Package Pmv :: Module pdb2pqrCommands :: Class SetupPdb2Pqr

Class SetupPdb2Pqr

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)

source code

None

Overrides: mvCommand.MVCommand.__init__

checkDependencies(self)

source code

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)

source code

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)

source code

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)

source code

None

doit(self, mol, **kw)

source code

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)

source code

None

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

source code

None

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

source code

None

build_hydrogen(self, mol, h)

source code

None

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

source code

None

build_atom(self, mol, atom, rout)

source code

None

buildFormDescr(self, formName)

source code

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)

source code

Default callback function called by the gui

Overrides: mvCommand.MVCommand.guiCallback

Class SetupPdb2Pqr

__init__(self) (Constructor)

checkDependencies(self)

onAddCmdToViewer(self)

__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)

checkForResults(self)

doit(self, mol, **kw)

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)

guiCallback(self)

init(self)
(Constructor)

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)