Change optimization target to Volume diameter (Å), no optimization as default, and add openings_cutoff parameter

Author: jvsguerra

AtomPacker/__init__.py

@@ -9,7 +9,7 @@
 the resulting structures.
 """
 
-__version__ = "0.4.2"
+__version__ = "0.4.3"
 __name__ = "AtomPacker"
 license = "GNU GPL-3.0 License"
 

AtomPacker/structure/Cage.py

@@ -274,8 +274,8 @@ def pack(
         b: float | None = None,
         c: float | None = None,
         clashing_tolerance: float = 0.0,
-        angles: numpy.ndarray | list[float] | None = None,
-        translations: numpy.ndarray | list[float] | None = None,
+        angles: numpy.ndarray | list[float] = [0.0],
+        translations: numpy.ndarray | list[float] = [0.0],
         optsave: bool = False,
         optdir: str | None = None,
         verbose: bool = False,
@@ -299,12 +299,16 @@ def pack(
         clashing_tolerance : float, optional
             Minimum allowed distance (Å) between cluster and cage atoms.
             Default is 0.0.
-        angles : numpy.ndarray | list[float] | None, optional
-            Rotation angles for cluster optimization. If None, uses [-75, -50,
-            -25, 0, 25, 50, 75].
-        translations : numpy.ndarray | list[float] | None, optional
-            Translation values for cluster optimization. If None, uses
-            [-0.2, 0.0, 0.2].
+        angles : numpy.ndarray | list[float], optional
+            Rotation angles for cluster optimization. If not specified, no optimization
+            is performed. Default is [0.0].
+            If specified, angles should be a list or numpy array of angles in degrees.
+            Example: [-75, -50, -25, 0, 25, 50, 75].
+        translations : numpy.ndarray | list[float], optional
+            Translation values for cluster optimization. If not specified, no optimization
+            is performed. Default is [0.0].
+            If specified, translations should be a list or numpy array of translation
+            values in Angstroms. Example: [-0.2, 0.0, 0.2].
         optsave : bool, optional
             If True, saves each optimization step as a PDB file. Default is
             False.
@@ -556,8 +560,8 @@ def _build_cluster(
         lattice_constants: tuple[float, float] | tuple[float] | None,
         center: numpy.ndarray,
         clashing_tolerance: float = 0.0,
-        angles: numpy.ndarray | list[float] | None = None,
-        translations: numpy.ndarray | list[float] | None = None,
+        angles: numpy.ndarray | list[float] = [0.0],
+        translations: numpy.ndarray | list[float] = [0.0],
         optsave: bool = False,
         optdir: str | None = None,
         verbose: bool = False,
@@ -582,12 +586,16 @@ def _build_cluster(
         clashing_tolerance : float, optional
             Minimum allowed distance (Å) between cluster and cage atoms.
             Default is 0.0.
-        angles : numpy.ndarray | list[float] | None, optional
-            Rotation angles for cluster optimization. If None, uses [-75, -50,
-            -25, 0, 25, 50, 75].
-        translations : numpy.ndarray | list[float] | None, optional
-            Translation values for cluster optimization. If None, uses
-            [-0.2, 0.0, 0.2].
+        angles : numpy.ndarray | list[float], optional
+            Rotation angles for cluster optimization. If not specified, no optimization
+            is performed. Default is [0.0].
+            If specified, angles should be a list or numpy array of angles in degrees.
+            Example: [-75, -50, -25, 0, 25, 50, 75].
+        translations : numpy.ndarray | list[float], optional
+            Translation values for cluster optimization. If not specified, no optimization
+            is performed. Default is [0.0].
+            If specified, translations should be a list or numpy array of translation
+            values in Angstroms. Example: [-0.2, 0.0, 0.2].
         optsave : bool, optional
             If True, saves each optimization step as a PDB file. Default is
             False.
@@ -670,13 +678,6 @@ def _build_cluster(
         # Get lattice constants for nanocluster
         cluster.info.update({"lattice_constants": lattice_constants})
 
-        # Create rotation angles and translations for the cluster
-        if angles is None:
-            angles = numpy.arange(start=-75, stop=90, step=25)
-
-        if translations is None:
-            translations = numpy.arange(start=-0.2, stop=0.21, step=0.2)
-
         # Iterate over all possible combinations of angles and translations
         log = []
         combinations = list(
@@ -747,8 +748,8 @@ def _build_cluster(
         # Convert optimization to DataFrame
         log = pandas.DataFrame(log)
 
-        # Get the best cluster based on the maximum diameter
-        idx = log["Maximum diameter (Å)"].idxmax()
+        # Get the best cluster based on the volume diameter
+        idx = log["Volume diameter (Å)"].idxmax()
         x, y, z, phi, theta, psi = log.loc[idx, ["x", "y", "z", "phi", "theta", "psi"]]
 
         # Rotate and translate the cluster

AtomPacker/structure/Cavity.py

@@ -100,7 +100,7 @@ def volume(self) -> numpy.float64:
             )
         return ((self.grid > 1).sum() * (self._step**3)).round(2)
 
-    def detect_openings(self, verbose: bool = False) -> None:
+    def detect_openings(self, openings_cutoff: int = 1, verbose: bool = False) -> None:
         """
         Detect openings in the cavity.
 
@@ -110,6 +110,9 @@ def detect_openings(self, verbose: bool = False) -> None:
 
         Parameters
         ----------
+        openings_cutoff : float, optional
+            The cutoff value for detecting openings (default is 1). The minimum
+            number of points in an opening to be considered valid.
         verbose : bool, optional
             If True, print detailed information during processing (default is False).
 
@@ -121,7 +124,13 @@ def detect_openings(self, verbose: bool = False) -> None:
         if self.grid.max() > 2:
             warnings.warn("Cavity has more than one cavity.")
 
-        self.openings = Openings(self.grid, self._step, self._vertices, verbose=verbose)
+        self.openings = Openings(
+            self.grid,
+            self._step,
+            self._vertices,
+            openings_cutoff=openings_cutoff,
+            verbose=verbose,
+        )
 
     def preview(
         self,

AtomPacker/structure/Openings.py

@@ -29,7 +29,14 @@ class Openings:
     their properties, and exporting openings data.
     """
 
-    def __init__(self, cavities: numpy.ndarray, step: float, vertices: numpy.ndarray, verbose: bool = False):
+    def __init__(
+        self,
+        cavities: numpy.ndarray,
+        step: float,
+        vertices: numpy.ndarray,
+        openings_cutoff: float = 1,
+        verbose: bool = False,
+    ):
         """
         Create a new `AtomPacker.Openings` object.
 
@@ -41,14 +48,19 @@ def __init__(self, cavities: numpy.ndarray, step: float, vertices: numpy.ndarray
             The step size of the grid.
         vertices : numpy.ndarray
             The vertices (origin, X-axis, Y-axis, Z-axis) of the grid.
+        openings_cutoff : float, optional
+            The cutoff value for detecting openings (default is 1). The minimum
+            number of points in an opening to be considered valid.
         verbose : bool, optional
             If True, print detailed information during processing (default is False).
         """
         self.nopenings: int
         self.grid: numpy.ndarray
         self.areas: dict[str, float]
 
-        self.nopenings, self.grid, self.areas = self._detect(cavities, step, verbose=verbose)
+        self.nopenings, self.grid, self.areas = self._detect(
+            cavities, step, openings_cutoff=openings_cutoff, verbose=verbose
+        )
         self.diameters: dict[str, float] = self._get_diameter()
 
         self._step: float = step
@@ -162,6 +174,7 @@ def _detect(
         self,
         cavities: numpy.ndarray,
         step: float,
+        openings_cutoff: float = 1,
         verbose: bool = False,
     ) -> tuple[int, numpy.ndarray, dict[str, float]]:
         """
@@ -173,6 +186,9 @@ def _detect(
             The cavity points.
         step : float
             The step size of the grid.
+        openings_cutoff : float, optional
+            The cutoff value for detecting openings (default is 1). The minimum
+            number of points in an opening to be considered valid.
         verbose : bool, optional
             If True, print detailed information during processing (default is False).
 
@@ -192,7 +208,13 @@ def _detect(
         depths, _, _ = depth(cavities, step, verbose=verbose)
 
         # Calculate openings and area of openings
-        nopenings, grid, aopenings = openings(cavities, depths, step=step, verbose=verbose)
+        nopenings, grid, aopenings = openings(
+            cavities,
+            depths,
+            step=step,
+            openings_cutoff=openings_cutoff,
+            verbose=verbose,
+        )
 
         # Flatten and sort opening areas
         areas = {