Commit c67e4126 authored by eric pellegrini's avatar eric pellegrini
Browse files

The job plugin can now be plugged into the viewer or on the data plugin

The DataInfoPlugin is now OK
Bug fix with pubsub.sendMessage wrong keyword
Improved the AtomListSelectionDialog
Removed unuseful pubsub calls from the molecular viewer
parent 9e9c7fe1
...@@ -54,7 +54,7 @@ class DensityProfile(IJob): ...@@ -54,7 +54,7 @@ class DensityProfile(IJob):
category = ('Structure',) category = ('Structure',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -47,7 +47,7 @@ class DipoleAutoCorrelationFunction(IJob): ...@@ -47,7 +47,7 @@ class DipoleAutoCorrelationFunction(IJob):
category = ('Infrared',) category = ('Infrared',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -57,7 +57,7 @@ class DynamicCoherentStructureFactor(IJob): ...@@ -57,7 +57,7 @@ class DynamicCoherentStructureFactor(IJob):
category = ('Scattering',) category = ('Scattering',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -52,7 +52,7 @@ class DynamicIncoherentStructureFactor(IJob): ...@@ -52,7 +52,7 @@ class DynamicIncoherentStructureFactor(IJob):
category = ('Scattering',) category = ('Scattering',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory']=('mmtk_trajectory',{}) settings['trajectory']=('mmtk_trajectory',{})
......
...@@ -88,7 +88,7 @@ class Eccentricity(IJob): ...@@ -88,7 +88,7 @@ class Eccentricity(IJob):
category = ('Structure',) category = ('Structure',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -56,7 +56,7 @@ class ElasticIncoherentStructureFactor(IJob): ...@@ -56,7 +56,7 @@ class ElasticIncoherentStructureFactor(IJob):
# The category of the analysis. # The category of the analysis.
category = ('Scattering',) category = ('Scattering',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -52,7 +52,7 @@ class GaussianDynamicIncoherentStructureFactor(IJob): ...@@ -52,7 +52,7 @@ class GaussianDynamicIncoherentStructureFactor(IJob):
category = ('Scattering',) category = ('Scattering',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -49,7 +49,7 @@ class GeneralAutoCorrelationFunction(IJob): ...@@ -49,7 +49,7 @@ class GeneralAutoCorrelationFunction(IJob):
category = ('Dynamics',) category = ('Dynamics',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -65,7 +65,7 @@ class GlobalMotionFilteredTrajectory(IJob): ...@@ -65,7 +65,7 @@ class GlobalMotionFilteredTrajectory(IJob):
category = ('Trajectory',) category = ('Trajectory',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -107,7 +107,7 @@ class IJob(Configurable): ...@@ -107,7 +107,7 @@ class IJob(Configurable):
section = "job" section = "job"
ancestor = 'molecular_viewer' ancestor = ["molecular_viewer"]
@staticmethod @staticmethod
def define_unique_name(): def define_unique_name():
...@@ -498,7 +498,7 @@ class %s(IJob): ...@@ -498,7 +498,7 @@ class %s(IJob):
# You should enter the category under which your job will be references. # You should enter the category under which your job will be references.
category = ('My jobs',) category = ('My jobs',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
# You should enter the configuration of your job here # You should enter the configuration of your job here
# Here a basic example of a job that will use a MMTK trajectory, a frame selection and an output file in NetCDF and ASCII file formats # Here a basic example of a job that will use a MMTK trajectory, a frame selection and an output file in NetCDF and ASCII file formats
......
...@@ -72,7 +72,7 @@ class McStasVirtualInstrument(IJob): ...@@ -72,7 +72,7 @@ class McStasVirtualInstrument(IJob):
category = ('Virtual Instruments',) category = ('Virtual Instruments',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')}) settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')})
......
...@@ -70,7 +70,7 @@ class MeanSquareDisplacement(IJob): ...@@ -70,7 +70,7 @@ class MeanSquareDisplacement(IJob):
category = ('Dynamics',) category = ('Dynamics',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory","molecular_viewer"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory']=('mmtk_trajectory',{}) settings['trajectory']=('mmtk_trajectory',{})
......
...@@ -58,7 +58,7 @@ class MolecularTrace(IJob): ...@@ -58,7 +58,7 @@ class MolecularTrace(IJob):
category = ('Structure',) category = ('Structure',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -77,7 +77,7 @@ class OrderParameter(IJob): ...@@ -77,7 +77,7 @@ class OrderParameter(IJob):
category = ('Dynamics',) category = ('Dynamics',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')}) settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')})
......
...@@ -57,7 +57,7 @@ class PairDistributionFunction(DistanceHistogram): ...@@ -57,7 +57,7 @@ class PairDistributionFunction(DistanceHistogram):
category = ('Structure',) category = ('Structure',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
def finalize(self): def finalize(self):
""" """
......
...@@ -49,7 +49,7 @@ class PositionAutoCorrelationFunction(IJob): ...@@ -49,7 +49,7 @@ class PositionAutoCorrelationFunction(IJob):
category = ('Dynamics',) category = ('Dynamics',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -51,7 +51,7 @@ class RadiusOfGyration(IJob): ...@@ -51,7 +51,7 @@ class RadiusOfGyration(IJob):
category = ('Structure',) category = ('Structure',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
...@@ -54,7 +54,7 @@ class RefoldedMembraneTrajectory(IJob): ...@@ -54,7 +54,7 @@ class RefoldedMembraneTrajectory(IJob):
category = ('Macromolecules','Lipids') category = ('Macromolecules','Lipids')
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{'default':os.path.join('..','..','..','Data','Trajectories','MMTK','dmpc_in_periodic_universe.nc')}) settings['trajectory'] = ('mmtk_trajectory',{'default':os.path.join('..','..','..','Data','Trajectories','MMTK','dmpc_in_periodic_universe.nc')})
......
...@@ -55,7 +55,7 @@ class RigidBodyTrajectory(IJob): ...@@ -55,7 +55,7 @@ class RigidBodyTrajectory(IJob):
category = ('Trajectory',) category = ('Trajectory',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory']=('mmtk_trajectory',{}) settings['trajectory']=('mmtk_trajectory',{})
......
...@@ -54,7 +54,7 @@ class RootMeanSquareDeviation(IJob): ...@@ -54,7 +54,7 @@ class RootMeanSquareDeviation(IJob):
category = ('Structure',) category = ('Structure',)
ancestor = "mmtk_trajectory" ancestor = ["mmtk_trajectory"]
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['trajectory'] = ('mmtk_trajectory',{}) settings['trajectory'] = ('mmtk_trajectory',{})
......
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