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# Copyright (c) 2012, Anders S. Christensen
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import structure_tools as struct
import sys
def calculate_chemical_shifts(chain):
# Calculate all phi/psi angles once
phi_psi_angles = struct.get_phi_psi_angles(chain)
# Calculate all chi-angles once
chi_angles = struct.get_chi_angles(chain)
# Loop over residue in chain:
for residue in chain:
res_id = residue.id[1]
res_name = residue.get_resname()
# Do something ...
#
# print res_name, res_id, phi_psi_angles[res_id], chi_angles[res_id]
# Retur something ...
return []
def main():
try:
pdb_filename = sys.argv[1]
# Load chain (as Bio.PDB chain-type) from pdb-file
chain = struct.load_chain(pdb_filename)
print 'Loaded chain from file:', pdb_filename
except:
print 'ERROR: Problem loading chain from file:', pdb_filename
raise SystemExit
# Calculate chemical shifts
chemical_shifts = calculate_chemical_shifts(chain)
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