Strip trailing new lines and update example for realsitic pressure

NiklasKappel · Apr 25, 2024 · 2687e66 · 2687e66
1 parent e6ee6d5
commit 2687e66
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Showing 6 changed files with 768 additions and 44 deletions.
diff --git a/README.md b/README.md
@@ -14,18 +14,20 @@ pip install molbox
 from molbox import Box, MolBox
 from molbox.lammps_data import write_lammps_data
 from molbox.rdkit_3d_ops import create_3d_mol_from_smiles, rotate_mol
+from rdkit import Chem
 from scipy.spatial.transform import Rotation
 
 
 def main():
-    box = Box([0, 0, 0], [10, 10, 10])
+    box = Box([0, 0, 0], [175, 175, 175])
     o2_box = MolBox(box=box)
     o2_mol = create_3d_mol_from_smiles("O=O")
-    num_mols = 32
+    num_mols = 128
     for _ in range(num_mols):
-        rotation = Rotation.random(random_state=42)
+        rotation = Rotation.random()
         new_mol = rotate_mol(o2_mol, rotation, "COM")
         o2_box.add_mol_randomly(new_mol)
+    Chem.MolToMolFile(o2_box.mol, "examples/o2_box.mol")
     write_lammps_data(o2_box, "examples/o2_box.lmpdat")
 
 

diff --git a/examples/create_o2_box.py b/examples/create_o2_box.py
@@ -6,10 +6,10 @@
 
 
 def main():
-    box = Box([0, 0, 0], [10, 10, 10])
+    box = Box([0, 0, 0], [175, 175, 175])
     o2_box = MolBox(box=box)
     o2_mol = create_3d_mol_from_smiles("O=O")
-    num_mols = 8
+    num_mols = 128
     for _ in range(num_mols):
         rotation = Rotation.random()
         new_mol = rotate_mol(o2_mol, rotation, "COM")