Package Pmv :: Module sdCommands :: Class ReadMolIndexedPolygons
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Class ReadMolIndexedPolygons

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ViewerFramework.VFCommand.Command --+    
                                    |    
                  mvCommand.MVCommand --+
                                        |
                                       ReadMolIndexedPolygons
Known Subclasses:
ReadBlur, ReadDockdata, ReadHarmony, ReadMSMS


Package : Pmv
Module  : sdCommands
Class   : ReadMolIndexedPolygons
Command : readMolIndexedPolygons

Description:
Class to read two files (defining vertices and faces) to generate
a MolIndexedPolygons instance and assign it to a molecule. Polygon
vertices are assigned to atoms in the molecule and vice versa. The
first six columns of the vertices file contain vertex coordinates
and surface normals. The remaining columns contain surface
properties.

Synopsis:
  None <- ReadMolIndexedPolygons(molName, vertfile, trifile, propertyList=[], name=None, **kw)
  molName        : name of the molecule to which the polygon belongs
  vertfile       : name of the file containing list of vertices and surface properties
  trifile        : file containing faces (i.e. vertex connectivity)
  atom_index     : file containing correspondence between surface points and atoms
                   (in the format output using cluster -d -a)
                   If absent, the correspondences will be calculated
  propertyList   : list of names to give the surface properties (columns 7+ of the vertex file)
  name           : name to give the geometry. Defaults to the vertex file name.
  
Keywords: geometry, harmony



Instance Methods [hide private]
  __init__(self)
  pickedVerticesToAtoms(self, geom, vertInd)
Function called to convert a picked vertex into an atom
  pickedVerticesToBonds(self, geom, parts, vertex)
  atomPropToVertices(self, geom, atoms, propName, propIndex=None)
Function called to map atomic properties to the vertices of the geometry
  onAddObjectToViewer(self, obj)
Adds the Molindexedpolygons geometry to represent the molindexedpolygons surface of a molecule
  doit(self, molName, vertfile, trifile, atom_index=None, propertyList=[], name=None, display=1)
virtual method.
  guiCallback(self)
Doesn't handle property lists yet.
  __call__(self, molName, vertfile, trifile, atom_file=None, propertyList=[], name=None, **kw)
None <- readMolIndexedPolygons(nodes, vertfile, trifile, atom_file, propertyList, name,**kw) nodes : TreeNodeSet holding a molecule vertfile: vertices and normals trifile : one-based triangulation file atom_file: (optional) output of cluster assigning atoms to vertices propertyList: list of names of surface properties in the vertfile

Inherited from mvCommand.MVCommand: strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __repr__, addCallbackAfter, addCallbackBefore, addUndoCall, afterDoit, beforeDoit, buildFormDescr, 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]

__init__(self)
(Constructor)

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None
Overrides: mvCommand.MVCommand.__init__

pickedVerticesToAtoms(self, geom, vertInd)

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Function called to convert a picked vertex into an atom

pickedVerticesToBonds(self, geom, parts, vertex)

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None

atomPropToVertices(self, geom, atoms, propName, propIndex=None)

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Function called to map atomic properties to the vertices of the geometry

onAddObjectToViewer(self, obj)

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Adds the Molindexedpolygons geometry to represent the molindexedpolygons surface of a molecule

doit(self, molName, vertfile, trifile, atom_index=None, propertyList=[], name=None, display=1)

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virtual method. Has to be implemented by the sub classes
Overrides: ViewerFramework.VFCommand.Command.doit
(inherited documentation)

guiCallback(self)

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Doesn't handle property lists yet. These have to be done on the command line
Overrides: mvCommand.MVCommand.guiCallback

__call__(self, molName, vertfile, trifile, atom_file=None, propertyList=[], name=None, **kw)
(Call operator)

source code 
None <- readMolIndexedPolygons(nodes, vertfile, trifile, atom_file, propertyList, name,**kw) nodes : TreeNodeSet holding a molecule vertfile: vertices and normals trifile : one-based triangulation file atom_file: (optional) output of cluster assigning atoms to vertices propertyList: list of names of surface properties in the vertfile
Overrides: ViewerFramework.VFCommand.Command.__call__