Rename function

cmeutils/gsd_utils.py

@@ -86,7 +86,7 @@ def get_all_types(gsd_file=None, snap=None, gsd_frame=-1):
     return snap.particles.types
 
 
-def snap_molecule_cluster(gsd_file=None, snap=None, gsd_frame=-1):
+def get_molecule_cluster(gsd_file=None, snap=None, gsd_frame=-1):
     """Find molecule index for each particle.
 
     Compute clusters of bonded molecules and return an array of the molecule

cmeutils/structure.py

@@ -114,7 +114,7 @@ def gsd_rdf(
         type_B = snap.particles.typeid == snap.particles.types.index(B_name)
 
         if exclude_bonded:
-            molecules = gsd_utils.snap_molecule_cluster(snap=snap)
+            molecules = gsd_utils.get_molecule_cluster(snap=snap)
             molecules_A = molecules[type_A]
             molecules_B = molecules[type_B]
 
@@ -164,7 +164,7 @@ def get_centers(gsdfile, new_gsdfile):
     """
     with gsd.hoomd.open(new_gsdfile, 'wb') as new_traj, gsd.hoomd.open(gsdfile, 'rb') as traj:
         snap = traj[0]
-        cluster_idx = gsd_utils.snap_molecule_cluster(snap=snap)
+        cluster_idx = gsd_utils.get_molecule_cluster(snap=snap)
         for snap in traj:
             new_snap = gsd.hoomd.Snapshot()
             new_snap.configuration.box = snap.configuration.box
@@ -285,20 +285,20 @@ def all_atom_rdf(gsdfile,
                  bins=100,
                  ):
     """Compute intermolecular RDF from a GSD file.
-    
+
     This function calculates the radial distribution function given a GSD file
     for all atoms. By default it will calculate the RDF
     for the entire trajectory.
     It is assumed that the bonding, number of particles, and simulation box do
     not change during the simulation.
-    
+
     Parameters
     ----------
     gsdfile : str
         Filename of the GSD trajectory.
     start : int, default 0
         Starting frame index for accumulating the RDF. Negative numbers index
-        from the end. 
+        from the end.
     stop : int, default -1
         Final frame index for accumulating the RDF. If None, the last frame
         will be used.
@@ -308,7 +308,7 @@ def all_atom_rdf(gsdfile,
         Minimum radius of RDF.
     bins : int, default 100
         Number of bins to use when calculating the RDF.
-        
+
     Returns
     -------
     freud.density.RDF

cmeutils/tests/test_gsd.py

@@ -5,7 +5,7 @@
 
 from base_test import BaseTest
 from cmeutils.gsd_utils import (
-    get_type_position, snap_molecule_cluster, get_all_types, _validate_inputs,
+    get_type_position, get_molecule_cluster, get_all_types, _validate_inputs,
     snap_delete_types, xml_to_gsd
 )
 
@@ -45,8 +45,8 @@ def test_get_all_types(self, gsdfile):
         types = get_all_types(gsdfile)
         assert types == ["A", "B"]
 
-    def test_snap_molecule_cluster(self, gsdfile_bond):
-        cluster = snap_molecule_cluster(gsd_file=gsdfile_bond)
+    def test_get_molecule_cluster(self, gsdfile_bond):
+        cluster = get_molecule_cluster(gsd_file=gsdfile_bond)
         assert np.array_equal(cluster, [1, 0, 1, 0, 0])
 
     def test_snap_delete_types(self, snap):