Add a method to create Compounds from coxeter shape objects

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ ci:
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.21
+  rev: v0.15.22
   hooks:
     # Run the linter.
     - id: ruff

.readthedocs.yml

@@ -5,9 +5,9 @@ formats:
 conda:
   environment: docs/docs-env.yml
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "mambaforge-4.10"
+    python: "mambaforge-latest"
 sphinx:
   builder: html
   configuration: docs/conf.py

docs/conf.py

@@ -158,8 +158,8 @@
 # built documents.
 #
 
-version = "1.3.0"
-release = "1.3.0"
+version = "1.4.0"
+release = "1.4.0"
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

mbuild/__init__.py

@@ -18,7 +18,7 @@
 from mbuild.port import Port
 from mbuild.recipes import recipes
 
-__version__ = "1.3.1"
+__version__ = "1.4.0"
 __date__ = "2025-11-10"
 
 

mbuild/conversion.py

@@ -493,6 +493,54 @@ def load_file(
     return compound
 
 
+def from_coxeter(shape, compound=None, ref_length=1, element=None, name=None):
+    """Backend-specific loading function for Coxeter.
+
+    Vertices are placed as particles and edges become bonds. The shape is
+    scaled so that its longest edge has length ``ref_length``, independent of
+    coxeter's native (unit-volume / unit-area) normalization.
+
+    Parameters
+    ----------
+    shape : coxeter.shapes
+        Any member of coxeter.shapes that exposes ``vertices`` and ``edges``.
+    compound : mb.Compound, optional, default=None
+        Host mb.Compound to load into. A new one is created if left as ``None``.
+    ref_length : float, optional, default=1
+        Target length of the longest edge, in the compound's units.
+    element : str, optional, default=None
+        The element symbol that sets the particle type for the particles.
+        If None, a generic bead-type is used.
+    name : str, optional, default="X"
+        Sets the particle name, but not the element.
+        Use this instead of ``element`` for non-atomistic particles.
+    """
+    if compound is None:
+        compound = mb.Compound()
+
+    scale = ref_length / shape.edge_lengths.max()
+
+    particles = []
+    for v in shape.vertices:
+        p = mb.Compound(pos=np.asarray(v) * scale)
+        if element:
+            p.element = element_from_symbol(element)
+            if not name:
+                p.name = element
+            else:
+                p.name = name
+        elif name:
+            p.name = name
+        compound.add(p)
+        particles.append(p)
+
+    for edge in shape.edges:
+        p1 = particles[int(edge[0])]
+        p2 = particles[int(edge[1])]
+        compound.add_bond(particle_pair=(p1, p2))
+    return compound
+
+
 def from_parmed(
     structure, compound=None, coords_only=False, infer_hierarchy=True, **kwargs
 ):

mbuild/packing.py

@@ -1196,15 +1196,15 @@ def _run_packmol(input_text, filled_xyz, temp_file, packmol_file):
         ):
             shutil.copyfileobj(inp_file, new_file)
 
-    proc = Popen(
-        f"{PACKMOL} < {packmol_inp.name}",
-        stdin=PIPE,
-        stdout=PIPE,
-        stderr=PIPE,
-        universal_newlines=True,
-        shell=True,
-    )
-    out, err = proc.communicate()
+    with open(packmol_inp.name) as inp_file:
+        proc = Popen(
+            [PACKMOL],
+            stdin=inp_file,
+            stdout=PIPE,
+            stderr=PIPE,
+            universal_newlines=True,
+        )
+        out, err = proc.communicate()
 
     if "WITHOUT PERFECT PACKING" in out:
         logger.warning(

mbuild/periodic_kdtree.py

@@ -383,7 +383,7 @@ def query_ball_point(self, x, r, p=2.0, eps=0):
             return self.__query_ball_point(x, r, p, eps)
         else:
             retshape = x.shape[:-1]
-            result = np.empty(retshape, dtype=np.object)
+            result = np.empty(retshape, dtype=object)
             for c in np.ndindex(retshape):
                 result[c] = self.__query_ball_point(x[c], r, p, eps)
             return result

pyproject.toml

@@ -29,7 +29,7 @@ classifiers=[
     "Operating System :: MacOS",
 ]
 urls = {Homepage = "https://github.com/mosdef-hub/mbuild"}
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dynamic = ["version"]
 
 [tool.setuptools]

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.3.0
+current_version = 1.4.0
 commit = True
 tag = True
 message = Bump to version {new_version}