Package Pmv :: Module fileCommands :: Class MoleculeReader

Class MoleculeReader

ViewerFramework.VFCommand.Command --+        
                                    |        
                  mvCommand.MVCommand --+    
                                        |    
                           MoleculeLoader --+
                                            |
                                           MoleculeReader

Command to read molecule
    
Package : Pmv
    
Module  : fileCommands
    
Class   : MoleculeReader
    
Command :readMolecule
    
Synopsis:

        mols <- readMolecule(filename,parser=None, **kw)
    
Required Arguments:

    filename --- path to a file describing a molecule

    parser  --- you can specify the parser to use to parse the file has to be one of 'PDB', 'PDBQ', 'PDBQS','PDBQT', 'PQR', 'MOL2'.This is useful when your file doesn't have the correct extension.

Instance Methods

[hide private]

__init__(self)

onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.

buildFormDescr(self, formName)
descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command.

guiCallback(self, event=None, *args, **kw)

__call__(self, filename, parser=None, **kw)
mols <- readMolecule(filename,parser=None, **kw) filename --- path to a file describing a molecule parser --- you can specify the parser to use to parse the file has to be one of 'PDB', 'PDBQ', 'PDBQS','PDBQT', 'PQR', 'MOL2'.

doit(self, filename, parser=None, ask=True)
virtual method.

Inherited from MoleculeLoader: onRemoveObjectFromViewer

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]

lastDir = None

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly

Method Details

[hide private]

init(self)
(Constructor)

source code

None

Overrides: MoleculeLoader.__init__

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)

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, event=None, *args, **kw)

source code

None

Overrides: MoleculeLoader.guiCallback

call(self, filename, parser=None, **kw)
(Call operator)

source code

mols <- readMolecule(filename,parser=None, **kw)
           
filename --- path to a file describing a molecule
           
parser --- you can specify the parser to use to parse the file
                     has to be one of 'PDB', 'PDBQ', 'PDBQS','PDBQT', 'PQR', 'MOL2'.
                     This is useful when your file doesn't have the correct
                     extension.

Overrides: ViewerFramework.VFCommand.Command.__call__

doit(self, filename, parser=None, ask=True)

source code

virtual method. Has to be implemented by the sub classes

Overrides: ViewerFramework.VFCommand.Command.doit: (inherited documentation)

Class Variable Details

[hide private]

lastDir

None

Value:

None

Class MoleculeReader

__init__(self) (Constructor)

onAddCmdToViewer(self)

buildFormDescr(self, formName)

guiCallback(self, event=None, *args, **kw)

__call__(self, filename, parser=None, **kw) (Call operator)

doit(self, filename, parser=None, ask=True)

lastDir

init(self)
(Constructor)

call(self, filename, parser=None, **kw)
(Call operator)