Update AtomPacker package

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"

AtomPacker/__init__.py

@@ -4,7 +4,7 @@
 
 __author__ = """João V S Guerra"""
 __email__ = '[email protected]'
-__version__ = '0.1.0'
+__version__ = '0.1.1'
 
 from . import AtomPacker
 from .AtomPacker import PackmolStructure, CavityDetector, AtomPacker

README.md

@@ -34,9 +34,7 @@ pip install -e AtomPacker
 
 ## Usage
 
-There are two pipelines available to pack nanoparticle atoms inside a supramolecular cage:
-
-### 1. Packing nanoparticle atoms freely with packmol and filter atoms inside the cavity;
+Packing nanoparticle atoms freely with packmol and filter atoms inside the cavity
 
 ```python
 from AtomPacker import *
@@ -69,42 +67,6 @@ ap.packing(replicates=10)
 print(ap.summary)
 ```
 
-### 2. Packing nanoparticle atoms with packmol inside a boundary and filter atoms inside the cavity;
-
-```python
-from AtomPacker import *
-
-# Load supramolecular cage into PackmolStructure object
-smc = PackmolStructure(
-    os.path.join("data", "C1.pdb"),
-    number=1,
-    instructions=["center", "fixed 0. 0. 0. 0. 0. 0."],
-)
-
-# Load nanoparticle atoms into PackmolStructure object
-# NOTE: You must set an appropriate number of atoms to fill the cavity and define a sphere that contains the whole supramolecular cage
-np_atom = PackmolStructure(
-    os.path.join("data", "Au.pdb"), number=40, instructions=["inside sphere 0. 0. 0. 6."]
-)
-
-# Create a CavityDetector with detection parameters appropriate for the supramolecular cage
-cd = CavityDetector(step=0.25, probe_in=1.4, probe_out=10.0, removal_distance=1.0, volume_cutoff=5.0, vdw=None)
-
-# Create the AtomPacked object
-# NOTE: For gold, atom radius is 1.36 Å
-ap = AtomPacker(smc, np_atom, np_atom_radius=1.36, cavity_detector=cd,
-basedir="pipeline-2")
-
-# Add a boundary to pack nanoparticle atoms
-ap.add_boundary()
-
-# Run Packing algorithm with 10 replicates
-ap.packing(replicates=10)
-
-# Show number of packed atoms
-print(ap.summary)
-```
-
 ## Citing
 
 If you find `AtomPacker` useful for you, please cite the following sources:

pyproject.toml

@@ -6,7 +6,8 @@ build-backend = "setuptools.build_meta"
 name = "AtomPacker"
 description = "A python package for packing atoms into a supramolecular cage"
 authors = [
-    { name = "João Victor da Silva Guerra", email = "[email protected]" },
+    { name = "João Victor da Silva Guerra" },
+    { name = "Gabriel Ernesto Jara" },
 ]
 maintainers = [
     { name = "João Victor da Silva Guerra", email = "[email protected]" },
@@ -29,11 +30,11 @@ classifiers = [
     "Programming Language :: Python :: 3 :: Only",
 ]
 dependencies = [
-    "MDAnalysis==2.6.1",
-    "numpy==1.26.1",
-    "pyKVFinder==0.6.8",
-    "pandas==2.1.1",
-    "scipy==1.11.2",
+    "MDAnalysis==2.7.0",
+    "numpy==1.26.3",
+    "pyKVFinder==0.6.11",
+    "pandas==2.1.4",
+    "scipy==1.11.4",
 ]
 dynamic = ["version"]
 

tests/conftest.py

@@ -8,8 +8,7 @@
 def clean_directories():
     # Define the directories to remove
     directories_to_remove = [
-        "tests/pipeline-1",
-        "tests/pipeline-2",
+        "tests/pipeline",
         # Add more directories to remove as needed
     ]
 

tests/test_pipeline_1.py → tests/test_pipeline.py

@@ -57,20 +57,20 @@ def test_pipeline_1(np_atom_params):
         np_atom,
         np_atom_radius=np_atom_radius,
         cavity_detector=cd,
-        basedir=os.path.join(HERE, "pipeline-1", basename),
+        basedir=os.path.join(HERE, "pipeline", basename),
     )
 
     # Run Packing algorithm
     ap.packing(replicates=REPLICATES)
 
     # Perform assertions to check if files were created for the specified np_atom and np_atom_radius
-    assert os.path.exists(os.path.join(HERE, "pipeline-1", basename, "PackedAtoms.csv"))
-    assert os.path.exists(os.path.join(HERE, "pipeline-1", basename, "cavity.pdb"))
-    assert os.path.exists(os.path.join(HERE, "pipeline-1", basename, "packmol.inp"))
-    assert os.path.exists(os.path.join(HERE, "pipeline-1", basename, "packmol.stdout"))
+    assert os.path.exists(os.path.join(HERE, "pipeline", basename, "PackedAtoms.csv"))
+    assert os.path.exists(os.path.join(HERE, "pipeline", basename, "cavity.pdb"))
+    assert os.path.exists(os.path.join(HERE, "pipeline", basename, "packmol.inp"))
+    assert os.path.exists(os.path.join(HERE, "pipeline", basename, "packmol.stdout"))
     for replicate in range(REPLICATES):
         assert os.path.exists(
-            os.path.join(HERE, "pipeline-1", basename, f"packed{replicate}.pdb")
+            os.path.join(HERE, "pipeline", basename, f"packed{replicate}.pdb")
         )