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ViewerFramework.VFCommand.Command --+ | mvCommand.MVCommand --+ | ComputeSecondaryStructureCommand
The computeSecondaryStructure command gets the information on the secondary structure of each molecule contained in the current selection.This information is then used to create object describing the various secondary structure elements. Package : Pmv Module : secondaryStructureCommands Class : ComputeSecondaryStructureCommand Command name : computeSecondaryStructure Description: The SS element object belonging to a chain are then grouped into sets. A new level is added in the 4 level hierarchy... The information is taken from the file when available or using stride when available.This command can be used as an interactive command. Synopsis: None <--- ComputeSS(nodes, molMode={}, **kw) Required Arguments: nodes --- any set for MolKit nodes describing molecular components Optional Arguments: molmode --- dictionary key: molecule name, value : 'From File' or 'From Stride'. Required Packages: MolKit, DejaVu, mglutil, OpenGL, Tkinter, Pmw, types, ViewerFramework Known bugs: None Examples: mol = mv.Mols[0] mv.computeSecondaryStructure(mv.getSelection())
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onRemoveObjectFromViewer(self,
obj) Method to delete sets created by this command. |
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onAddCmdToViewer(self) method called when an instance of this command is added to the viewer. |
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__call__(self,
nodes,
molModes=None,
**kw) None <--- computeSecondaryStructure(nodes, molModes = None, **kw) nodes --- TreeNodeSet holding the current selection. |
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doit(self,
nodes,
molModes=None) virtual method. |
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| savesets(self, mol) | ||
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clean(self,
mol) This method is called when getting the secondary structure information using stride after having from file and vice versa. |
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buildFormDescr(self,
formName) Build the form description for the given form name. |
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guiCallback(self) Default callback function called by the gui |
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Inherited from Inherited from Inherited from |
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Inherited from |
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None <--- computeSecondaryStructure(nodes, molModes = None, **kw) nodes --- TreeNodeSet holding the current selection. moldMode --- dictionary {name of the protein: 'From File' or From Stride'}, 'From File' to get the information from the file, 'From Stride' to use stride.
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