Package Pmv :: Module APBSCommands
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Module APBSCommands

source code

GUI for Adaptive Poisson-Boltzmann Solver 

Minimal documentation follows. 
Consult APBS or PMV documentation for more detail. 
More documentation is planned for later releases.

How to set up an APBS run:

1. (Calculation tab) There are three types of calculations available:
   electrostatic potential, binding energy, and solvation energy.
   Select whichever is of interest.
2. (Calculation tab) Under Molecules, select PQR files corresponding to
   the molecules of interest. Note that binding energy requires three PQRs:
   one for the complex, and one for each compound.
3. (Grid tab) Autocenter and Autosize generate grid parameters based on
   the current selection in PMV. You may also manually set these parameters.
   It is wise to check that your machine has the system resources required to
   perform the run.
4. (Physics tab) Enter the ions of interest and change the listed parameters
   as desired.
5. (Calculation tab) All files will be stored in the specified project folder.
   Unique project folder names are automatically generated.
6. (Calculation tab) If you wish to modify the the run you created in the GUI
   later, save the profile.
7. (Calculation tab) To run APBS separately from the GUI, use the write APBS
   parameter file button, which writes to the project folder. Then call apbs
   (in say, a shell) on that file.
8. (Calculation tab) Run APBS!

:see: `The epydoc webpage <http://epydoc.sourceforge.net>`__



Classes [hide private]
  APBSCmdToWebService
This object takes an APBSParams instance the Pmv.APBSCommands.py
  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.
  APBSRun
APBSRun runs Adaptive Poisson-Boltzmann Solver (APBS)...
  APBSMap_Potential_to_MSMS
APBSMapPotential2MSMS maps APBS Potential into MSMS Surface...
  APBSDisplay_Isocontours
APBSDisplayIsocontours displays APBS Potential Isocontours...
  APBSDisplayOrthoSlice
APBSDisplayOrthoslice displays APBS Potential Orthoslice...
  APBSVolumeRender
APBSVolumeRender ...
  APBSLoad_Profile
APBSLoadProfile loads APBS parameters...
  APBSSave_Profile
APBSSaveProfile saves APBS parameters...
  APBSWrite_APBS_Parameter_File
APBSOutputWrite writes APBS input file...
  APBSPreferences
APBSPreferences allows to change APBS Preferences...

Functions [hide private]
  closestMatch(value, _set)
Returns an element of the set that is closest to the supplied value
  initModule(viewer)
  change_Menu_state(self, state)

Variables [hide private]
  APBS_ssl = True
  ResourceFolder = '/home/sargis/.mgltools/1.4.6'
  APBS_proxy = '/home/sargis/.mgltools/1.4.6/ws/proxy_gama'
  PROFILES = ('Default',)
  APBSservicesFound = True
  state_GUI = 'disabled'
  blinker = 0
  cascadeName = 'Electrostatics'
  APBSSetupGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSRun_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSMap_Potential_to_MSMS_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSDisplay_Isocontours_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSDisplayOrthoSlice_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSVolumeRender_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSLoad_Profile_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSSave_Profile_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSWrite_Parameter_File_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  APBSPreferences_GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...
  test = <UTpackages.UTvolrend.UTVolumeLibrary.VolumeRenderer...
  flag = True

Function Details [hide private]

closestMatch(value, _set)

source code 
Returns an element of the set that is closest to the supplied value

initModule(viewer)

source code 
None

change_Menu_state(self, state)

source code 
None

Variables Details [hide private]

APBS_ssl

None
Value:
True                                                                   
      

ResourceFolder

None
Value:
'/home/sargis/.mgltools/1.4.6'                                         
      

APBS_proxy

None
Value:
'/home/sargis/.mgltools/1.4.6/ws/proxy_gama'                           
      

PROFILES

None
Value:
('Default',)                                                           
      

APBSservicesFound

None
Value:
True                                                                   
      

state_GUI

None
Value:
'disabled'                                                             
      

blinker

None
Value:
0                                                                     
      

cascadeName

None
Value:
'Electrostatics'                                                       
      

APBSSetupGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f860c>          
      

APBSRun_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f810c>          
      

APBSMap_Potential_to_MSMS_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f88cc>          
      

APBSDisplay_Isocontours_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f88ec>          
      

APBSDisplayOrthoSlice_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f892c>          
      

APBSVolumeRender_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f896c>          
      

APBSLoad_Profile_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f89ac>          
      

APBSSave_Profile_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f89ec>          
      

APBSWrite_Parameter_File_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f8a2c>          
      

APBSPreferences_GUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb32f8a6c>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb32f810c>
,
  'name': 'APBSRun'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb32f88cc>
,
  'name': 'APBSMapPotential2MSMS'},
...                                                                    
      

test

None
Value:
<UTpackages.UTvolrend.UTVolumeLibrary.VolumeRenderer; proxy of <Swig O
bject of type 'VolumeRenderer *' at 0xaa2cf38> >                       
      

flag

None
Value:
True