Package Pmv :: Module sdCommands :: Class ReadMolIndexedPolygons

Class ReadMolIndexedPolygons

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)

source code

None

Overrides: mvCommand.MVCommand.__init__

pickedVerticesToAtoms(self, geom, vertInd)

source code

Function called to convert a picked vertex into an atom

pickedVerticesToBonds(self, geom, parts, vertex)

source code

None

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

source code

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

onAddObjectToViewer(self, obj)

source code

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)

source code

virtual method. Has to be implemented by the sub classes

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

guiCallback(self)

source code

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__

Class ReadMolIndexedPolygons

__init__(self) (Constructor)

pickedVerticesToAtoms(self, geom, vertInd)

pickedVerticesToBonds(self, geom, parts, vertex)

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

onAddObjectToViewer(self, obj)

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

guiCallback(self)

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

init(self)
(Constructor)

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