The job plugins can now be plugged in a data plugin or in a molecular

viewer
Bug fix when closing a lugin pane
Bug fix with DL_POLY converter plugin

MDANSE/Framework/Jobs/AngularCorrelation.py

@@ -65,9 +65,9 @@ class AngularCorrelation(IJob):
     
     label = "Angular Correlation"
 
-    category = ('Dynamics',)
+    category = ('Analysis','Dynamics',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()    
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/AreaPerMolecule.py

@@ -54,9 +54,9 @@ class AreaPerMolecule(IJob):
 
     label = "Area Per Molecule"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{'default':os.path.join('..','..','..','Data','Trajectories','MMTK','dmpc_in_periodic_universe.nc')})

MDANSE/Framework/Jobs/BoxTranslatedTrajectory.py

@@ -51,9 +51,9 @@ class BoxCenteredTrajectory(IJob):
     
     label = "Box Translated Trajectory"
 
-    category = ('Trajectory',)
+    category = ('Analysis','Trajectory',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/CenterOfMassesTrajectory.py

@@ -49,9 +49,9 @@ class CenterOfMassesTrajectory(IJob):
     
     label = "Center Of Masses Trajectory"
 
-    category = ('Trajectory',)
+    category = ('Analysis','Trajectory',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/Converters/DL_POLY.py

@@ -287,7 +287,7 @@ class DL_POLYConverter(Converter):
 
     type = 'dl_poly'
     
-    label = "DL_POLY"
+    label = "DL-POLY"
 
     settings = collections.OrderedDict()   
     settings['field_file'] = ('input_file',{'wildcard':"FIELD files|FIELD*|All files|*",

MDANSE/Framework/Jobs/CoordinationNumber.py

@@ -46,9 +46,9 @@ class CoordinationNumber(DistanceHistogram):
 
     label = "Coordination Number"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]        
+    ancestor = ["mmtk_trajectory","molecular_viewer"]        
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/CroppedTrajectory.py

@@ -47,9 +47,9 @@ class CroppedTrajectory(IJob):
     
     label = "Cropped Trajectory"
 
-    category = ('Trajectory',)
+    category = ('Analysis','Trajectory',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/CurrentCorrelationFunction.py

@@ -54,9 +54,9 @@ class CurrentCorrelationFunction(IJob):
     
     label = "Current Correlation Function"
 
-    category = ('Scattering',)
+    category = ('Analysis','Scattering',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/Density.py

@@ -45,9 +45,9 @@ class Density(IJob):
     
     label = "Density"
 
-    category = ('Thermodynamics',)
+    category = ('Analysis','Thermodynamics',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/DensityOfStates.py

@@ -49,9 +49,9 @@ class DensityOfStates(IJob):
     
     label = "Density Of States"
 
-    category = ('Dynamics',)
+    category = ('Analysis','Dynamics',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/DensityProfile.py

@@ -52,9 +52,9 @@ class DensityProfile(IJob):
 
     label = "Density Profile"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py

@@ -45,9 +45,9 @@ class DipoleAutoCorrelationFunction(IJob):
 
     label = "Dipole AutoCorrelation Function"
     
-    category = ('Infrared',)
+    category = ('Analysis','Infrared',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py

@@ -55,9 +55,9 @@ class DynamicCoherentStructureFactor(IJob):
     
     label = "Dynamic Coherent Structure Factor"
 
-    category = ('Scattering',)
+    category = ('Analysis','Scattering',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/DynamicIncoherentStructureFactor.py

@@ -50,9 +50,9 @@ class DynamicIncoherentStructureFactor(IJob):
     
     label = "Dynamic Incoherent Structure Factor"
 
-    category = ('Scattering',)
+    category = ('Analysis','Scattering',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory']=('mmtk_trajectory',{})

MDANSE/Framework/Jobs/Eccentricity.py

@@ -86,9 +86,9 @@ class Eccentricity(IJob):
 
     label = "Eccentricity"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/ElasticIncoherentStructureFactor.py

@@ -54,9 +54,9 @@ class ElasticIncoherentStructureFactor(IJob):
     label = "Elastic Incoherent Structure Factor"
 
     # The category of the analysis.
-    category = ('Scattering',)
+    category = ('Analysis','Scattering',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/GaussianDynamicIncoherentStructureFactor.py

@@ -50,9 +50,9 @@ class GaussianDynamicIncoherentStructureFactor(IJob):
     
     label = "Gaussian Dynamic Incoherent Structure Factor"
 
-    category = ('Scattering',)
+    category = ('Analysis','Scattering',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/GeneralAutoCorrelationFunction.py

@@ -47,9 +47,9 @@ class GeneralAutoCorrelationFunction(IJob):
     
     label = "General AutoCorrelation Function"
 
-    category = ('Dynamics',)
+    category = ('Analysis','Dynamics',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/GlobalMotionFilteredTrajectory.py

@@ -63,9 +63,9 @@ class GlobalMotionFilteredTrajectory(IJob):
     
     label = "Global Motion Filtered Trajectory"
 
-    category = ('Trajectory',)
+    category = ('Analysis','Trajectory',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
         
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/JobStatus.py

@@ -32,12 +32,7 @@ class JobStatus(Status):
         
         self.save_status()
                     
-    def finish_status(self,message):
-
-        status = message
-
-        if status != self:
-            return
+    def finish_status(self):
 
         self.cleanup()
                     
@@ -47,9 +42,7 @@ class JobStatus(Status):
         return self._state    
 
     def cleanup(self):
-        
-        return
-                
+                        
         try:
             os.unlink(self._state['temporary_file'])
         except:

MDANSE/Framework/Jobs/McStasVirtualInstrument.py

@@ -70,9 +70,9 @@ class McStasVirtualInstrument(IJob):
     
     label = "McStas Virtual Instrument"
 
-    category = ('Virtual Instruments',)
+    category = ('Analysis','Virtual Instruments',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')})

MDANSE/Framework/Jobs/MeanSquareDisplacement.py

@@ -48,7 +48,7 @@ class MeanSquareDisplacement(IJob):
     since molecules undergo collisions. The path is to a good approximation to a random walk. 
     
     Mathematically, a random walk is a series of steps where each step is taken in a completely 
-    random direction from the one before, as analysed by Albert Einstein 
+    random direction from the one before, as analyzed by Albert Einstein 
     in a study of Brownian motion. The MSD of a particle in this case 
     is proportional to the time elapsed:
     
@@ -68,7 +68,7 @@ class MeanSquareDisplacement(IJob):
     
     label = "Mean Square Displacement"
 
-    category = ('Dynamics',)
+    category = ('Analysis','Dynamics',)
     
     ancestor = ["mmtk_trajectory","molecular_viewer"]
     

MDANSE/Framework/Jobs/MolecularTrace.py

@@ -56,9 +56,9 @@ class MolecularTrace(IJob):
 
     label = "Molecular Trace"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/OrderParameter.py

@@ -75,9 +75,9 @@ class OrderParameter(IJob):
     
     label = "Order parameter"
 
-    category = ('Dynamics',)
+    category = ('Analysis','Dynamics',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')})

MDANSE/Framework/Jobs/PairDistributionFunction.py

@@ -55,9 +55,9 @@ class PairDistributionFunction(DistanceHistogram):
 
     label = "Pair Distribution Function"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]  
+    ancestor = ["mmtk_trajectory","molecular_viewer"]  
     
     def finalize(self):
         """

MDANSE/Framework/Jobs/PositionAutoCorrelationFunction.py

@@ -47,9 +47,9 @@ class PositionAutoCorrelationFunction(IJob):
     
     label = "Position AutoCorrelation Function"
 
-    category = ('Dynamics',)
+    category = ('Analysis','Dynamics',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()      
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/RadiusOfGyration.py

@@ -49,9 +49,9 @@ class RadiusOfGyration(IJob):
 
     label = "Radius of Gyration"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/RefoldedMembraneTrajectory.py

@@ -52,9 +52,9 @@ class RefoldedMembraneTrajectory(IJob):
     
     label = "Refolded Membrane Trajectory"
 
-    category = ('Macromolecules','Lipids')
+    category = ('Analysis','Macromolecules','Lipids')
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{'default':os.path.join('..','..','..','Data','Trajectories','MMTK','dmpc_in_periodic_universe.nc')})

MDANSE/Framework/Jobs/RigidBodyTrajectory.py

@@ -53,9 +53,9 @@ class RigidBodyTrajectory(IJob):
     
     label = 'Rigid Body Trajectory'
 
-    category = ('Trajectory',)
+    category = ('Analysis','Trajectory',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory']=('mmtk_trajectory',{})

MDANSE/Framework/Jobs/RootMeanSquareDeviation.py

@@ -52,9 +52,9 @@ class RootMeanSquareDeviation(IJob):
 
     label = "Root Mean Square Deviation"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/RootMeanSquareFluctuation.py

@@ -48,9 +48,9 @@ class RootMeanSquareFluctuation(IJob):
 
     label = "Root Mean Square Fluctuation"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/SolventAccessibleSurface.py

@@ -64,9 +64,9 @@ class SolventAccessibleSurface(IJob):
 
     label = "Solvent Accessible Surface"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/SpatialDensity.py

@@ -37,7 +37,7 @@ import numpy
 
 from MDANSE.Extensions import sd_fast_calc
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Geometry import build_cartesian_axes, center_of_mass
+from MDANSE.Mathematics.Geometry import build_cartesian_axes
 
 class SpatialDensity(IJob):
     """The Spatial Density (SD) computes the 3D histograms of atomic coordinates of the a given set of target molecules 
@@ -58,9 +58,9 @@ class SpatialDensity(IJob):
     
     label = "Spatial Density"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')})

MDANSE/Framework/Jobs/StaticStructureFactor.py

@@ -47,9 +47,9 @@ class StaticStructureFactor(DistanceHistogram):
 
     label = "Static Structure Factor"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/StructureFactorFromScatteringFunction.py

@@ -45,9 +45,9 @@ class StructureFactorFromScatteringFunction(IJob):
     
     label = "Structure Factor From Scattering Function"
 
-    category = ('Scattering',)
+    category = ('Analysis','Scattering',)
     
-    ancestor = ["netcdf_data"]
+    ancestor = ["netcdf_data","mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['netcdf_input_file'] = ('netcdf_input_file', {'variables':['time','f(q,t)_total'],

MDANSE/Framework/Jobs/Temperature.py

@@ -55,9 +55,9 @@ class Temperature(IJob):
     
     label = "Temperature"
 
-    category = ('Thermodynamics',)
+    category = ('Analysis','Thermodynamics',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
             
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/UnfoldedTrajectory.py

@@ -64,9 +64,9 @@ class UnfoldedTrajectory(IJob):
     
     label = "Unfolded Trajectory"
 
-    category = ('Trajectory',)
+    category = ('Analysis','Trajectory',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
         
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/VelocityAutoCorrelationFunction.py

@@ -70,9 +70,9 @@ class VelocityAutoCorrelationFunction(IJob):
     
     label = "Velocity AutoCorrelation Function"
 
-    category = ('Dynamics',)
+    category = ('Analysis','Dynamics',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/Voronoi.py

@@ -61,9 +61,9 @@ class Voronoi(IJob):
 
     label = "Voronoi"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
 
     settings = collections.OrderedDict()   
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Jobs/XRayStaticStructureFactor.py

@@ -66,9 +66,9 @@ class StaticStructureFactor(DistanceHistogram):
 
     label = "XRay Static Structure Factor"
     
-    category = ('Structure',)
+    category = ('Analysis','Structure',)
     
-    ancestor = ["mmtk_trajectory"]
+    ancestor = ["mmtk_trajectory","molecular_viewer"]
     
     settings = collections.OrderedDict()
     settings['trajectory'] = ('mmtk_trajectory',{})

MDANSE/Framework/Plugins/DataPlugin.py

@@ -31,9 +31,7 @@ Created on Mar 30, 2015
 '''
 
 import wx
-import wx.aui as wxaui
 
-from MDANSE import REGISTRY
 from MDANSE.Externals.pubsub import pub
 
 from MDANSE.GUI import DATA_CONTROLLER
@@ -53,7 +51,7 @@ def get_data_plugin(window):
                     
 class DataPlugin(IPlugin):
     
-    type = 'data'
+    type = None
         
     ancestor = []
     
@@ -95,31 +93,7 @@ class DataPlugin(IPlugin):
     @property
     def dataplugin(self):
         return self
-    
-    def drop(self, pluginName):
-                                        
-        # If no plugin match the name of the dropped plugin, do nothing.
-        plugin = REGISTRY["plugin"].get(pluginName,None)
-        
-        if plugin is None:
-            return
         
-        klasses = tuple([REGISTRY['plugin'][anc] for anc in plugin.ancestor])
-        if not issubclass(self.__class__,klasses):
-            return
-                                                            
-        plugin = plugin(self)
-        
-        self._mgr.AddPane(plugin, wxaui.AuiPaneInfo().Caption(getattr(plugin, "label", pluginName)))
-
-        self._mgr.Update()
-        
-        plugin.plug()
-        
-        plugin.SetFocus()
-        
-        self._currentWindow = plugin
-    
     def on_changing_pane(self, event):
         
         window = plugin_parent(event.GetWindow())
@@ -128,5 +102,5 @@ class DataPlugin(IPlugin):
             return
         
         self._currentWindow = window
-                                    
+
         pub.sendMessage('msg_set_plugins_tree', plugin=window)

MDANSE/Framework/Plugins/IPlugin.py

@@ -114,22 +114,13 @@ class IPlugin(wx.Panel):
     def parent(self):
         return self._parent
     
-    def close_children(self):
-
-        childrenPlugins = [p.window for p in self._mgr.GetAllPanes()]
-        
-        for plugin in childrenPlugins:
-            try:
-                plugin.close_children()
-            except AttributeError:
-                continue
-            
-        self.close()
-
     def is_parent(self,window):
             
         if window == self:
             return True
+
+        if window is None:
+            return False