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ViewerFramework.VFCommand.Command --+ | mvCommand.MVCommand --+ | ViewerFramework.VFCommand.ICOM --+ | | | mvCommand.MVICOM --+ | | | mvCommand.MVAtomICOM --+ | BuildBondsByDistance
This command creates the bonds between atoms of the given set of nodes and connect the residues when necessary. The cut_off distance is based on the bond order radius of the two atoms to be bound. The command will use the bhtree functionality to find the pairs of atoms to be found when available.This command can be applied on a current selection or used interactively when bound to the mouse event. Package : Pmv Module : bondsCommands Class : BuildBondsByDistance Command : buildBondsByDistance Synopsis: None<---buildBondsByDistance( nodes, display = True, **kw) Required Arguments: nodes --- any set for MolKit nodes describing molecular components display --- when set to 1 the displayLines command is called and th bonds are displayed as lines. Optional Arguments: kw --- any of the additional optional keywords supported by commands (see ViewerFramework.VFCommands.Command documentation). Required Commands: displayLines Known bugs: None Examples: mol = mv.Mols[ 0 ] mv.buildBondsByDistance(mol, display=1)
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| __init__(self, func=None) | ||
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onAddCmdToViewer(self) method called when an instance of this command is added to the viewer. |
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doit(self,
nodes,
display=False) virtual method. |
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__call__(self,
nodes,
display=False,
**kw) None <- buildBondsByDistance(nodes, display=1,**kw) nodes : TreeNodeSet holding the current selection display : Boolean flag if set to True the displayLines commands are called. |
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guiCallback(self,
event=None) Default callback function called by the gui |
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Inherited from Inherited from Inherited from Inherited from Inherited from |
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Inherited from |
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None <- buildBondsByDistance(nodes, display=1,**kw) nodes : TreeNodeSet holding the current selection display : Boolean flag if set to True the displayLines commands are called. The buildBondsByDistance commands connects atoms and residues in the given set of nodes based on the covalent radius of each atoms to be connected.
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