def main():
res = VibTools.SNFResults(outname='Ala10/snf.out',
restartname='Ala10/restart',
coordfile='Ala10/coord')
res.read()
plots = []
# numbers of the amide I modes
ml = range(241, 250)
modes = res.modes.get_subset(ml)
lv = VibTools.LocVib(modes, 'PM')
lv.localize()
lv.sort_by_residue()
lv.adjust_signs()
# vibrational coupling constants
cmat = lv.get_couplingmat()
print
print "Vibrational coupling matrix [in cm-1]"
print_mat(cmat)
# intensity coupling constants
lma = VibTools.LocModeAnalysis(res, 'ROA', lv.locmodes)
intcmat = lma.get_intensity_coupling_matrix()
print
print "Intensity coupling matrix for ROA backscattering"
print_mat(1000.0 * intcmat)
def localize_subset(modes, subset):
# method that takes normal modes
# and a range of modes, returns them
# localized + the cmat
tmpmodes = modes.get_subset(subset)
tmploc = VibTools.LocVib(tmpmodes, 'PM')
tmploc.localize()
tmploc.sort_by_residue()
tmploc.adjust_signs()
tmpcmat = tmploc.get_couplingmat(hessian=True)
return tmploc.locmodes.modes_mw, tmploc.locmodes.freqs, tmpcmat
def main():
res = VibTools.SNFResults(outname='Ala10/snf.out',
restartname='Ala10/restart',
coordfile='Ala10/coord')
res.read()
# numbers of amide I normal modes (found with composition.py)
ml = range(241, 250)
modes = res.modes.get_subset(ml)
backint = res.get_backscattering_int(modes=modes)
lv = VibTools.LocVib(modes, 'PM')
lv.localize()
lv.sort_by_residue()
lv.adjust_signs()
print
print "Composition of localized modes: "
lv.locmodes.print_attype2_composition()
lv.locmodes.print_residue_composition()
# write localized modes to g98-style file
lv.locmodes.write_g98out(filename="locmodes-amide1.out")
backint_loc = res.get_backscattering_int(modes=lv.locmodes)
print
print "ROA backscattering intensities of normal modes and localized modes"
print
print " normal modes | localized modes "
print " freq int | freq int"
n = 0
for i, f, bi, f_loc, bi_loc in zip(ml, modes.freqs, backint * 1e3,
lv.locmodes.freqs, backint_loc * 1e3):
n = n + 1
print r"%i %6.1f %8.2f | %2i %6.1f %8.2f" % (i, f, bi, n, f_loc,
bi_loc)
print
print "Total ROA Int : ", backint.sum() * 1e3