Added new PDB examples

Improved the ClassRegistry import mechanism (avoid conflict with distro
module with the same name)
Improved the performance of the molecular viewer
Removed unused import
Bug fix in QVectors widgets

MDANSE/Core/ClassRegistry.py

@@ -32,6 +32,7 @@ Created on Mar 30, 2015
 
 import abc
 import glob
+import imp
 import inspect
 import os
 import sys
@@ -112,7 +113,7 @@ class ClassRegistry(abc.ABCMeta):
         '''
         Update the classes registry by importing all the modules contained in a given package.
         
-        Only the classes that are metaclassed by ClassRegistry will be registered.
+        Only the classes metaclassed by :py:class:`~MDANSE.Core.ClassRegistry.ClassRegistry` will be registered.
         
         :param packageDir: the package for which all modules should be imported
         :type packageDir: str
@@ -125,16 +126,22 @@ class ClassRegistry(abc.ABCMeta):
             if moduleFile == '__init__.py':
                 continue
      
-            moduleName, moduleExt = os.path.splitext(moduleFile)
+            moduleName, _ = os.path.splitext(moduleFile)
             
             if moduleDir not in sys.path:        
                 sys.path.append(moduleDir)
 
+
             # Any error that may occur here has to be caught. In such case the module is skipped.    
             try:
-                __import__(moduleName, locals(), globals())
+                filehandler,path,description = imp.find_module(moduleName, [moduleDir])
+                mod = imp.load_module(moduleName,filehandler,path,description)
             except:
                 continue
+            else:
+                if not os.path.samefile(os.path.dirname(mod.__file__),moduleDir):
+                    print "A module with name %s is already present in your distribution with %s path." % (moduleName,)
+
     
     @classmethod
     def info(cls, interface):

MDANSE/Core/Error.py

@@ -32,7 +32,7 @@ Created on Mar 30, 2015
 
 class Error(Exception):
     '''
-    Base class for handling exception occuring in MDANSE.
+    Base class for handling exception occurring in MDANSE.
     
     Any exception defined in MDANSE should derive from it in order to be properly handled
     in the GUI application.

MDANSE/Core/Platform.py

@@ -39,7 +39,6 @@ import os
 import re
 import subprocess
 import tempfile
-import types
 
 from MDANSE.Core.Error import Error
 

MDANSE/Framework/Configurable.py

@@ -56,7 +56,7 @@ class Configurable(object):
     
     settings = collections.OrderedDict()
     
-    def __init__(self):
+    def __init__(self,settings=None):
         '''
         Constructor
         '''
@@ -65,6 +65,9 @@ class Configurable(object):
                                      
         self._configured=False
         
+        if settings is not None:
+            self.settings = settings
+        
         self.build_configuration()
         
     def build_configuration(self):

MDANSE/Framework/Jobs/Converters/PDB.py

@@ -66,11 +66,11 @@ class PDBConverter(Converter):
         self.numberOfSteps = self.configuration['nb_frame']["number"]
 
         # Create all objects from the PDB file.  
-        pdb_config = PDBFile(self.configuration['pdb_file']['filename'], model =  0)
+        pdb_config = PDBFile(self.configuration['pdb_file']['filename'], model=0)
 
         # Create the universe.
         self._universe = pdb_config.createUnitCellUniverse()
-        
+                
         # Construct system
         self._universe.addObject(pdb_config.createAll(None, 1))
         
@@ -95,7 +95,7 @@ class PDBConverter(Converter):
         pdb_config = PDBFile(self.configuration['pdb_file']['filename'], model=frame)
         uni = pdb_config.createUnitCellUniverse()
         uni.addObject(pdb_config.createAll(None, 1))
-        
+                
         univ_config  = Configuration(self._universe, uni.configuration().array)
         
         self._universe.setConfiguration(univ_config)

MDANSE/Framework/Jobs/IJob.py

@@ -106,6 +106,8 @@ class IJob(Configurable):
     type = "job"
     
     section = "job"
+    
+    ancestor = 'molecular_viewer'
         
     @staticmethod
     def define_unique_name():
@@ -294,7 +296,7 @@ class IJob(Configurable):
         f.write('\n')
     
         f.write('job = REGISTRY[%r][%r]()\n' % ('job',cls.type))
-        f.write('job.run(parameters,status=False)')
+        f.write('job.run(parameters,status=True)')
          
         f.close()
         

MDANSE/Framework/Plugins/JobPlugin.py

@@ -27,12 +27,13 @@
 ''' 
 Created on Apr 14, 2015
 
-:author: Eric C. ellegrini
+:author: Eric C. Pellegrini
 '''
 
 import os
 import subprocess               
 import sys
+import tempfile
 import time
 
 import wx
@@ -40,8 +41,9 @@ import wx.aui as aui
 
 from MDANSE import PLATFORM,REGISTRY
 from MDANSE.Externals.pubsub import pub
-
 from MDANSE.Framework.Plugins.ComponentPlugin import ComponentPlugin
+from MDANSE.GUI import DATA_CONTROLLER
+from MDANSE.GUI.WorkingPanel import WorkingPanel
 from MDANSE.GUI.ComboWidgets.ConfigurationPanel import ConfigurationPanel
 from MDANSE.GUI.ComboWidgets.JobHelpFrame import JobHelpFrame
 
@@ -106,10 +108,11 @@ class JobPlugin(ComponentPlugin):
             return
         
         name = self._job.define_unique_name()
-        
-        script = os.path.join(PLATFORM.jobscripts_directory(),name)+'.py'
-                
-        self._job.save(script, parameters)
+
+        handle,filename = tempfile.mkstemp(prefix="MDANSE_%s.py" % name, text=True)
+        os.close(handle)
+                        
+        self._job.save(filename, parameters)
                                 
         if PLATFORM.name == "windows":
             startupinfo = subprocess.STARTUPINFO()
@@ -118,7 +121,7 @@ class JobPlugin(ComponentPlugin):
         else:
             startupinfo = None
         
-        subprocess.Popen([sys.executable, script], startupinfo=startupinfo, stdin=subprocess.PIPE,stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        subprocess.Popen([sys.executable, filename], startupinfo=startupinfo, stdin=subprocess.PIPE,stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
         time.sleep(1)
 
@@ -159,7 +162,7 @@ class JobPlugin(ComponentPlugin):
         
 class JobFrame(wx.Frame):
     
-    def __init__(self, parent, jobType, datakey):
+    def __init__(self, parent, jobType, datakey=None):
                 
         wx.Frame.__init__(self, parent, wx.ID_ANY, size = (800,400), style=wx.DEFAULT_DIALOG_STYLE|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX|wx.RESIZE_BORDER)
 
@@ -167,9 +170,10 @@ class JobFrame(wx.Frame):
         
         self._datakey = datakey
 
-        data = REGISTRY['input_data']['mmtk_trajectory'](self._datakey)
-                                    
-        DATA_CONTROLLER[filename] = data
+        if self._datakey is not None:
+            data = REGISTRY['input_data']['mmtk_trajectory'](self._datakey)
+                                        
+            DATA_CONTROLLER[filename] = data
 
         self.build_dialog()
 
@@ -196,13 +200,10 @@ class JobFrame(wx.Frame):
             self.Destroy()           
         
 if __name__ == "__main__":
-
-    from MDANSE.GUI import DATA_CONTROLLER
-    from MDANSE.GUI.WorkingPanel import WorkingPanel
             
     filename = os.path.join(os.path.dirname(PLATFORM.package_directory()),'Data','Trajectories','MMTK','protein_in_periodic_universe.nc')
     
     app = wx.App(False)
-    f = JobFrame(None,'mvi',filename)
+    f = JobFrame(None,'msd',filename)
     f.Show()
     app.MainLoop()            
\ No newline at end of file

MDANSE/Framework/Plugins/MolecularViewerPlugin.py

@@ -94,7 +94,7 @@ class SelectionBox(vtk.vtkBoxWidget):
                     
         outlineMapper = vtk.vtkPolyDataMapper()
         outlineMapper.SetInputConnection(outline.GetOutputPort())
-        self.box=vtk.vtkActor()
+        self.box=vtk.vtkLODActor()
         self.box.SetMapper( outlineMapper )
         self.box.GetProperty().SetColor(1,1,1)
         self.box.PickableOff()
@@ -159,7 +159,7 @@ class MolecularViewerPanel(ComponentPlugin):
     category = ("Viewer",)
                 
     # 0 line / 1 sphere / 2 tube / 3 sphere + tube / 4 sphere + line
-    _rendmod = 3
+    _rendmod = 0
     
     def __init__(self, parent, *args, **kwargs):
         
@@ -290,21 +290,41 @@ class MolecularViewerPanel(ComponentPlugin):
         
         # The number of atoms of the universe stored by the trajectory.
         self._nAtoms = trajectory.universe.numberOfAtoms()
-                                   
-        self.coords = trajectory.universe.contiguousObjectConfiguration().array
-
+        
+        self._resolution = int(numpy.sqrt(300000.0 / self._nAtoms))
+        if self._resolution > 10:
+            self._resolution = 10
+        
+        if self._resolution < 4:
+            self._resolution = 4
+                             
         # The array that will store the color and alpha scale for all the atoms.
         self._atomsColours , self._lut= self.build_ColorTransferFunction()
         self.atomsColours = numpy.copy(self._atomsColours)
                         
         # The array that will store the scale for all the atoms.
         self._atomsScales = numpy.array([ELEMENTS[at.symbol,'vdw_radius'] for at in self._atoms]).astype(numpy.float32)
+
+        scalars = ndarray_to_vtkarray(self.atomsColours, self._atomsScales, self._nAtoms) 
+
+        bonds = vtk.vtkCellArray()
+        for at in self._atoms:
+            idx1 = at.index
+            for bat in at.bondedTo():
+                idx2 = bat.index
+                line = vtk.vtkLine()
+                line.GetPointIds().SetId(0,idx1)
+                line.GetPointIds().SetId(1,idx2)
+                bonds.InsertNextCell(line)
+
+        self._polydata = vtk.vtkPolyData()
+        self._polydata.GetPointData().SetScalars(scalars)
+        self._polydata.SetLines(bonds)
              
         self.clear_universe()
         
         self._trajectory = trajectory
-        
-        # Set the configuration and display it.        
+
         self.set_configuration(frame)
         
         self.enable_info_picking()
@@ -803,7 +823,7 @@ class MolecularViewerPanel(ComponentPlugin):
         outline_mapper = vtk.vtkPolyDataMapper()
         outline_mapper.SetInputConnection(outline.GetOutputPort())
         
-        outline_actor = vtk.vtkActor()
+        outline_actor = vtk.vtkLODActor()
         outline_actor.SetMapper(outline_mapper)
         outline_actor.GetProperty().SetColor(1,0,0)
         outline_actor.GetProperty().SetLineWidth(3)
@@ -834,45 +854,25 @@ class MolecularViewerPanel(ComponentPlugin):
         outline_mapper = vtk.vtkPolyDataMapper()
         outline_mapper.SetInputConnection(outline.GetOutputPort())
         
-        outline_actor = vtk.vtkActor()
+        outline_actor = vtk.vtkLODActor()
         outline_actor.SetMapper(outline_mapper)
         outline_actor.GetProperty().SetColor(1,1,1)
         outline_actor.GetProperty().SetLineWidth(3)
         
         return outline_actor
      
-    def build_polydata(self):   
+    def build_scene(self):   
         '''
         build a vtkPolyData object for a given frame of the trajectory
         '''
         
-        self._polydata = vtk.vtkPolyData()
-        
-        # Converts the numpy coordinates into a vtk array
-        coords, self.vtkids = ndarray_to_vtkpoints(self.coords)
-        self._polydata.SetPoints(coords)
-        del coords
-        
-        scalars = ndarray_to_vtkarray(self.atomsColours, self._atomsScales, self._nAtoms) 
-        self._polydata.GetPointData().SetScalars(scalars) 
-        del scalars
-        
-        bonds = []
-        for at in self._atoms:
-            for bat in at.bondedTo():
-                if set([at.index,bat.index]) not in bonds:
-                    bonds.append([at.index,bat.index])
-        bonds = ndarray_to_vtkcellarray(bonds)
-        self._polydata.SetLines(bonds)
-        del bonds
-        
         rendmod = self._rendmod
         
-        actor_list = []
-        line_acteur=None
-        ball_acteur=None
-        tube_acteur=None
-        
+        actorList = []
+        lineActor=None
+        ballActor=None
+        tubeActor=None
+                
         if rendmod in [0,4] :
             line_mapper = vtk.vtkPolyDataMapper()
             if vtk.vtkVersion.GetVTKMajorVersion()<6:
@@ -883,15 +883,17 @@ class MolecularViewerPanel(ComponentPlugin):
             line_mapper.SetLookupTable(self._lut)
             line_mapper.ScalarVisibilityOn()
             line_mapper.ColorByArrayComponent("scalars", 1)
-            line_acteur = vtk.vtkActor()
-            line_acteur.GetProperty().SetLineWidth(3)
-            line_acteur.SetMapper(line_mapper)
-            actor_list.append(line_acteur)
+            lineActor = vtk.vtkLODActor()
+            lineActor.GetProperty().SetLineWidth(3)
+            lineActor.SetMapper(line_mapper)
+            actorList.append(lineActor)
             
         if rendmod in [1,3,4]:
             sphere = vtk.vtkSphereSource()
             sphere.SetCenter(0, 0, 0)
             sphere.SetRadius(0.2)
+            sphere.SetThetaResolution(self._resolution)
+            sphere.SetPhiResolution(self._resolution)
             glyph = vtk.vtkGlyph3D()
             if vtk.vtkVersion.GetVTKMajorVersion()<6:
                 glyph.SetInput(self._polydata)
@@ -909,13 +911,15 @@ class MolecularViewerPanel(ComponentPlugin):
             sphere_mapper.SetInputConnection(glyph.GetOutputPort())            
             sphere_mapper.ScalarVisibilityOn()
             sphere_mapper.ColorByArrayComponent("scalars", 1)
-            ball_acteur = vtk.vtkActor()
-            ball_acteur.SetMapper(sphere_mapper)
-            ball_acteur.GetProperty().SetAmbient(0.2)
-            ball_acteur.GetProperty().SetDiffuse(0.5)
-            ball_acteur.GetProperty().SetSpecular(0.3)
-            actor_list.append(ball_acteur)
+            ballActor = vtk.vtkLODActor()
+            ballActor.SetMapper(sphere_mapper)
+            ballActor.GetProperty().SetAmbient(0.2)
+            ballActor.GetProperty().SetDiffuse(0.5)
+            ballActor.GetProperty().SetSpecular(0.3)
+            ballActor.SetNumberOfCloudPoints(30000)
+            actorList.append(ballActor)
             self.glyph = glyph
+            
         if rendmod in [2,3] :
             tubes = vtk.vtkTubeFilter()
             if vtk.vtkVersion.GetVTKMajorVersion()<6:
@@ -930,46 +934,45 @@ class MolecularViewerPanel(ComponentPlugin):
             else:
                 tubes.SetCapping(0)
                 tubes.SetRadius(0.01)
+            tubes.SetNumberOfSides(self._resolution)
             tube_mapper = vtk.vtkPolyDataMapper()
             tube_mapper.SetLookupTable(self._lut)
             tube_mapper.SetInputConnection(tubes.GetOutputPort())
             tube_mapper.ScalarVisibilityOn()
             tube_mapper.ColorByArrayComponent("scalars", 1)
-            tube_acteur = vtk.vtkActor()
-            tube_acteur.SetMapper(tube_mapper)
-            tube_acteur.GetProperty().SetAmbient(0.2)
-            tube_acteur.GetProperty().SetDiffuse(0.5)
-            tube_acteur.GetProperty().SetSpecular(0.3)
-            actor_list.append(tube_acteur)
+            tubeActor = vtk.vtkLODActor()
+            tubeActor.SetMapper(tube_mapper)
+            tubeActor.GetProperty().SetAmbient(0.2)
+            tubeActor.GetProperty().SetDiffuse(0.5)
+            tubeActor.GetProperty().SetSpecular(0.3)
+            actorList.append(tubeActor)
             self.tubes = tubes
         
-        self.picking_domain = {0:line_acteur,1:ball_acteur,2:tube_acteur,3:ball_acteur,4:ball_acteur}[rendmod]
+        self.picking_domain = [lineActor,ballActor,tubeActor,ballActor,ballActor][rendmod]
         
         basis_vector = self._trajectory.universe.basisVectors()
         if not basis_vector is None:
             self.bbox = self.build_bbox(basis_vector)
             if not self.display_bbox:
                 self.bbox.VisibilityOff()
-            actor_list.append(self.bbox)
+            actorList.append(self.bbox)
             
         assembly = vtk.vtkAssembly()
-        for actor in actor_list:
+        for actor in actorList:
             assembly.AddPart(actor)
-        
-        #self.build_real_bbox(assembly)
-        
+                
         return assembly
     
     def clear_universe(self):
 
-        if not hasattr(self, "molecule"):
+        if not hasattr(self, "_actors"):
             return 
         
-        self.molecule.VisibilityOff()
-        self.molecule.ReleaseGraphicsResources(self.get_renwin())
-        self._renderer.RemoveActor(self.molecule)
+        self._actors.VisibilityOff()
+        self._actors.ReleaseGraphicsResources(self.get_renwin())
+        self._renderer.RemoveActor(self._actors)
         
-        del self.molecule 
+        del self._actors
   
     def show_universe(self):
         '''
@@ -979,10 +982,10 @@ class MolecularViewerPanel(ComponentPlugin):
         self.clear_universe()
         
         # creating new polydata
-        self.molecule = self.build_polydata()
+        self._actors = self.build_scene()
 
         # adding polydata to renderer
-        self._renderer.AddActor(self.molecule)
+        self._renderer.AddActor(self._actors)
         
         # rendering
         self._iren.Render()
@@ -997,8 +1000,17 @@ class MolecularViewerPanel(ComponentPlugin):
         
         self._currentFrame = frame % len(self._trajectory)
         self._trajectory.universe.setConfiguration(self._trajectory.configuration[self._currentFrame])
-        self.coords = self._trajectory.universe.contiguousObjectConfiguration().array
-                        
+
+        coords = self._trajectory.universe.contiguousObjectConfiguration().array
+
+        points = vtk.vtkPoints()
+        points.SetNumberOfPoints(self._nAtoms)
+        for i in range(self._nAtoms):
+            x,y,z = coords[i]
+            points.SetPoint(i,x,y,z)
+
+        self._polydata.SetPoints(points)
+                                
         # Reset the view.                        
         self.show_universe()        
 
@@ -1018,7 +1030,7 @@ def ndarray_to_vtkarray(colors, radius, nbat):
     color_scalars = vtk.vtkFloatArray()
     color_scalars.SetNumberOfValues(colors.shape[0])
     for i,c in enumerate(colors):
-            color_scalars.SetValue(i,c)
+        color_scalars.SetValue(i,c)
     color_scalars.SetName("colors")
     
     # some radii

MDANSE/Framework/Widgets/AtomsListWidget.py

@@ -245,7 +245,7 @@ if __name__ == "__main__":
     
     app = wx.App(False)
                 
-    p = AtomsListDialog(None,t,3)
+    p = AtomsListDialog(None,t,10)
                 
     p.ShowModal()
     

MDANSE/Framework/Widgets/QVectorsWidget.py

@@ -222,6 +222,7 @@ class QVectorsDialog(UserDefinitionsDialog):
             return
         
         self._ud['parameters'] = (qPanel.generator.type,qPanel.parameters)
+        self._ud['generator'] = qPanel.generator.type
         self._ud['q_vectors'] = qPanel.grid.GetTable().data
         self._ud['is_lattice'] = qPanel.generator.is_lattice
                 

MDANSE/Logging/Logger.py

@@ -47,7 +47,7 @@ class Logger(object):
     def __call__(self,message,level="info",loggers=None):
 
         lvl = Logger.levels.get(level,None)
-
+        
         # If the logging level is unkwnown, skip that log
         if lvl is None:
             return

MDANSE/MolecularDynamics/Trajectory.py

@@ -44,7 +44,8 @@ def build_connectivity(universe ,tolerance=0.05):
 
     scannedObjects = [obj for obj in universe.objectList() if isinstance(obj,AtomCluster)]
     singleAtomsObjects = [obj for obj in universe.objectList() if isinstance(obj,Atom) or obj.numberOfAtoms()==1]
-    scannedObjects.append(Collection(singleAtomsObjects))
+    if singleAtomsObjects:
+        scannedObjects.append(Collection(singleAtomsObjects))
                 
     for obj in scannedObjects:
                                                         

MDANSE/__init__.py

@@ -32,13 +32,13 @@ Created on Mar 26, 2015
 
 from __pkginfo__ import __version__, __author__, __date__
 
+from MDANSE.Logging.Logger import LOGGER
+
 from MDANSE.Core.Platform import PLATFORM
 from MDANSE.Core.ClassRegistry import ClassRegistry as REGISTRY
 
 from MDANSE.Data.ElementsDatabase import ELEMENTS
 
-from MDANSE.Logging.Logger import LOGGER
-
 from MDANSE.Core.Preferences import PREFERENCES
 
 import Framework