Package Pmv :: Module fileCommands :: Class PDBQTWriter

[frames] | no frames]

Class PDBQTWriter

ViewerFramework.VFCommand.Command --+        
                                    |        
                  mvCommand.MVCommand --+    
                                        |    
                                PDBWriter --+
                                            |
                                           PDBQTWriter

Command to write PDBQT files using a PDBQT spec compliant writer
    
Package : Pmv
    
Module  : fileCommands
    
Class   : PDBQTWriter
    
Command : write PDBQT
    
Synopsis:

        None <--- writePDBQT( nodes, filename=None, sort=True,
                          pdbRec=['ATOM', 'HETATM', 'CONECT'],
                          bondOrigin='all', ssOrigin=None, **kw)

    
Required argument:

        nodes --- TreeNodeSet holding the current selection
        
    
Optional arguments:

        filename --- name of the PDB file (default=None). If None is given
                  The name of the molecule plus the .pdb extension will be used

        sort --- Boolean flag to either sort or not the nodes before writing
                  the PDB file (default=True)

        pdbRec --- List of the PDB Record to save in the PDB file.
                  (default: ['ATOM', 'HETATM', 'CONECT']

        bondOrigin --- string or list specifying the origin of the bonds to save
                    as CONECT records in the PDB file. Can be 'all' or a tuple


        ssOrigin --- Flag to specify the origin of the secondary structure
                    information to be saved in the HELIX, SHEET and TURN
                    record. Can either be None, File or Stride.

Instance Methods

doit(self, nodes, filename=None, sort=True, pdbRec=['ATOM','HETATM','CONECT'], bondOrigin='all', ssOrigin=None, transformed=False)
virtual method.

__call__(self, nodes, filename=None, sort=True, pdbRec=['ATOM','HETATM','CONECT'], bondOrigin='all', ssOrigin=None, transformed=False, **kw)
None <- writePDBQT( nodes, filename=None, sort=True, pdbRec=['ATOM', 'HETATM', 'CONECT'], bondOrigin='all', ssOrigin=None, **kw) Required Argument: nodes --- TreeNodeSet holding the current selection Optional Arguments: filename --- name of the PDB file (default=None).

guiCallback(self)

Inherited from PDBWriter: __init__, add_cb, buildFormDescr, dismiss_cb, remove_cb, setEntry_cb, setNewCoords, showPDBHelp

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, onAddCmdToViewer, onAddNewCmd, onCmdRun, setLastUsedValues, setupUndoAfter, setupUndoBefore, showForm, tkCb, updateGeom, warningMsg

Class Variables

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly

Method Details

doit(self, nodes, filename=None, sort=True, pdbRec=['ATOM','HETATM','CONECT'], bondOrigin='all', ssOrigin=None, transformed=False)

virtual method. Has to be implemented by the sub classes

Overrides: PDBWriter.doit

call(self, nodes, filename=None, sort=True, pdbRec=['ATOM','HETATM','CONECT'], bondOrigin='all', ssOrigin=None, transformed=False, **kw)
(Call operator)

None <- writePDBQT( nodes, filename=None, sort=True,
                          pdbRec=['ATOM', 'HETATM', 'CONECT'],
                          bondOrigin='all', ssOrigin=None, **kw)

        
Required Argument:

        nodes --- TreeNodeSet holding the current selection
        
        
Optional Arguments:

        filename --- name of the PDB file (default=None). If None is given
                  The name of the molecule plus the .pdb extension will be used

        sort --- Boolean flag to either sort or not the nodes before writing
                  the PDB file (default=True)

        pdbRec --- List of the PDB Record to save in the PDB file.
                  (default: ['ATOM', 'HETATM', 'CONECT']

        bondOrigin --- string or list specifying the origin of the bonds to save
                    as CONECT records in the PDB file. Can be 'all' or a tuple


        ssOrigin --- Flag to specify the origin of the secondary structure
                    information to be saved in the HELIX, SHEET and TURN
                    record. Can either be None, File or Stride.

Overrides: PDBWriter.__call__

guiCallback(self)

None

Overrides: PDBWriter.guiCallback