Package Pmv :: Module fileCommands
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Module fileCommands

source code


This Module implements commands to load molecules from files in the following
formats:
    PDB: Brookhaven Data Bank format
    PQR: Don Bashford's modified PDB format used by MEAD
    PDBQ: Autodock file format
    PDBQS: Autodock file format
    PDBQT: Autodock file format
    MMCIF: Macromolecular Crystallographic Information File
The module implements commands to save molecules in additional formats:    
    STL: Stereolithography file format



Classes [hide private]
  MoleculeLoader
Base class for all the classes in this module
  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.
  PDBReader
Command to load PDB files using a PDB spec compliant parser...
  MMCIFReader
This command reads macromolecular Crystallographic Information File (mmCIF)...
  GROReader
This command reads macromolecular Crystallographic Information File (mmCIF)...
  PDBQReader
Command to load AutoDock PDBQ files.
  PDBQSReader
Command to load AutoDock PDBQS files...
  PDBQTReader
Command to load AutoDock PDBQT files...
  PQRReader
Command to load MEAD PQR files...
  MOL2Reader
Command to load MOL2 files...
  PDBWriter
Command to write the given molecule or the given subset of atoms of one molecule as PDB file.
  PQRWriter
Command to write PQR files using a PQR spec compliant writer...
  PDBQWriter
Command to write PDBQ files using a PDBQ spec compliant writer Package : Pmv Module : fileCommands Class : PDBQWriter Command : writePDBQ Synopsis: None <- writePDBQ( 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).
  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).
  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).
  SaveMMCIF
This command writes macromolecular Crystallographic Information File (mmCIF).
  STLWriter
Command to write coords&normals of currently displayed geometries as...
  VRML2Writer
Command to save currently displayed geometries in VRML 2.0 format...
  readFromWebCommand
Command to read pdb from ftp://ftp.rcsb.org...

Functions [hide private]
  initModule(viewer)

Variables [hide private]
  pdbDescr = "\nBy default the PDB writer will create the followi...
  MoleculeReaderGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  pdbReaderGuiDescr = {'menyEntryLabel': 'Read PDB ...', 'menuButtonName':...
  pdbqReaderGuiDescr = {'menyEntryLabel': 'Read PDBQ ...', 'menuButtonName'...
  pdbqsReaderGuiDescr = {'menyEntryLabel': 'Read PDBQS ...', 'menuButtonName...
  pdbqtReaderGuiDescr = {'menyEntryLabel': 'Read PDBQT ...', 'menuButtonName...
  pqrReaderGuiDescr = {'menyEntryLabel': 'Read PQR ...', 'menuButtonName':...
  mol2ReaderGuiDescr = {'menyEntryLabel': 'Read MOL2 ...', 'menuButtonName'...
  pdbWriterDescr = {'menyEntryLabel': 'Write PDB ...', 'menuButtonName'...
  PDBWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  pqrWriterDescr = {'menyEntryLabel': 'Write PQR ...', 'menuButtonName'...
  PQRWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  pdbqWriterGuiDescr = {'menyEntryLabel': 'Write PDBQ ...', 'menuButtonName...
  PDBQWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  pdbqsWriterGuiDescr = {'menyEntryLabel': 'Write PDBS ...', 'menuButtonName...
  PDBQSWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  pdbqtWriterGuiDescr = {'menyEntryLabel': 'Write PDBQT ...', 'menuButtonNam...
  PDBQTWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  SaveMMCIFGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  stlWriterGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'File'...
  STLWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  vrml2WriterGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'File'...
  VRML2WriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  readFromWebGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details [hide private]

initModule(viewer)

source code 
None

Variables Details [hide private]

pdbDescr

None
Value:
"""
By default the PDB writer will create the following records:
- ATOM and TER records
- CONECT records when bond information is available (bonds have been b
uilt by distance,
  the user defined bond information or the original file contained con
nectivity information.
- HELIX, SHEET, TURN when secondary structure information is available
...                                                                    
      

MoleculeReaderGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751582c>          
      

pdbReaderGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Read PDB ...',
 'widgetType': 'Menu'}                                                 
      

pdbqReaderGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Read PDBQ ...',
 'widgetType': 'Menu'}                                                 
      

pdbqsReaderGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Read PDBQS ...',
 'widgetType': 'Menu'}                                                 
      

pdbqtReaderGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Read PDBQT ...',
 'widgetType': 'Menu'}                                                 
      

pqrReaderGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Read PQR ...',
 'widgetType': 'Menu'}                                                 
      

mol2ReaderGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Read MOL2 ...',
 'widgetType': 'Menu'}                                                 
      

pdbWriterDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Write PDB ...',
 'widgetType': 'Menu'}                                                 
      

PDBWriterGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bbec>          
      

pqrWriterDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Write PQR ...',
 'widgetType': 'Menu'}                                                 
      

PQRWriterGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bc2c>          
      

pdbqWriterGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Write PDBQ ...',
 'widgetType': 'Menu'}                                                 
      

PDBQWriterGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bc6c>          
      

pdbqsWriterGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Write PDBS ...',
 'widgetType': 'Menu'}                                                 
      

PDBQSWriterGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bcac>          
      

pdbqtWriterGuiDescr

None
Value:
{'index': 0,
 'menuButtonName': 'File',
 'menyBarName': 'menuRoot',
 'menyEntryLabel': 'Write PDBQT ...',
 'widgetType': 'Menu'}                                                 
      

PDBQTWriterGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bcec>          
      

SaveMMCIFGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bd2c>          
      

stlWriterGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'File',
 'menuEntryLabel': 'Write STL',
 'widgetType': 'Menu'}                                                 
      

STLWriterGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bd6c>          
      

vrml2WriterGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'File',
 'menuEntryLabel': 'Write VRML 2.0',
 'widgetType': 'Menu'}                                                 
      

VRML2WriterGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bdac>          
      

readFromWebGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb751bdec>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb751bbec>
,
  'name': 'writePDB'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb751bc6c>
,
  'name': 'writePDBQ'},
...