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- calcSA(rSolvent=1.2, sel='known')
calculate the total effective surface area of the given selection.
Radii are calculated as documented for create_SurfaceArea.
- create_SurfaceArea(rSolvent=1.2, sel='known', radiusType='allatom')
create a surfaceArea.SurfaceArea object with the specified
solvent radius. Surface area calculations will include atoms specified
by the atomSel.AtomSel sel.
if radiusType is allatom, radii are set to be rSolvent + 0.5 * sigma of
the NONBond parameter - of all XPLOR type-based parameters read in thus
far.
if radiusType is heavyatom, the radii from McCammon, Wolynes and Karplus,
Biochem. 18, 927-942 (1979) are used, and protons positions are not
considered.
- dumpVMDRadii(sa)
dump radius info in VMD format to file named 'radius.vmd'
- initializeChemTypeRadii()
- readXplorRadii(filename)
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