generate points function is modified

anooplab · Aug 6, 2024 · 1bc5927 · 1bc5927
1 parent 030a81a
commit 1bc5927
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Showing 5 changed files with 78 additions and 242 deletions.
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/pyar.iml b/.idea/pyar.iml
diff --git a/pyar/scripts/pyar-clustering b/pyar/scripts/pyar-clustering
@@ -36,7 +36,7 @@ if len(input_files) < 2:
 mols = []
 for each_file in input_files:
     mol = Molecule.from_xyz(each_file)
-    mol.energy = pyar.data_analysis.clustering.read_energy_from_xyz_file(each_file)
+    mol.energy = pyar.data_analysis.clustering_file(each_file)
     mols.append(mol)
 
 pyar.data_analysis.clustering.plot_energy_histogram(mols)

diff --git a/pyar/scripts/pyar-tabu b/pyar/scripts/pyar-tabu
@@ -68,7 +68,7 @@ def tabu_function():
     tabu_on = args.tabu == 'y:'
     grid_on = False
     pts = pyar.tabu.generate_points(number_of_trial_orientations,
-                                    tabu_on, grid_on, False)
+                                    tabu_on, d_threshold=1.0)
     if args.plot:
         pyar.tabu.plot_points(pts, os.getcwd())
 
@@ -86,8 +86,7 @@ def tabu_function():
     if args.make_composite:
         for i in range(8):
             pts = pyar.tabu.generate_points(number_of_trial_orientations,
-                                            tabu_on=True, grid_on=True,
-                                            check_angle=False)
+                                            tabu_on=True, d_threshold=1.0)
             result = pyar.tabu.create_composite_molecule(seed, monomer,
                                                          pts, d_scale=d_scale)
             result.title = f"trial_{i:03d}"