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Pydoc: module hbPotTools

hbPotTools

index

Helper functions for creating and analyzing hbPot.HBPot energy terms.

Functions

create_HBPot( name, selection='not PSEUDO', configFilename='da.dat', threshold='99.95', verbose=1 ): create and return a hbPot.HBPot energy term with instanceName name, and
covering atoms specified in selection.

Arguments: name
           selection="not PSEUDO",
           configFilename="da.dat",
           threshold='99.95',
           verbose=1

   selection - the term can be applied to a subset of atoms by specifying
               an alternate value.
   configFilename - file which specifies donors and acceptors for selected
                    residues and a mapping of all pairs to a
                    hbSurf.HBSurf energy surface.
   threshold      - percentage threshold used to determine whether a
                    hydrogen bond is violated. If the energy for a
                    particular geometry is larger than that corresponding
                    to threshold percent of the input datapoints, it is
                    considered to be violated. Valid values are currently
                    '98', '99' and '99.95'.

hBondInfo(term): Return a pretty-printed string with information on each detected hydrogen
bond.

readConfigFile(configFilename): Read file defining hydrogen bond acceptors, donors and mappings of
acceptor/donor pairs to database surface. Acceptor lines are of the format

    acceptor aName sel1 [sel2]

where aName is an arbitrary label for the acceptor, sel1 is an
atom selection string (atomSelLang), and sel2 is an optional second
selection string which defines the bound-to atom. The second selection string
is necessary if the acceptor is bound to more than one atom. If sel2 is
specified, sel1 must be enclosed in parentheses.

Donor lines are of the form

    donor dName sel

where dName is a label for the donor and sel is the selection string.

Mappings from acceptor/donor pairs to database source are of the form

    mapping aName:dName deltaResid filename

where aName and dName are one of the acceptor or donor labels, respectively,
or the "*" character to match any. The deltaResid argument specifies a
difference in primary sequence of the donor and acceptor residues, or
the "*" character to match any. The filename argument specifies a file for
the hydrogen bonding potential of mean force relative to the FIX...

Data
		dbDir = '/home/schwitrs/xplor/databases/hbPot/current' environ = environ({'ARCH': 'Linux_x86_64', 'NUM_THREADS': ...ocal/lib:/home/schwitrs/lib/Linux_x86_64/trunk'})