Merge pull request #2017 from jamesmkrieger/parallel_insty

more Parallel InSty fixes

prody/proteins/interactions.py

@@ -1004,6 +1004,10 @@ def calcSaltBridges(atoms, **kwargs):
     distA = kwargs.pop('distA', distSB)
 
     atoms_KRED = atoms.select('protein and ((resname ASP GLU LYS ARG and not backbone and not name OXT NE "C.*" and noh) or (resname HIS HSE HSD HSP and name NE2))')
+    if atoms_KRED is None:
+        LOGGER.warn('There are no side chain heavy atoms for residues K, R, E, D and H, so not salt bridges are calculated')
+        return []
+
     charged_residues = list(set(zip(atoms_KRED.getResnums(), atoms_KRED.getChids())))
 
     LOGGER.info('Calculating salt bridges.')
@@ -1735,8 +1739,9 @@ def calcInteractionsMultipleFrames(atoms, interaction_type, trajectory, **kwargs
         if isinstance(trajectory, Atomic):
             trajectory = Ensemble(trajectory)
 
-        nfi = trajectory._nfi    
-        trajectory.reset()
+        if isinstance(trajectory, Trajectory):
+            nfi = trajectory._nfi
+            trajectory.reset()
         numFrames = trajectory._n_csets
 
         if stop_frame == -1:
@@ -1745,7 +1750,7 @@ def calcInteractionsMultipleFrames(atoms, interaction_type, trajectory, **kwargs
             traj = trajectory[start_frame:stop_frame+1]
 
         atoms_copy = atoms.copy()
-        def analyseFrame(j0, start_frame, frame0, interactions_all):
+        def analyseFrame(j0, frame0, interactions_all):
             LOGGER.info('Frame: {0}'.format(j0))
             atoms_copy.setCoords(frame0.getCoords())
             protein = atoms_copy.select('protein')
@@ -1755,13 +1760,10 @@ def analyseFrame(j0, start_frame, frame0, interactions_all):
         if max_proc == 1:
             interactions_all = []
             for j0, frame0 in enumerate(traj, start=start_frame):
-                interactions_all.append([])
-                analyseFrame(j0, start_frame, frame0, interactions_all)
+                analyseFrame(j0, frame0, interactions_all)
         else:
             with mp.Manager() as manager:
                 interactions_all = manager.list()
-                for j0, frame0 in enumerate(traj, start=start_frame):
-                    interactions_all.append([])
 
                 j0 = start_frame
                 while j0 < traj.numConfs()+start_frame:
@@ -1770,8 +1772,7 @@ def analyseFrame(j0, start_frame, frame0, interactions_all):
                     for _ in range(max_proc):
                         frame0 = traj[j0-start_frame]
 
-                        p = mp.Process(target=analyseFrame, args=(j0, start_frame,
-                                                                 frame0,
+                        p = mp.Process(target=analyseFrame, args=(j0, frame0,
                                                                  interactions_all))
                         p.start()
                         processes.append(p)
@@ -1785,7 +1786,8 @@ def analyseFrame(j0, start_frame, frame0, interactions_all):
 
                 interactions_all = interactions_all[:]
 
-        trajectory._nfi = nfi
+        if isinstance(trajectory, Trajectory):
+            trajectory._nfi = nfi
 
     else:
         if atoms.numCoordsets() > 1:
@@ -1796,16 +1798,19 @@ def analyseFrame(i, interactions_all):
                 interactions = interactions_dic[interaction_type](protein, **kwargs)
                 interactions_all.append(interactions)
 
+            if stop_frame == -1:
+                stop_frame = atoms.numCoordsets()
+
             if max_proc == 1:
                 interactions_all = []
-                for i in range(len(atoms.getCoordsets()[start_frame:stop_frame])):
+                for i in range(len(atoms.getCoordsets()[start_frame:stop_frame+1])):
                     analyseFrame(i, interactions_all)
             else:
                 with mp.Manager() as manager:
                     interactions_all = manager.list()
 
                     i = start_frame
-                    while i < len(atoms.getCoordsets()[start_frame:stop_frame]):
+                    while i < len(atoms.getCoordsets()[start_frame:stop_frame+1]):
                         processes = []
                         for _ in range(max_proc):
                             p = mp.Process(target=analyseFrame, args=(i, interactions_all))
@@ -3127,8 +3132,9 @@ def calcSminaBindingAffinity(atoms, trajectory=None, **kwargs):
         if isinstance(trajectory, Atomic):
             trajectory = Ensemble(trajectory)
 
-        nfi = trajectory._nfi
-        trajectory.reset()
+        if isinstance(trajectory, Trajectory):
+            nfi = trajectory._nfi
+            trajectory.reset()
         numFrames = trajectory._n_csets
 
         if stop_frame == -1:
@@ -3164,7 +3170,8 @@ def calcSminaBindingAffinity(atoms, trajectory=None, **kwargs):
                 bindingAffinity.append(data['Affinity'])
                 data_final.append(data)
 
-        trajectory._nfi = nfi
+        if isinstance(trajectory, Trajectory):
+            trajectory._nfi = nfi
 
     else:
         if atoms.numCoordsets() == 1:
@@ -5178,9 +5185,10 @@ def calcProteinInteractionsTrajectory(self, atoms, trajectory=None, filename=Non
         if isinstance(trajectory, Atomic):
             trajectory = Ensemble(trajectory)
 
-        #nfi = trajectory._nfi
-        #trajectory.reset()
-        #numFrames = trajectory._n_csets
+        if isinstance(trajectory, Trajectory):
+            nfi = trajectory._nfi
+            trajectory.reset()
+        numFrames = trajectory._n_csets
 
         if stop_frame == -1:
             traj = trajectory[start_frame:]
@@ -5286,6 +5294,9 @@ def analyseFrame(j0, frame0, interactions_all, interactions_nb, j0_list):
             with open(str(filename)+'.pkl', 'wb') as f:
                 pickle.dump(self._interactions_traj, f)  
             LOGGER.info('File with interactions saved.')
+
+        if isinstance(trajectory, Trajectory):
+            trajectory._nfi = nfi
 
         return interactions_nb
 
@@ -5790,8 +5801,9 @@ def calcLigandInteractionsTrajectory(self, atoms, trajectory=None, **kwargs):
             if isinstance(trajectory, Atomic):
                 trajectory = Ensemble(trajectory)
 
-            nfi = trajectory._nfi
-            trajectory.reset()
+            if isinstance(trajectory, Trajectory):
+                nfi = trajectory._nfi
+                trajectory.reset()
             numFrames = trajectory._n_csets
 
             if stop_frame == -1: