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ViewerFramework.VFCommand.Command --+ | mvCommand.MVCommand --+ | BuildHydrogenBonds
This command finds hydrogen donor atoms within 2.4*percentCutoff angstrom distance of hydrogen acceptor atoms. It builds and returns a dictionary atDict whose keys are hydrogen atoms (or hydrogenbond donor atoms if there are no hydrogens) and whose values are potential h-bond acceptors and distances to these atoms, respectively Package : Pmv Module : hbondCommands Class : BuildHydrogenBonds Command : buildHbonds Synopsis: atDict <- buildHbonds(group1, group2, paramDict, **kw) Required Arguments: group1 --- atoms group2 --- atoms paramDict --- a dictionary with these keys and default values keywords -- distCutoff: 2.25 hydrogen--acceptor distance distCutoff2: 3.00 donor... acceptor distance d2min: 120 <min theta for sp2 hybridized donors> d2max: 180 <max theta for sp2 hybridized donors> d3min: 120 <min theta for sp3 hybridized donors> d3max: 170 <max theta for sp3 hybridized donors> a2min: 120 <min phi for sp2 hybridized donors> a2max: 150 <max phi for sp2 hybridized donors> a3min: 100 <min phi for sp3 hybridized donors> a3max: 150 <max phi for sp3 hybridized donors> donorTypes = allDonors acceptorTypes = allAcceptors reset: remove all previous hbonds
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onAddCmdToViewer(self) method called when an instance of this command is added to the viewer. |
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| reset(self) | ||
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doit(self,
group1,
group2,
paramDict,
reset) virtual method. |
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__call__(self,
group1,
group2=None,
paramDict={},
reset=1,
**kw) atDict <--- buildHbonds(group1, group2, paramDict, **kw) |
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Inherited from Inherited from Inherited from |
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Inherited from |
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atDict <--- buildHbonds(group1, group2, paramDict, **kw) group1 --- atoms group2 --- atoms paramDict --- a dictionary with these keys and default values keywprds --- distCutoff: 2.25 hydrogen--acceptor distance distCutoff2: 3.00 donor... acceptor distance d2min: 120 <min theta for sp2 hybridized donors> d2max: 180 <max theta for sp2 hybridized donors> d3min: 120 <min theta for sp3 hybridized donors> d3max: 170 <max theta for sp3 hybridized donors> a2min: 120 <min phi for sp2 hybridized donors> a2max: 150 <max phi for sp2 hybridized donors> a3min: 100 <min phi for sp3 hybridized donors> a3max: 150 <max phi for sp3 hybridized donors> donorTypes = allDonors acceptorTypes = allAcceptors reset: remove all previous hbonds
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