setAtoms fixes

prody/ensemble/functions.py

@@ -46,7 +46,7 @@ def saveEnsemble(ensemble, filename=None, **kwargs):
                           '_padding', '_ionicStrength', '_force_field', '_tolerance',
                           '_maxIterations', '_sim', '_temp', '_t_steps', '_outlier',
                           '_mzscore', '_v1', '_parallel', '_idx_cg', '_n_cg', '_cycle',
-                          '_time', '_targeted', '_tmdk'])
+                          '_time', '_targeted', '_tmdk', '_topology', '_positions'])
     if isinstance(ensemble, AdaptiveHybrid):
         attr_list.extend(['_atomsB', '_defvecs', '_resetFmin', '_rmsds'])
         atomsB = dict_['_atomsB']
@@ -168,7 +168,7 @@ def loadEnsemble(filename, **kwargs):
                     '_rmsd', '_n_gens', '_maxclust', '_threshold', '_sol',
                     '_sim', '_temp', '_t_steps', '_outlier', '_mzscore', '_v1',
                     '_parallel', '_idx_ca', '_n_ca', '_cycle', '_time', '_targeted',
-                    '_tmdk']
+                    '_tmdk', '_topology', '_positions']
 
             for attr in attrs:
                 if attr in attr_dict.files:

prody/hybrid/adaptive.py

@@ -544,9 +544,9 @@ def _sample(self, conf, **kwargs):
 
         return coordsets
 
-    def setAtoms(self, atomsA, atomsB, pH=7.0, **kwargs):
+    def setAtoms(self, atomsA, atomsB=None, pH=7.0, **kwargs):
         aligned = kwargs.get('aligned', False)
-        if not aligned:
+        if not aligned and atomsB is not None:
             T = calcTransformation(atomsA.ca, atomsB.ca, weights=atomsA.ca.getFlags("mapped"))
             _ = applyTransformation(T, atomsA)
 
@@ -555,6 +555,9 @@ def setAtoms(self, atomsA, atomsB, pH=7.0, **kwargs):
             self._atomsB = atomsB
         else:
             for i, atoms in enumerate([atomsA, atomsB]):
+                if i == 1 and atomsB is None:
+                    break
+
                 atoms = atoms.select('not hetatm')
 
                 self._nuc = atoms.select('nucleotide')
@@ -628,17 +631,17 @@ def _fix(self, atoms, i):
         self._topology = fixed.topology
         self._positions = fixed.positions
 
-    def getAtomsA(self):
-
+    def getAtomsA(self, selected=True):
         'Returns atoms for structure A (main atoms).'
+        return super(AdaptiveHybrid, self).getAtoms(selected)
 
-        return self._atoms
-
-    def getAtomsB(self):
-
+    def getAtomsB(self, selected=True):
         'Returns atoms for structure B.'
-
-        return self._atomsB
+        if self._atomsB is None:
+            return None
+        if self._indices is None or not selected:
+            return self._atomsB
+        return self._atomsB[self._indices]
 
     def getRMSDsB(self):
         if self._confs is None or self._coords is None:

prody/hybrid/clustenm.py

@@ -125,11 +125,9 @@ 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):
 

prody/hybrid/hybrid.py

@@ -36,18 +36,20 @@
 from scipy.cluster.hierarchy import fcluster, linkage
 
 from prody import LOGGER
+
 from prody.dynamics.anm import ANM
 from prody.dynamics.gnm import GNM, ZERO
 from prody.dynamics.rtb import RTB
 from prody.dynamics.imanm import imANM
 from prody.dynamics.exanm import exANM
 from prody.dynamics.editing import extendModel
 from prody.dynamics.sampling import sampleModes
-from prody.atomic import AtomGroup
+
+from prody.atomic import AtomGroup, Atomic
 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 prody.proteins import writePDB, writePDBStream, parsePDBStream, EMDMAP
+from prody.utilities import createStringIO, importLA, mad, getCoords
 
 la = importLA()
 norm = la.norm
@@ -115,17 +117,15 @@ def __getitem__(self, index):
 
         return super(Hybrid, self).__getitem__(index)
 
-    def getAtoms(self):
-
+    def getAtoms(self, selected=True):
         'Returns atoms.'
-
-        return self._atoms
+        return super(Hybrid, self).getAtoms(selected)
 
     def _isBuilt(self):
 
         return self._confs is not None
 
-    def setAtoms(self, atoms, pH=7.0):
+    def setAtoms(self, atoms):
 
         '''
         Sets atoms.
@@ -135,6 +135,7 @@ def setAtoms(self, atoms, pH=7.0):
         :arg pH: pH based on which to select protonation states for adding missing hydrogens, default is 7.0.
         :type pH: float
         '''
+        super(Hybrid, self).setAtoms(atoms)
 
     def getTitle(self):
 
@@ -164,7 +165,38 @@ def setTitle(self, title):
         self._title = title
 
     def _fix(self, atoms):
-        ''''''
+
+        try:
+            from pdbfixer import PDBFixer
+            from simtk.openmm.app import PDBFile
+        except ImportError:
+            raise ImportError('Please install PDBFixer and OpenMM in order to use ClustENM.')
+
+        stream = createStringIO()
+        title = atoms.getTitle()
+        writePDBStream(stream, atoms)
+        stream.seek(0)
+        fixed = PDBFixer(pdbfile=stream)
+        stream.close()
+
+        fixed.missingResidues = {}
+        fixed.findNonstandardResidues()
+        fixed.replaceNonstandardResidues()
+        fixed.removeHeterogens(False)
+        fixed.findMissingAtoms()
+        fixed.addMissingAtoms()
+        fixed.addMissingHydrogens(self._ph)
+
+        stream = createStringIO()
+        PDBFile.writeFile(fixed.topology, fixed.positions,
+                          stream, keepIds=True)
+        stream.seek(0)
+        self._atoms = parsePDBStream(stream)
+        self._atoms.setTitle(title)
+        stream.close()
+
+        self._topology = fixed.topology
+        self._positions = fixed.positions
 
     def _prep_sim(self, coords, external_forces=[]):