Package Pmv :: Module coarseMolSurfaceCommands :: Class coarseMolSurface
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Class coarseMolSurface

source code

ViewerFramework.VFCommand.Command --+    
                                    |    
                  mvCommand.MVCommand --+
                                        |
                                       coarseMolSurface

Command to compute a coarse molecular surface. Selected atoms are first blurred as gaussians into a grid. The grid is then isocontoured at a user specified value. An indexed polygon geometry is added to the viewer.

Instance Methods [hide private]
  __init__(self, func=None)
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  loadNetwork(self)
  onAddObjectToViewer(self, obj)
  guiCallback(self)
  buildFormDescr(self, formName="default")
descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command.
  doit(self, **kw)
list of keywords: nodes, surfName, perMol, gridZise, isovalue, resolution, bindGeom, immediate, padding.
  __call__(self, **kw)
None <- mv.coarseMolSurface(**kw) list of available keywords: nodes -- atomic fragment; surfName -- string - name of created surface; perMol -- True or False; if True, a surface is computed for each molecule having at least one node in the current selection, else the surface is computed for the current selection; gridZise -- integer; Size of computed grid will be: gridSize x gridSize x gridSize; isovalue -- can be one of the following: 'fast approximation', 'precise value' or a numeric value specifying the isovalue; resolution -- resolution of the blurred surface - a negative value; bindGeom -- True or False; if True - the surface is bound to the selected molecule.
  perMol_cb(self, event=None)
calback of perMol check button of the input form
  mode_cb(self, event=None)
callback of the input form's immediate mode check button
  select_surfname(self, surfName)
callback of surface name ComboBox
  set_gridsize(self)
callback of the 'grid size' entry field
  set_resolution(self, val)
callback of the input form's resolution radio buttons
  set_isovalue(self, val)
callback of the input form's isovalue radio buttons
  set_padding(self, val)
callback of the thumbwheel widget for setting padding around the molecule.
  set_custom_isovalue(self, val)
callback of the thumbwheel widget used for setting custom isovalue
  set_custom_resolution(self, val)
callback of the thumbwheel widget used for setting custom resolution
  dismiss(self, event=None)
Withdraws the input form
  bind_cb(self)
callback of the 'bind surface to molecule' check button
  get_precise_isovalue(self, resolution)
Computes precise isovalue using methods from computeIsovalue.py
  entryValidate(self, text)
Method to validate the name of the msms surface.
  compute(self, event=None)
callback of 'Compute' button of the input form
  disableThumbWheel(self, tw)
disables a thumbwheel widgets used to specify custom resolution/isovalue
  enableThumbWheel(self, tw, val=None)
enables a thumbwheel widgets used to specify custom resolution/isovalue
  piecewiseLinearInterpOnIsovalue(self, x)
Piecewise linear interpretation on isovalue that is a function blobbyness.

Inherited from mvCommand.MVCommand: strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __repr__, addCallbackAfter, addCallbackBefore, addUndoCall, afterDoit, beforeDoit, buildLogArgList, checkDependencies, cleanup, customizeGUI, doitWrapper, getArguments, getHelp, getLastUsedValues, getLogArgs, getValNamedArgs, log, logString, onAddNewCmd, onCmdRun, setLastUsedValues, setupUndoAfter, setupUndoBefore, showForm, tkCb, updateGeom, warningMsg


Class Variables [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

__init__(self, func=None)
(Constructor)

source code 
None
Overrides: mvCommand.MVCommand.__init__

onAddCmdToViewer(self)

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method called when an instance of this command is added to the viewer. This enable viewer-addition time initializations
Overrides: ViewerFramework.VFCommand.Command.onAddCmdToViewer
(inherited documentation)

loadNetwork(self)

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None

onAddObjectToViewer(self, obj)

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None

guiCallback(self)

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None
Overrides: mvCommand.MVCommand.guiCallback

buildFormDescr(self, formName="default")

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descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command. This is where the inputFormDescr is created and the description of the widgets appended. If a command has several inputForm buildFormDescr should build all the inputFormDescr and you do a if / elif check to know which one to create. formName : string name of the form corresponding to this descr.
Overrides: ViewerFramework.VFCommand.Command.buildFormDescr
(inherited documentation)

doit(self, **kw)

source code 
list of keywords: nodes, surfName, perMol, gridZise, isovalue, resolution, bindGeom, immediate, padding.
Overrides: ViewerFramework.VFCommand.Command.doit

__call__(self, **kw)
(Call operator)

source code 
None <- mv.coarseMolSurface(**kw)

list of available keywords:
nodes    -- atomic fragment; 

surfName -- string - name of created surface; 

perMol   -- True or False; if True, a surface is computed for each 
            molecule having at least one node in the current selection,
            else the surface is computed for the current selection;

gridZise -- integer; Size of computed grid will be: gridSize x gridSize x gridSize;

isovalue -- can be one of the following: 'fast approximation', 'precise value' or
              a numeric value specifying the isovalue;

resolution -- resolution of the blurred surface - a negative value; 

bindGeom   -- True or False; if True - the surface is bound to the selected molecule.

Overrides: ViewerFramework.VFCommand.Command.__call__

perMol_cb(self, event=None)

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calback of perMol check button of the input form

mode_cb(self, event=None)

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callback of the input form's immediate mode check button

select_surfname(self, surfName)

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callback of surface name ComboBox

set_gridsize(self)

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callback of the 'grid size' entry field

set_resolution(self, val)

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callback of the input form's resolution radio buttons

set_isovalue(self, val)

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callback of the input form's isovalue radio buttons

set_padding(self, val)

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callback of the thumbwheel widget for setting padding around the molecule.

set_custom_isovalue(self, val)

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callback of the thumbwheel widget used for setting custom isovalue

set_custom_resolution(self, val)

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callback of the thumbwheel widget used for setting custom resolution

dismiss(self, event=None)

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Withdraws the input form

bind_cb(self)

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callback of the 'bind surface to molecule' check button

get_precise_isovalue(self, resolution)

source code 
Computes precise isovalue using methods from computeIsovalue.py

entryValidate(self, text)

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Method to validate the name of the msms surface. This name will be used by other command to build Pmw widget so it can't contain an '_'.

compute(self, event=None)

source code 
callback of 'Compute' button of the input form

disableThumbWheel(self, tw)

source code 
disables a thumbwheel widgets used to specify custom resolution/isovalue

enableThumbWheel(self, tw, val=None)

source code 
enables a thumbwheel widgets used to specify custom resolution/isovalue

piecewiseLinearInterpOnIsovalue(self, x)

source code 
Piecewise linear interpretation on isovalue that is a function blobbyness.