reduce changes to clustenm

prody/dynamics/clustenm.py

@@ -43,20 +43,18 @@
 from .exanm import exANM
 from .editing import extendModel
 from .sampling import sampleModes
-
-from prody.measure.transform import calcTransformation, applyTransformation, calcRMSD
-from prody.proteins.pdbfile import writePDB, writePDBStream, parsePDBStream
-
+from prody.atomic import AtomGroup
+from prody.measure import calcTransformation, applyTransformation, calcRMSD
+from prody.ensemble import Ensemble
+from prody.proteins import writePDB, parsePDB, writePDBStream, parsePDBStream
 from prody.utilities import createStringIO, importLA, mad
 
-from .hybrid import Hybrid
-
 la = importLA()
 norm = la.norm
 
 __all__ = ['ClustENM', 'ClustRTB', 'ClustImANM', 'ClustExANM']
 
-class ClustENM(Hybrid):
+class ClustENM(Ensemble):
 
     '''
     ClustENMv2 is the new version of ClustENM(v1) conformation sampling algorithm [KZ16]_.
@@ -125,9 +123,10 @@ def __getitem__(self, index):
 
         return super(ClustENM, self).__getitem__(index)
 
-    def getAtoms(self, selected=True):
+    def getAtoms(self):
         'Returns atoms.'
-        return super(ClustENM, self).getAtoms(selected)
+
+        return self._atoms
 
     def _isBuilt(self):
 
@@ -893,17 +892,17 @@ 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 ints can be given, e.g. (10, 30, 50) for subsequent generations.
+            A tuple of int's 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, tuple
+        :type maxclust: int or a tuple of int's
 
         :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, tuple
+        :type threshold: float or tuple of floats.
 
         :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 +920,7 @@ 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: tuple
+        :type force_field: a tuple of str
         
         :arg tolerance: Energy tolerance to which the system should be minimized, default is 10.0 kJ/mole.
         :type tolerance: float
@@ -941,12 +940,12 @@ 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 ints can be given, e.g. (3000, 5000, 7000) for subsequent generations.
-        :type t_steps_g: int, tuple
+            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
 
         :arg outlier: Exclusion of conformers detected as outliers in each generation.
             Default is True for implicit solvent. Outliers, if any, are detected by