Merge pull request #1307 from jamesmkrieger/clustenm_fix

clustenm fixes

prody/dynamics/clustenm.py

@@ -123,11 +123,9 @@ def __getitem__(self, index):
 
         return super(ClustENM, self).__getitem__(index)
 
-    def getAtoms(self):
-
+    def getAtoms(self, selected=True):
         'Returns atoms.'
-
-        return self._atoms
+        return super(ClustENM, self).getAtoms(selected)
 
     def _isBuilt(self):
 
@@ -893,17 +891,17 @@ def run(self, cutoff=15., n_modes=3, gamma=1., n_confs=50, rmsd=1.0,
         :type n_gens: int
 
         :arg maxclust: Maximum number of clusters for each generation, default in None.
-            A tuple of int's can be given, e.g. (10, 30, 50) for subsequent generations.
+            A tuple of ints can be given, e.g. (10, 30, 50) for subsequent generations.
             Warning: Either maxclust or RMSD threshold should be given! For large number of
             generations and/or structures, specifying maxclust is more efficient.
-        :type maxclust: int or a tuple of int's
+        :type maxclust: int, tuple
 
         :arg threshold: RMSD threshold to apply when forming clusters, default is None.
             This parameter has been used in ClustENMv1, setting it to 75% of the maximum RMSD
             value used for sampling. A tuple of floats can be given, e.g. (1.5, 2.0, 2.5)
             for subsequent generations.
             Warning: This threshold should be chosen carefully in ClustENMv2 for efficiency.
-        :type threshold: float or tuple of floats.
+        :type threshold: float, tuple
 
         :arg solvent: Solvent model to be used. If it is set to 'imp' (default),
             implicit solvent model will be used, whereas 'exp' stands for explicit solvent model.
@@ -921,7 +919,7 @@ def run(self, cutoff=15., n_modes=3, gamma=1., n_confs=50, rmsd=1.0,
         :arg force_field: Implicit solvent force field is ('amber99sbildn.xml', 'amber99_obc.xml'). 
             Explicit solvent force field is ('amber14-all.xml', 'amber14/tip3pfb.xml').
             Experimental feature: Forcefields already implemented in OpenMM can be used. 
-        :type force_field: a tuple of str
+        :type force_field: tuple
         
         :arg tolerance: Energy tolerance to which the system should be minimized, default is 10.0 kJ/mole.
         :type tolerance: float
@@ -941,12 +939,12 @@ def run(self, cutoff=15., n_modes=3, gamma=1., n_confs=50, rmsd=1.0,
         :arg t_steps_i: Duration of MD simulation (number of time steps) for the starting structure
             following the heating-up phase, default is 1000. Each time step is 2.0 fs.
             Note: Default value reduces possible drift from the starting structure. 
-        :type t_steps_i : int
+        :type t_steps_i: int
 
         :arg t_steps_g: Duration of MD simulations (number of time steps) to run for each conformer
             following the heating-up phase, default is 7500. Each time step is 2.0 fs.
-            A tuple of int's can be given, e.g. (3000, 5000, 7000) for subsequent generations.
-        :type t_steps_g: int or tuple of int's
+            A tuple of ints can be given, e.g. (3000, 5000, 7000) for subsequent generations.
+        :type t_steps_g: int, tuple
 
         :arg outlier: Exclusion of conformers detected as outliers in each generation.
             Default is True for implicit solvent. Outliers, if any, are detected by
@@ -985,7 +983,7 @@ def run(self, cutoff=15., n_modes=3, gamma=1., n_confs=50, rmsd=1.0,
         self._targeted = kwargs.pop('targeted', False)
         self._tmdk = kwargs.pop('tmdk', 15.)
 
-        if maxclust is None and threshold is None:
+        if maxclust is None and threshold is None and n_gens > 0:
             raise ValueError('Either maxclust or threshold should be set!')
 
         if maxclust is None: