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# Retrieve atomic fluctuation information from a PDBConfiguration object.
#
from MMTK import *
from MMTK.PDB import PDBConfiguration
from Scientific import N
# Read a PDB file containing ANISOU records.
conf = PDBConfiguration('1G66.pdb')
# By passing the applyTo methods of MMTK.PDB a dictionary argument
# atom_map, one obtains a dictionary from MMTK atom objects to the
# corresponding PDB atom objects. This dictionary can be used to
# retrieve additional atom data from the PDB file.
atom_map = {}
for c in conf.peptide_chains:
# Create a PeptideChain object
chain = c.createPeptideChain()
# Retrieve the atom_map dictionary
# Note: this also redefines the configuration, but in this
# application that makes no difference since it is the same
# that was defined in the previous line.
c.applyTo(chain, atom_map=atom_map)
# Print the B factor and the trace of the anisotropic displacement
# tensor for each atom for which both are available. They should
# be equal, but due to the limited precision in PDB files
# there can be small differences.
for atom in chain.atomList():
try:
pdb_atom = atom_map[atom]
except KeyError:
print atom, " not in PDB file"
continue
b_factor = pdb_atom.properties['temperature_factor'] * Units.Ang**2
try:
u_trace = pdb_atom.properties['u'].trace()/3. * Units.Ang**2
except KeyError:
u_trace = "[no ANISOU record]"
print atom, b_factor/(8*N.pi**2), u_trace
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