Updated MDAnalysis select_atoms syntax in code and tests.

tylerjereddy · Dec 17, 2015 · ccb47fe · ccb47fe
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/diffusion_analysis.py b/diffusion_analysis.py
@@ -261,9 +261,9 @@ def mean_square_displacement_by_species(coordinate_file_path, trajectory_file_pa
     if not contiguous_protein_selection:
         MDA_residue_selection_dictionary = {}
         for particle_name, selection_string in dict_particle_selection_strings.iteritems():
-            MDA_selection = universe_object.selectAtoms(selection_string)
+            MDA_selection = universe_object.select_atoms(selection_string)
             MDA_selection_residue_list = MDA_selection.residues #have to break it down by residues, otherwise would end up with centroid of all particles of a given name
-            list_per_residue_selection_objects = [residue.selectAtoms(selection_string) for residue in MDA_selection_residue_list] #the MDA selection objects PER residue
+            list_per_residue_selection_objects = [residue.select_atoms(selection_string) for residue in MDA_selection_residue_list] #the MDA selection objects PER residue
             MDA_residue_selection_dictionary[particle_name] = list_per_residue_selection_objects
 
         def centroid_array_production(current_MDA_selection_dictionary): #actually my modification of this for the github workflow won't work--it will find the centroid of ALL the particles with the same name
@@ -275,7 +275,7 @@ def centroid_array_production(current_MDA_selection_dictionary): #actually my mo
             return dictionary_centroid_arrays
 
     else: #dealing with proteins, where we don't want a breakdown by residue
-        protein_selection = universe_object.selectAtoms(contiguous_protein_selection)
+        protein_selection = universe_object.select_atoms(contiguous_protein_selection)
 
 
     dict_MSD_values = {'MSD_value_dict':{},'MSD_std_dict':{},'frame_skip_value_list':[]} #for overall storage of MSD average / standard deviation values for this replicate

diff --git a/test_diffusion_analysis.py b/test_diffusion_analysis.py
@@ -119,10 +119,10 @@ def test_protein_centroid_data_structure(self):
         universe_object = MDAnalysis.Universe(self.simple_gro_path, self.simple_xtc_path)
         protein_centroids = []
         for i in range(5):
-            prot_sele = universe_object.selectAtoms('bynum {}:{}'.format(i*18+1, (i+1)*18) )
+            prot_sele = universe_object.select_atoms('bynum {}:{}'.format(i*18+1, (i+1)*18) )
             protein_centroids.append(prot_sele.centroid())
         # now get the same data from the diffusion_analysis script
-        all_prot_sele = universe_object.selectAtoms('bynum 1:90')
+        all_prot_sele = universe_object.select_atoms('bynum 1:90')
         num_protein_copies = 5
         dictionary_centroid_arrays = diffusion_analysis.centroid_array_production_protein(all_prot_sele, num_protein_copies )
         # ..and compare