Package Pmv :: Module hbondCommands :: Class BuildHydrogenBonds
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Class BuildHydrogenBonds

source code

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

    



Instance Methods [hide private]
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  reset(self)
  doit(self, group1, group2, paramDict, reset)
virtual method.
  __call__(self, group1, group2=None, paramDict={}, reset=1, **kw)
atDict <--- buildHbonds(group1, group2, paramDict, **kw)

Inherited from mvCommand.MVCommand: __init__, guiCallback, strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __repr__, addCallbackAfter, addCallbackBefore, addUndoCall, afterDoit, beforeDoit, buildFormDescr, buildLogArgList, checkDependencies, cleanup, customizeGUI, doitWrapper, getArguments, getHelp, getLastUsedValues, getLogArgs, getValNamedArgs, log, logString, onAddNewCmd, onCmdRun, setLastUsedValues, setupUndoAfter, setupUndoBefore, showForm, tkCb, updateGeom, warningMsg


Class Variables [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

onAddCmdToViewer(self)

source code 
method called when an instance of this command is added to the viewer. This enable viewer-addition time initializations
Overrides: ViewerFramework.VFCommand.Command.onAddCmdToViewer
(inherited documentation)

reset(self)

source code 
None

doit(self, group1, group2, paramDict, reset)

source code 
virtual method. Has to be implemented by the sub classes
Overrides: ViewerFramework.VFCommand.Command.doit
(inherited documentation)

__call__(self, group1, group2=None, paramDict={}, reset=1, **kw)
(Call operator)

source code 

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
Overrides: ViewerFramework.VFCommand.Command.__call__