Package Pmv :: Module fileCommands :: Class PDBQSWriter
[hide private]
[frames] | no frames]

Class PDBQSWriter

source code

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

Command to write PDBQS files using a PDBQS spec compliant writer
    
Package : Pmv
    
Module  : fileCommands
    
Class   : PDBQSWriter
    
Command : writePDBQS
    
Synopsis:

        None <- writePDBQS( 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 [hide private]
  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 <- writePDBQS( 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 [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

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

source code 
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)

source code 
None <- writePDBQS( 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)

source code 
None
Overrides: PDBWriter.guiCallback