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ViewerFramework.VFCommand.Command --+ | mvCommand.MVCommand --+ | ModifyTermini
This class detects residues within a chain which are not bonded to a previous residue in the chain and those not bonded to a subsequent residue in the chain. It calls ModifyNTerminus to edit hydrogens bonded to the nitrogen atom of the first kind of residue and ModifyCTerminus to edit hydrogens bonded terminal carbon in the second kind of intra-chain breaks. Package : Pmv Module : repairCommands Class : ModifyTermini Command : modifyTermini Synopsis: None<- modifyTermini(res, check, **kw) Required Arguments: nodes to be checked for intrachain deletions. check --- if check, each molecule in nodes.top is checked to be sure that each of its residues is a standard type. If not, looking for peptide connection breaks doesn't make sense so command exits with an error.If the user's molecule has non-standard residues, he can call this with check=0...
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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,
check=1,
**kw) None<- modifyTermini(res, check, **kw) |
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doit(self,
nodes,
check) virtual method. |
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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<- modifyTermini(res, check, **kw) nodes to be checked for intrachain deletions. check --- if check, each molecule in nodes.top is checked to be sure that each of its residues is a standard type. If not, looking for peptide connection breaks doesn't make sense so command exits with an error.If the user's molecule has non-standard residues, he can call this with check=0...
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