Python: module pairDHPotTools
Functions for creating and analyzing the screened electrostatic Debye-Hueckel
term pairDHPot.PairDHPot.
Functions |
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- analyze(potList)
- perform analysis of PairDHPot terms and return nicely formatted
summary.
- create_PairDHPot(name, selection='not PSEUDO', selPairs=[], moveTol=0.5, charges=None, dielectricConst=78, ionicStrength=1, tempK=300, rOn=20, verbose=False)
- Return an instance of pairDHPot.PairDHPot.
The selection argument specifies which atoms are included in the
nonbonded calculation. moveTol specifies the maximum atom
displacement before the nonbonded list is recalculated. The selPairs argument is an optional sequence of pairs
of atom selection strings which specify particular pairs of atoms
to compute interactions between. The actual selections used will
be the intersections of the selection argument and each selection
pair entry.
The other optional arguments are
charges - a sequence with length len(selection).
rOn - specifies the internuclear distance at which energy
truncation begins.
dielectricConst - unitless dielectric constant.
ionicStrength - ionic strength in FIX units.
tempK - temperature in K - used to calculate Debye lengths
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