Package Pmv :: Module APBSCommands :: Class APBSSetup
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Class APBSSetup

source code

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

APBSSetup setups all necessary parameters for Adaptive Poisson-Boltzmann 
Solver (APBS)

    
Package : Pmv
    
Module  : APBSCommands
    
Class   : APBSSetup
    
Command name : APBSSetup
    
Synopsis:

    None <--- APBSSetup(**kw)

    
Description:

   Pmv-->APBS-->Setup creates Pmw.NoteBook with three tabbed pages:

   Calculation, Grid and Physics.
    
   Calculation page contains the following groups: 
        
   Mathematics - is used to setup up Calculation type (kw['calculationType']),
   Poisson-Boltzmann equation type (kw['pbeType']), Boundary conditions 
   (kw['boundaryConditions']),Charge discretization (kw['chargeDiscretization'])
   Surface-based coefficients (kw['surfaceCalculation']), and Spline window in
   Angstroms (kw['splineWindow'], present only when surfaceCalculation is set to 
   'Spline-based')
   Molecules - allows to select molecule(s)
   Output - sets output file formats
   Profiles - is used to add, remove, load, save and run different profiles
   APBS Web Services - is present only when APBSService_services module is 
   installed. It allows APBS to be run remotely
   
   Grid page contains the following groups:
   
   General - lets you select number of grid point along X, Y and Z directions
   Coarse Grid - allows changing the length and the center of the coarse grid. 
   It also allows to autoceter, autosize as well as visualize the coarse grid.
   Fine Grid - dos the same for the fine grid
   System Resources - shows total grid point and memory to be allocated for APBS
    
   Grid page contains the following groups:
       
   Parameters - allows to change protein and solevent dielectric constants, 
   solvent radius and system temperature
   Ions - allows to add and/or remove different ions
   



Instance Methods [hide private]
  __init__(self, func=None)
Constructor for class APBSSetup
  doit(self, **kw)
doit function
  __call__(self, **kw)
Call method
  onAddObjectToViewer(self, object)
Called when object is added to viewer
  onRemoveObjectFromViewer(self, object)
Called when object is removed from viewer
  onAddCmdToViewer(self)
Called when APBSSetup are added to viewer
  guiCallback(self)
GUI callback for APBSSetup
  dismiss(self, event=None)
Withdraws 'default' GUI
  coarseResolutionX(self)
Returns coarse grid resolution in X direction
  coarseResolutionY(self)
Returns coarse grid resolution in Y direction
  coarseResolutionZ(self)
Returns coarse grid resolution in Z direction
  fineResolutionX(self)
Returns fine grid resolution in X direction
  fineResolutionY(self)
Returns fine grid resolution in Y direction
  fineResolutionZ(self)
Returns fine grid resolution in Z direction
  memoryToBeAllocated(self)
Returns memory to be allocated for APBS run
  totalGridPoints(self)
Returns total number of grid points
  autocenterCoarseGrid(self)
Autocenters coarse grid
  autosizeCoarseGrid(self)
Autosizes coarse grid
  autocenterFineGrid(self)
Autocenters fine grid
  autosizeFineGrid(self)
Autosizes fine grid
  getCoords(self)
Returns coordinates of atoms included in calculation
  refreshCalculationPage(self)
Refreshes calculation page
  testCalculationWidgets(self)
Tests calculation widgets
  calculationParamUpdate(self, selectItem=0)
Updates calculation parameters
  refreshGridPage(self)
Refreshes grid page
  testGridWidgets(self)
Tests grid widget
  gridParamUpdate(self, selectItem=0)
Updates grid parameters.
  refreshPhysicsPage(self)
Refreshes physics page
  testPhysicsWidgets(self)
Tests physics widget
  physicsParamUpdate(self)
Updates physics parameter.
  refreshAll(self, cmdForm=None)
Refreshes calculation, grid and physics pages
  paramUpdateAll(self)
Updates all parameters.
  setOutputFiles(self)
Sets output files using outputFilesForm GUI
  addIon(self)
Adds an Ion
  removeIon(self)
Removes an Ion
  moleculeListSelect(self, molName)
None <--- moleculeListSelect(molName)
  molecule1Select(self)
Seclects molecule1 and setups molecule1Path
  molecule2Select(self)
Seclects molecule2 and setups molecule2Path
  complexSelect(self)
Seclects complex and setups complexPath
  apbsOutput(self, molecule1=None, molecule2=None, _complex=None)
Runs APBS using mglutil.popen2Threads.SysCmdInThread
  SaveResults(self, params_name)
Checks the queue for results until we get one
  select_profile(self, profile_name)
Selects profile
  add_profile(self)
Adds profile
  remove_profile(self)
Removes current profile
  saveProfile(self, Profilename="Default")
Saves current profile
  loadProfile(self, filename=None)
Loads profile
  apbsRunRemote(self)
Runs APBS Web Services in a thread and checks for the results
  runWS(self, address, params, mol1, mol2=None, _complex=None)
Runs APBS Web Services
  checkForRemoteResults(self)
Checks the queue for remote results until we get one
  Download(self)
  Download_and_Merge(self)
  buildFormDescr(self, formName)
Builds 'error','ionForm','outputFilesForm','moleculeSelect' and 'default' forms'
  SaltUpdate(self)
Toggles ParallelGroup widget
  changeMenuState(self, state)
Updates the state of DisplayIsocontours, MapPotential2MSMS and SisplayOrthoSlice manues.
  ParallelParamUpdate(self)
Toggles ParallelGroup widget
  WS_http(self, event)
Opens webbrowser at http://nbcr.sdsc.edu/services/apbs/apbs-py.html
  toggle_usrpass(self, event)
Toggles User Name and Parssword entry and label

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 
Constructor for class APBSSetup
Overrides: mvCommand.MVCommand.__init__

doit(self, **kw)

source code 
doit function
Overrides: ViewerFramework.VFCommand.Command.doit

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

source code 
Call method
Overrides: ViewerFramework.VFCommand.Command.__call__

onAddObjectToViewer(self, object)

source code 
Called when object is added to viewer

onRemoveObjectFromViewer(self, object)

source code 
Called when object is removed from viewer

onAddCmdToViewer(self)

source code 
Called when APBSSetup are added to viewer
Overrides: ViewerFramework.VFCommand.Command.onAddCmdToViewer

guiCallback(self)

source code 
GUI callback for APBSSetup
Overrides: mvCommand.MVCommand.guiCallback

dismiss(self, event=None)

source code 
Withdraws 'default' GUI

coarseResolutionX(self)

source code 
Returns coarse grid resolution in X direction

coarseResolutionY(self)

source code 
Returns coarse grid resolution in Y direction

coarseResolutionZ(self)

source code 
Returns coarse grid resolution in Z direction

fineResolutionX(self)

source code 
Returns fine grid resolution in X direction

fineResolutionY(self)

source code 
Returns fine grid resolution in Y direction

fineResolutionZ(self)

source code 
Returns fine grid resolution in Z direction

memoryToBeAllocated(self)

source code 
Returns memory to be allocated for APBS run

totalGridPoints(self)

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Returns total number of grid points

autocenterCoarseGrid(self)

source code 
Autocenters coarse grid

autosizeCoarseGrid(self)

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Autosizes coarse grid

autocenterFineGrid(self)

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Autocenters fine grid

autosizeFineGrid(self)

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Autosizes fine grid

getCoords(self)

source code 
Returns coordinates of atoms included in calculation

refreshCalculationPage(self)

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Refreshes calculation page

testCalculationWidgets(self)

source code 
Tests calculation widgets

calculationParamUpdate(self, selectItem=0)

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Updates calculation parameters

refreshGridPage(self)

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Refreshes grid page

testGridWidgets(self)

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Tests grid widget

gridParamUpdate(self, selectItem=0)

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Updates grid parameters. Returns "ERROR" is failed

refreshPhysicsPage(self)

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Refreshes physics page

testPhysicsWidgets(self)

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Tests physics widget

physicsParamUpdate(self)

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Updates physics parameter. Returns "ERROR" is failed

refreshAll(self, cmdForm=None)

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Refreshes calculation, grid and physics pages

paramUpdateAll(self)

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Updates all parameters. Returns "ERROR" if failed

setOutputFiles(self)

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Sets output files using outputFilesForm GUI

addIon(self)

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Adds an Ion

removeIon(self)

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Removes an Ion

moleculeListSelect(self, molName)

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None <--- moleculeListSelect(molName)

Selects molecule with molName.

If the molecule was not read as pqr file moleculeListSelect

molecule1Select(self)

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Seclects molecule1 and setups molecule1Path

molecule2Select(self)

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Seclects molecule2 and setups molecule2Path

complexSelect(self)

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Seclects complex and setups complexPath

apbsOutput(self, molecule1=None, molecule2=None, _complex=None)

source code 
Runs APBS using mglutil.popen2Threads.SysCmdInThread

SaveResults(self, params_name)

source code 
Checks the queue for results until we get one

select_profile(self, profile_name)

source code 
Selects profile

add_profile(self)

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Adds profile

remove_profile(self)

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Removes current profile

saveProfile(self, Profilename="Default")

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Saves current profile

loadProfile(self, filename=None)

source code 
Loads profile

apbsRunRemote(self)

source code 
Runs APBS Web Services in a thread and checks for the results

runWS(self, address, params, mol1, mol2=None, _complex=None)

source code 
Runs APBS Web Services

checkForRemoteResults(self)

source code 
Checks the queue for remote results until we get one

Download(self)

source code 
None

Download_and_Merge(self)

source code 
None

buildFormDescr(self, formName)

source code 
Builds 'error','ionForm','outputFilesForm','moleculeSelect' and 'default' forms'
Overrides: ViewerFramework.VFCommand.Command.buildFormDescr

SaltUpdate(self)

source code 
Toggles ParallelGroup widget

changeMenuState(self, state)

source code 
Updates the state of DisplayIsocontours, MapPotential2MSMS and SisplayOrthoSlice manues.

ParallelParamUpdate(self)

source code 
Toggles ParallelGroup widget

WS_http(self, event)

source code 
Opens webbrowser at http://nbcr.sdsc.edu/services/apbs/apbs-py.html

toggle_usrpass(self, event)

source code 
Toggles User Name and Parssword entry and label