr__(self) -> str:
         """Implement :func:`str(self)<str>` and :func:`repr(self)<repr>`."""
         obj = object.__repr__(self.obj)

CAT/attachment/optimize_rotmat.py

@@ -32,7 +32,7 @@ def _minimize_func(vec1: np.ndarray, vec2: np.ndarray, xyz: np.ndarray, anchor:
     xyz_new = xyz@rotmat
     xyz_new -= xyz_new[anchor]
 
-    # Apply the cost function: e^(|yz|)
+    # Apply the cost function: e^(||yz||)
     yz = xyz_new[:, 1:]
     distance = np.linalg.norm(yz, axis=1)
     return np.exp(distance).sum()

CAT/base.py

@@ -46,7 +46,7 @@
 
 from .multi_ligand import init_multi_ligand
 from .attachment.qd_opt import init_qd_opt
-from .attachment.ligand_opt import init_ligand_opt
+from .attachment.ligand_opt import init_ligand_opt, allign_axis
 from .attachment.distribution import distribute_idx
 from .attachment.ligand_attach import init_qd_construction
 from .attachment.ligand_anchoring import init_ligand_anchoring
@@ -295,6 +295,9 @@ def prep_ligand(ligand_df: SettingsDataFrame) -> SettingsDataFrame:
     # Optimize the ligands
     if optimize:
         init_ligand_opt(ligand_df)
+    else:
+        for lig in ligand_df[MOL]:
+            allign_axis(lig, lig.properties.dummies)
 
     # Perform a COSMO-RS calculation on the ligands
     if crs:

CAT/settings_dataframe.py

@@ -25,7 +25,7 @@
 
 """
 
-from typing import Optional
+from typing import Optional, Callable
 
 import pandas as pd
 
@@ -59,14 +59,14 @@ def __init__(self, data=None, index=None, dtype=None, name=None, copy=False, fas
         super().__init__(data, index, dtype, name, copy, fastpath)
 
     @property
-    def _constructor(self) -> 'SettingsSeries':
+    def _constructor(self) -> Callable[..., 'SettingsSeries']:
         """Construct a :class:`.SettingsSeries` instance."""
         def _series(*args, **kwargs) -> SettingsSeries:
             return SettingsSeries(*args, **kwargs).__finalize__(self)
         return _series
 
     @property
-    def _constructor_expanddim(self) -> 'SettingsDataFrame':
+    def _constructor_expanddim(self) -> Callable[..., 'SettingsDataFrame']:
         """Construct a :class:`.SettingsDataFrame` instance."""
         def _df(*args, **kwargs) -> SettingsDataFrame:
             return SettingsDataFrame(*args, **kwargs).__finalize__(self)
@@ -109,14 +109,14 @@ def __init__(self, data=None, index=None, columns=None, dtype=None, copy=False,
         super().__init__(data, index, columns, dtype, copy)
 
     @property
-    def _constructor(self) -> 'SettingsDataFrame':
+    def _constructor(self) -> Callable[..., 'SettingsDataFrame']:
         """Construct a :class:`.SettingsDataFrame` instance."""
         def _df(*args, **kwargs) -> SettingsDataFrame:
             return SettingsDataFrame(*args, **kwargs).__finalize__(self)
         return _df
 
     @property
-    def _constructor_sliced(self) -> 'SettingsSeries':
+    def _constructor_sliced(self) -> Callable[..., 'SettingsSeries']:
         """Construct a :class:`.SettingsSeries` instance."""
         def _series(*args, **kwargs) -> SettingsSeries:
             return SettingsSeries(*args, **kwargs).__finalize__(self)

CAT/utils.py

@@ -280,7 +280,7 @@ def restart_init(path: str, folder: str, hashing: str = 'input') -> None:
 @overload
 def cycle_accumulate(iterable: Iterable[T1]) -> Generator[T1, None, None]: ...
 @overload
-def cycle_accumulate(iterable: Iterable[T1], start: T1 = ...) -> Generator[T1, None, None]: ...
+def cycle_accumulate(iterable: Iterable[T1], start: T1) -> Generator[T1, None, None]: ...
 def cycle_accumulate(iterable, start=0):  # noqa: E302
     """Accumulate and return elements from **iterable** until it is exhausted.
 
@@ -547,5 +547,9 @@ def from_str(cls, version: str) -> 'VersionInfo':
             cls_name = version.__class__.__name__
             raise TypeError(f"'version' expected a string; observed type: {cls_name!r}")
 
-        args = (int(i) for i in version.split('.'))
-        return cls(*args)
+        try:
+            major, minor, micro = (int(i) for i in version.split('.'))
+        except (ValueError, TypeError) as ex:
+            raise ValueError("'version' expected a string consisting of three '.'-separated "
+                             f"integers (e.g. '0.8.2'); observed value: {version!r}") from ex
+        return cls(major=major, minor=minor, micro=micro)

CHANGELOG.rst

@@ -11,6 +11,13 @@ This project adheres to `Semantic Versioning <http://semver.org/>`_.
 * WiP: Added an option the import pre-built quantum dots.
 
 
+0.8.8
+*****
+* Fixed a bug where ligands weren't properly rotated when
+  using ``optional.ligand.optimize = False``.
+* Added tests for ``CAT.utils.SetAttr``.
+
+
 0.8.7
 *****
 * Replaced ``print()`` calls with ``logger.warning()`` in all dye-related functions.

README.rst

@@ -16,7 +16,7 @@
 
 
 ##############################
-Compound Attachment Tool 0.8.7
+Compound Attachment Tool 0.8.8
 ##############################
 
 **CAT** is a collection of tools designed for the construction of various chemical compounds.

docs/conf.py

@@ -69,7 +69,7 @@
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the built documents.
-release = '0.8.7'  # The full version, including alpha/beta/rc tags.
+release = '0.8.8'  # The full version, including alpha/beta/rc tags.
 version = release.rsplit('.', maxsplit=1)[0]
 
 

tests/test_setattr.py

@@ -0,0 +1,49 @@
+"""Tests for :class:`CAT._setattr.SetAttr`."""
+
+import copy
+import reprlib
+from assertionlib import assertion
+
+from CAT.utils import SetAttr
+
+
+class _Test:
+    a = True
+
+
+OBJ = SetAttr(_Test, 'a', False)
+
+
+def test_setattr() -> None:
+    """Test :class:`CAT._setattr.SetAttr`."""
+    assertion.is_(OBJ.obj, _Test)
+    assertion.eq(OBJ.name, 'a')
+    assertion.is_(OBJ.value, False)
+
+    assertion.is_(OBJ.attr, _Test.a)
+    try:
+        OBJ.attr = False
+        assertion.is_(OBJ.attr, False)
+    finally:
+        OBJ.attr = True
+
+    assertion.contains(repr(OBJ), SetAttr.__name__)
+    assertion.contains(repr(OBJ), object.__repr__(OBJ.obj))
+    assertion.contains(repr(OBJ), reprlib.repr(OBJ.value))
+    assertion.contains(repr(OBJ), 'a')
+
+    obj2 = SetAttr(_Test, 'a', False)
+    obj3 = SetAttr(_Test, 'a', True)
+    assertion.eq(OBJ, obj2)
+    assertion.ne(OBJ, obj3)
+    assertion.ne(OBJ, 0)
+
+    assertion.assert_(OBJ.__reduce__, exception=TypeError)
+    assertion.is_(copy.copy(OBJ), OBJ)
+    assertion.is_(copy.deepcopy(OBJ), OBJ)
+    assertion.truth(hash(OBJ))
+    assertion.eq(hash(OBJ), OBJ._hash)
+
+    with OBJ:
+        assertion.is_(_Test.a, False)
+    assertion.is_(_Test.a, True)