Class BuildHydrogenBonds

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