Package Pmv :: Module pdb2pqrCommands :: Class SetupPdb2Pqr
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Class SetupPdb2Pqr

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ViewerFramework.VFCommand.Command --+    
                                    |    
                  mvCommand.MVCommand --+
                                        |
                                       SetupPdb2Pqr

This command creates an instance of Pdb2Pqr protein class for a MolKit molecule

Instance Methods [hide private]
  __init__(self)
  checkDependencies(self)
virtual method.
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  __call__(self, mol, forcefield='amber', debump=1, hopt=1, hdebump=1, watopt=1, hbond=1, updateMol=0, newMol=0, filename=None, useThread=1, **kw)
None setup_Pdb2Pqr(mol, forcefield='amber', debump=1,...
  checkForResults(self)
  doit(self, mol, **kw)
virtual method.
  process(self, mol, pdblist, forcefield, debump, hopt, hdebump, watopt, hbond, filename, newMol, updateMol, useThread=1)
  update_molecule(self, mol, weakrefDict, hitlist, misslist, new_pmv_ats)
  build_all_hydrogens(self, mol, hlist, renumber, weakrefDict)
  build_hydrogen(self, mol, h)
  build_missing_atoms(self, mol, original_atoms, updated_atoms, rout, weakrefDict)
  build_atom(self, mol, atom, rout)
  buildFormDescr(self, formName)
descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command.
  guiCallback(self)
Default callback function called by the gui

Inherited from mvCommand.MVCommand: strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __repr__, addCallbackAfter, addCallbackBefore, addUndoCall, afterDoit, beforeDoit, buildLogArgList, 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)
(Constructor)

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None
Overrides: mvCommand.MVCommand.__init__

checkDependencies(self)

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virtual method. Has to be implemented by the sub classes. Method called when command is loaded, if all the dependencies are not found the command won't be loaded.
Overrides: ViewerFramework.VFCommand.Command.checkDependencies
(inherited documentation)

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)

__call__(self, mol, forcefield='amber', debump=1, hopt=1, hdebump=1, watopt=1, hbond=1, updateMol=0, newMol=0, filename=None, useThread=1, **kw)
(Call operator)

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None setup_Pdb2Pqr(mol, forcefield='amber', debump=1,
                            hopt=1, hdebump=1, watopt=1, hbond=1, 
                            updateMol=0, newMol=0, filename=None)
mol: pmv molecule 
forcefield: string specifying forcefield to use: 'amber', 'charm' or 'parse'
debump: whether to debump heavy atoms
hopt: whether to run hydrogen optimization
hdebump: whether to debump hydrogens  [if not, they are randomized]
watopt: whether to optimize water hydrogens
hbond: whether to print hydrogen bonding summary
updateMol: whether to update the current pmv molecule
newMol: whether to build a new updated copy of the pmv molecule
filename: if provided, a pqr file is written
useThread: allows threads to be turned off for testing purposes

returns  None
 

Overrides: ViewerFramework.VFCommand.Command.__call__

checkForResults(self)

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None

doit(self, mol, **kw)

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virtual method. Has to be implemented by the sub classes
Overrides: ViewerFramework.VFCommand.Command.doit
(inherited documentation)

process(self, mol, pdblist, forcefield, debump, hopt, hdebump, watopt, hbond, filename, newMol, updateMol, useThread=1)

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None

update_molecule(self, mol, weakrefDict, hitlist, misslist, new_pmv_ats)

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None

build_all_hydrogens(self, mol, hlist, renumber, weakrefDict)

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None

build_hydrogen(self, mol, h)

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None

build_missing_atoms(self, mol, original_atoms, updated_atoms, rout, weakrefDict)

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None

build_atom(self, mol, atom, rout)

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None

buildFormDescr(self, formName)

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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)

guiCallback(self)

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Default callback function called by the gui
Overrides: mvCommand.MVCommand.guiCallback