Merge pull request #86 from nlesc-nano/devel

 Fixed an issue where an incorrect offset was within _evaluate_distance()

CAT/attachment/ligand_attach.py

@@ -243,6 +243,8 @@ def get_name() -> str:
 
     # Attach the rotated ligands to the core, returning the resulting strucutre (PLAMS Molecule).
     lig_array = rot_mol(ligand, vec1, vec2, atoms_other=core.properties.dummies, idx=idx)
+    _evaluate_distance(lig_array, len(core))
+
     qd = core.copy()
     array_to_qd(ligand, lig_array, mol_out=qd)
     qd.round_coords()
@@ -466,12 +468,13 @@ def rotation_check_kdtree(xyz: np.ndarray, at_other: np.ndarray, k: int = 10):
         at_other_ = np.concatenate((at_other_, ar[idx_min]))
         ret[i] = ar[idx_min]
 
-    _evaluate_distance(ret, len(at_other))
     return ret
 
 
-def _evaluate_distance(xyz3D: np.ndarray, core_atom_count: int,
-                       threshold: float = 1.0, action: str = 'warn') -> Union[None, NoReturn]:
+def _evaluate_distance(xyz3D: np.ndarray,
+                       offset: int = 0,
+                       threshold: float = 1.0,
+                       action: str = 'warn') -> Union[None, NoReturn]:
     """Eavluate all the distance matrix of **xyz3D** and perform **action** when distances are below **threshold**."""  # noqa
     try:
         action_func = WARN_MAP[action]
@@ -492,7 +495,7 @@ def _evaluate_distance(xyz3D: np.ndarray, core_atom_count: int,
     bool_ar = dist < threshold
     if bool_ar.any():
         _idx2 = np.stack([np.arange(len(idx)), idx]).T
-        _idx2 += 1 + core_atom_count
+        _idx2 += 1 + offset
         _idx2.sort(axis=1)
 
         idx2 = np.unique(_idx2[bool_ar], axis=0)

CAT/data_handling/warn_map.py

@@ -1,13 +1,44 @@
+"""
+CAT.data_handling.warn_map
+==========================
+
+A module for managing exceptions and warnings in CAT.
+
+"""
 import warnings
 from types import MappingProxyType
-from typing import Mapping, Callable, NoReturn, Union
+from typing import Mapping, Callable, NoReturn, Union, Type
+
+from scm.plams import MoleculeError
 
 __all__ = ['WARN_MAP']
 
 
+class MoleculeWarning(Warning, MoleculeError):
+    """A :exc:`Warning` subclass for :class:`Molecule<scm.plams.mol.molecule.Molecule>` related errors."""  # noqa
+
+
+class ValueWarning(Warning, ValueError):
+    """A :exc:`Warning` subclass for :exc:`ValueError` related errors."""  # noqa
+
+
+#: Map an :exc:`Exception` type to a :exc:`Warning` type.
+CATEGORY_MAP: Mapping[Type[Exception], Type[Warning]] = MappingProxyType({
+    MoleculeError: MoleculeWarning,
+    ValueError: ValueWarning
+})
+
+
 def _warn(exc: Exception) -> None:
-    """Perform a warning using **exc**."""
-    warnings.warn(str(exc), category=RuntimeWarning, stacklevel=2)
+    """Perform a warning using **exc**.
+
+    When possible, the warning category will be derived from the passed Exception type
+    (see :data:`CATEGORY_MAP`).
+    Will default to :exc:`RuntimeWarning` otherwise.
+
+    """  # noqa
+    warnings.warn(str(exc), stacklevel=2,
+                  category=CATEGORY_MAP.get(type(exc), RuntimeWarning))
 
 
 def _raise(exc: Exception) -> NoReturn:
@@ -20,6 +51,8 @@ def _ignore(exc: Exception) -> None:
     return None
 
 
+#: Map a string to callable for either raising an :exc:`Exception`,
+#: displaying a :exc:`Warning` or doing nothing.
 WARN_MAP: Mapping[str, Callable[[Exception], Union[NoReturn, None]]] = MappingProxyType({
     'raise': _raise,
     'warn': _warn,

CAT/workflows/workflow_dicts.py

@@ -8,7 +8,7 @@
 
 import os
 from types import MappingProxyType
-from typing import Mapping, MutableMapping, Tuple
+from typing import Mapping, MutableMapping
 
 import yaml
 import numpy as np