Get atom radius from raw

AtomPacker/structure/Cage.py

@@ -531,6 +531,14 @@ def _build_cluster(
         # Translate the cluster to the center
         cluster.positions += center
 
+        # Get radii for nanocluster
+        distances = cluster.get_all_distances()
+        radii = (distances[distances > 0] / 2).min()
+        cluster.info.update({"radii": radii})
+
+        # Get lattice constants for nanocluster
+        cluster.info.update({"lattice_constants": lattice_constants})
+
         if optimize:
             # Create rotation angles and translations for the cluster
             if angles is None:

AtomPacker/structure/Cluster.py

@@ -11,12 +11,11 @@
 """
 
 import os
-from typing import Any, Dict, Tuple
+from typing import Any, Dict
 
 import ase
 import numpy
 import pandas
-from ase.data import atomic_numbers, covalent_radii
 from MDAnalysis import Universe
 from plotly.express import scatter_3d
 
@@ -53,7 +52,8 @@ def __init__(
         # Cluster information
         self.atom_type = cluster.get_chemical_symbols()[0]
         self.lattice_type = cluster.symmetry
-        self.lattice_constants = self._get_lattice_constants()
+        self.lattice_constants = cluster.info.get("lattice_constants")
+        self.radii = cluster.info.get("radii")
 
         # Atomic information: MDAnalysis Universe
         self.universe = self._get_universe()
@@ -214,7 +214,7 @@ def summary(self) -> pandas.DataFrame:
         return pandas.DataFrame.from_dict(
             {
                 "Atom Type": self.atom_type,
-                "Atom Radius": self._get_radii(),
+                "Atom Radius": self.radii,
                 "Cavity Volume (ų)": self._cavity.volume,
                 "Diameter (maximum)": self.diameter(method="maximum"),
                 "Diameter (shape)": self.diameter(method="shape"),
@@ -239,55 +239,7 @@ def _get_distances(self) -> numpy.ndarray:
             cluster.
         """
         # Calculate distances between atoms
-        distances = numpy.linalg.norm(
-            self._cluster.positions[:, numpy.newaxis, :]
-            - self._cluster.positions[numpy.newaxis, :, :],
-            axis=-1,
-        )
-
-        return distances
-
-    def _get_lattice_constants(
-        self,
-    ) -> Tuple[float, float, float] | Tuple[float, float] | float:
-        """
-        Get the lattice constants of the cluster.
-
-        Returns
-        -------
-        Tuple[float, float, float] | Tuple[float, float] | float
-            The lattice constants of the cluster.
-        """
-        if self.lattice_type == "hcp":
-            return (
-                self._cluster.lattice_basis[0, 0],
-                self._cluster.lattice_basis[2, 2],
-            )
-        elif self.lattice_type == "fcc":
-            return self._cluster.lattice_basis[0, 0]
-        elif self.lattice_type == "bcc":
-            return self._cluster.lattice_basis[0, 0]
-        elif self.lattice_type == "sc":
-            return self._cluster.lattice_basis[0, 0]
-
-    def _get_radii(self) -> float:
-        """
-        Get the radius of the atoms in the cluster.
-
-        Returns
-        -------
-        float
-            The radius of the atoms in the cluster.
-        """
-        if len(self._cluster) > 1:
-            # Calculate distances between atoms
-            distances = self._get_distances()
-            # Calculate radii, ignoring self-distances
-            radii = (distances[distances > 0] / 2).min()
-        else:
-            radii = covalent_radii[atomic_numbers[self._cluster.get_chemical_formula()]]
-
-        return radii
+        return self._cluster.get_all_distances()
 
     def _get_universe(self) -> Universe:
         """
@@ -322,7 +274,7 @@ def _get_universe(self) -> Universe:
         )  # atom type
         universe.add_TopologyAttr(
             "radii",
-            [self._get_radii()] * universe.atoms.n_atoms,  # atom radius
+            [self.radii] * universe.atoms.n_atoms,  # atom radius
         )
         universe.add_TopologyAttr("resids", [1])  # resids
         universe.add_TopologyAttr("resnums", [1])  # resnums

README.md

@@ -49,7 +49,7 @@ Packing nanoparticle atoms, based on ASE nanocluster, and filter atoms inside a
 # Uncomment to preview the cage structure.
 >>> # cage.preview()
 # 2: Detect cavity
->>> cage.detect_cavity(step=0.25, probe_in=1.4, probe_out=10.0, removal_distance=1.0, volume_cutoff=5.0)
+>>> cage.detect_cavity(step=0.6, probe_in=1.4, probe_out=10.0, removal_distance=1.0, volume_cutoff=5.0)
 # Uncomment to preview the cavity structure for detection quality control.
 >>> # cage.cavity.preview()
 # Show volume
@@ -123,13 +123,11 @@ class Cluster {
 + Universe universe
 + numpy.ndarray volume
 # Cavity cavity
-# ase.cluster.Cluster cluster
+# ase.cluster.Cluster _cluster
 + diameter(str method) float
 + preview(str renderer, float opacity, Dict~str,Any~ **kwargs) void
 + save(str filename) void
 # _get_distances() numpy.ndarray
-# _get_lattice_constants() Tuple~float~
-# _get_radii() float
 # _get_universe() Universe  
 }
 }

tests/test_cluster.py

@@ -5,7 +5,6 @@
 
 from AtomPacker import Cage, Cavity, Cluster
 from ase.cluster import FaceCenteredCubic
-from ase.data import atomic_numbers, covalent_radii
 
 DATADIR = os.path.join(os.path.abspath(os.path.dirname(__file__)), "data")
 
@@ -46,41 +45,24 @@ def cavity(grid, vertices):
     )
 
 
-@pytest.fixture  # 1 atom
-def atom():
-    return FaceCenteredCubic(
-        symbols="Au",
-        surfaces=[(1, 0, 0), (0, 1, 0), (0, 0, 1)],
-        layers=[0, 0, 0],
-        latticeconstant=4.08,
-    )
-
-
 @pytest.fixture  # 13 atoms
 def cluster():
-    return FaceCenteredCubic(
+    _cluster = FaceCenteredCubic(
         symbols="Au",
         surfaces=[(1, 0, 0), (0, 1, 0), (0, 0, 1)],
         layers=[1, 1, 1],
         latticeconstant=4.08,
     )
+    # Add radius to ase.cluster
+    distances = _cluster.get_all_distances()
+    radii = (distances[distances > 0] / 2).min()
+    _cluster.info.update({"radii": radii})
+    # Add lattice_constants to ase.cluster
+    _cluster.info.update({"lattice_constants": 4.08})
+    return _cluster
 
 
-def test_one_atom_cluster_distances(pdb, cavity, atom):
-    cage = Cage()
-    cage.load(pdb)
-
-    # Dummy Cavity
-    cage.cavity = cavity
-
-    # Dummy Cluster
-    cage.cluster = Cluster(atom, cavity)
-
-    # Check distances for one-atom cluster
-    assert cage.cluster._get_distances() == numpy.array([0])
-
-
-def test_multi_atom_cluster_distances(pdb, cavity, cluster):
+def test_cluster_distances(pdb, cavity, cluster):
     cage = Cage()
     cage.load(pdb)
 
@@ -92,25 +74,11 @@ def test_multi_atom_cluster_distances(pdb, cavity, cluster):
 
     # Check distances for multi-atom cluster
     assert (
-        cage.cluster._cluster.get_all_distances() == cage.cluster._get_distances()
+        cage.cluster._get_distances() == cage.cluster._cluster.get_all_distances()
     ).all()
 
 
-def test_one_atom_cluster_radii(pdb, cavity, atom):
-    cage = Cage()
-    cage.load(pdb)
-
-    # Dummy Cavity
-    cage.cavity = cavity
-
-    # Dummy Cluster
-    cage.cluster = Cluster(atom, cavity)
-
-    # Check radii for one-atom cluster
-    assert cage.cluster._get_radii() == [covalent_radii[atomic_numbers["Au"]]]
-
-
-def test_multi_atom_cluster_radii(pdb, cavity, cluster):
+def test_cluster_radii(pdb, cavity, cluster):
     cage = Cage()
     cage.load(pdb)
 
@@ -125,24 +93,10 @@ def test_multi_atom_cluster_radii(pdb, cavity, cluster):
     radii = distances[distances > 0].min() / 2
 
     # Check radii for multi-atom cluster
-    assert cage.cluster._get_radii() == radii
+    assert cage.cluster.radii == radii
 
 
-def test_one_atom_cluster_coordinates(pdb, cavity, atom):
-    cage = Cage()
-    cage.load(pdb)
-
-    # Dummy Cavity
-    cage.cavity = cavity
-
-    # Dummy Cluster
-    cage.cluster = Cluster(atom, cavity)
-
-    # Check coordinates
-    assert (cage.cluster.coordinates == numpy.array([0, 0, 0])).all()
-
-
-def test_multi_atom_cluster_coordinates(pdb, cavity, cluster):
+def test_cluster_coordinates(pdb, cavity, cluster):
     cage = Cage()
     cage.load(pdb)
 
@@ -165,26 +119,13 @@ def test_cluster_lattice_constants(pdb, cavity, cluster):
 
     # Dummy Cluster
     cage.cluster = Cluster(cluster, cavity)
+    print(cage.cluster.lattice_constants)
 
     # Check lattice constants
-    assert (cage.cluster.lattice_constants == 4.08).all()
-
-
-def test_one_atom_cluster_number_of_atoms(pdb, cavity, atom):
-    cage = Cage()
-    cage.load(pdb)
+    assert cage.cluster.lattice_constants == 4.08
 
-    # Dummy Cavity
-    cage.cavity = cavity
-
-    # Dummy Cluster
-    cage.cluster = Cluster(atom, cavity)
 
-    # Check number of atoms
-    assert cage.cluster.number_of_atoms == 1
-
-
-def test_multi_atom_cluster_number_of_atoms(pdb, cavity, cluster):
+def test_cluster_number_of_atoms(pdb, cavity, cluster):
     cage = Cage()
     cage.load(pdb)
 
@@ -198,28 +139,7 @@ def test_multi_atom_cluster_number_of_atoms(pdb, cavity, cluster):
     assert cage.cluster.number_of_atoms == 13
 
 
-def test_one_atom_cluster_maximum_number_of_atoms(pdb, cavity, atom):
-    cage = Cage()
-    cage.load(pdb)
-
-    # Dummy Cavity
-    cage.cavity = cavity
-
-    # Dummy Cluster
-    cage.cluster = Cluster(atom, cavity)
-
-    # Get maximum number of atoms
-    maximum_number_of_atoms = numpy.ceil(
-        numpy.prod(cage.cavity.grid.shape)
-        * 0.6**3
-        / (4 / 3 * numpy.pi * (cage.cluster._get_radii() ** 3)),
-    ).astype(int)
-
-    # Check maximum number of atoms
-    assert cage.cluster.maximum_number_of_atoms == maximum_number_of_atoms
-
-
-def test_multi_atom_cluster_maximum_number_of_atoms(pdb, cavity, cluster):
+def test_cluster_maximum_number_of_atoms(pdb, cavity, cluster):
     cage = Cage()
     cage.load(pdb)
 
@@ -233,7 +153,7 @@ def test_multi_atom_cluster_maximum_number_of_atoms(pdb, cavity, cluster):
     maximum_number_of_atoms = numpy.ceil(
         numpy.prod(cage.cavity.grid.shape)
         * 0.6**3
-        / (4 / 3 * numpy.pi * (cage.cluster._get_radii() ** 3)),
+        / (4 / 3 * numpy.pi * (cage.cluster.radii**3)),
     ).astype(int)
 
     # Check maximum number of atoms