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ViewerFramework.VFCommand.Command --+ | mvCommand.MVCommand --+ | ReadMolIndexedPolygons
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
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pickedVerticesToAtoms(self,
geom,
vertInd) Function called to convert a picked vertex into an atom |
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| pickedVerticesToBonds(self, geom, parts, vertex) | ||
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atomPropToVertices(self,
geom,
atoms,
propName,
propIndex=None) Function called to map atomic properties to the vertices of the geometry |
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onAddObjectToViewer(self,
obj) Adds the Molindexedpolygons geometry to represent the molindexedpolygons surface of a molecule |
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doit(self,
molName,
vertfile,
trifile,
atom_index=None,
propertyList=[],
name=None,
display=1) virtual method. |
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guiCallback(self) Doesn't handle property lists yet. |
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__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 |
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