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from MMTK import *
from MMTK.ChemicalObjects import Group
from Scientific.N import sqrt
residues = ['alanine', 'arginine', 'asparagine', 'aspartic_acid',
'cysteine', 'cystine_ss', 'glutamic_acid', 'glutamine',
'glycine', 'histidine', 'histidine_deltah',
'histidine_epsilonh', 'histidine_plus', 'isoleucine',
'leucine', 'lysine', 'methionine', 'phenylalanine',
'proline', 'serine', 'threonine', 'tryptophan',
'tyrosine', 'valine']
for r in residues:
binc = 0.
binc_deut = 0.
bcoh_sq = 0.
bcoh_deut_sq = 0.
mass = 0.
for a in Group(r).atomList():
binc = binc + a.b_incoherent/Units.fm
binc_deut = binc_deut + a.b_incoherent_deut/Units.fm
bcoh_sq = bcoh_sq + (a.b_coherent/Units.fm)**2
bcoh_deut_sq = bcoh_deut_sq + (a.b_coherent_deut/Units.fm)**2
mass = mass + a.mass()
print r
print "b_coherent = %f*fm" % sqrt(bcoh_sq)
print "b_incoherent = %f*fm" % binc
print "b_coherent_deut = %f*fm" % sqrt(bcoh_deut_sq)
print "b_incoherent_deut = %f*fm" % binc_deut
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