Bugfix where k-off convergence plots were not being generated. Also a…

…dded check that Amber parameters files have the correct extensions so that mdtraj can read them.

seekr2/converge.py

@@ -29,7 +29,7 @@ def converge(model, k_on_state=None, image_directory=None, verbose=False,
 
     if image_directory is None or image_directory == "" or not long_converge:
         return data_sample_list, times_dict
-
+        
     k_off_fig, ax = common_converge.plot_scalar_conv(
         k_off_conv, max_step_list, title="$k_{off}$ Convergence", 
         label="k_{off} (s^{-1})", timestep_in_ns=timestep_in_ns)

seekr2/modules/check.py

@@ -233,12 +233,13 @@ def load_structure_with_mdtraj(model, anchor, mode="pdb", coords_filename=None):
         return traj
 
     elif anchor.amber_params is not None:
-
-        if anchor.amber_params.prmtop_filename is not None:
+        if (anchor.amber_params.prmtop_filename is None) \
+                or (anchor.amber_params.prmtop_filename == ""):
+            return None
+        else:
             prmtop_filename = os.path.join(
                 building_directory, anchor.amber_params.prmtop_filename)
-        else:
-            return None
+
         if mode == "pdb":
             if anchor.amber_params.pdb_coordinates_filename is not None \
                     and anchor.amber_params.pdb_coordinates_filename != "":
@@ -249,7 +250,16 @@ def load_structure_with_mdtraj(model, anchor, mode="pdb", coords_filename=None):
             else:
                 # anchor has no structure files: at least test that mdtraj
                 #  can load the parm file
-                dummy = mdtraj.load(prmtop_filename)
+                if anchor.amber_params.prmtop_filename is None:
+                    return None
+                my_splitext = os.path.splitext(prmtop_filename)
+                assert len(my_splitext) == 2, \
+                    "File must have '.parm7' or '.prmtop extension: " \
+                    +f"{prmtop_filename}"
+                extension = my_splitext[1]
+                assert extension in [".parm7", ".prmtop"], \
+                    "File must have '.parm7' or '.prmtop' extension: " \
+                    +f"{prmtop_filename}"
                 return None
 
         elif mode == "elber_umbrella":

seekr2/modules/common_converge.py

@@ -394,7 +394,7 @@ def plot_scalar_conv(conv_values, conv_intervals, label, title, timestep_in_ns,
     ax : object
         matplotlib Axes object
     """
-    if not np.all(np.isfinite(conv_values)) or np.all(conv_values == 0):
+    if not np.any(np.isfinite(conv_values)) or np.all(conv_values == 0):
         return None, None
     fig, ax = plt.subplots()
     ax.plot(np.multiply(conv_intervals, timestep_in_ns), conv_values, 

seekr2/modules/elber_analyze.py

@@ -292,7 +292,7 @@ def monte_carlo_milestoning_error(
     if verbose: print("collecting ", num, " MCMC samples from ", 
                       num*(stride) + skip, " total moves")  
     new_data_sample = None
-    for counter in range(num * (stride) + skip):
+    for counter in range(num * (stride) + skip + 1):
         #if verbose: print("MCMC stepnum: ", counter)
         Qnew = markov_chain_monte_carlo\
             .irreversible_stochastic_matrix_algorithm_sample(Q, N, R)

seekr2/modules/mmvt_analyze.py

@@ -1148,7 +1148,7 @@ def monte_carlo_milestoning_error(
             mmvt_Qij_alpha[alpha])
         nonzero_indices_Q_alpha_list.append(nonzero_indices_Q_alpha)
 
-    for counter in range(num * (stride) + skip):
+    for counter in range(num * (stride) + skip + 1):
         new_data_sample = MMVT_data_sample(model)
         new_data_sample.N_alpha_beta = main_data_sample.N_alpha_beta
         new_data_sample.N_i_j_alpha = main_data_sample.N_i_j_alpha