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#
# Anna Dehof 2010-09-15
# read a NMR and assign the shifts to a proteins' atoms
#
import sys
from BALL import *
#### for use in BALLView
#system = getSystems()[0]
#### for command line use
# issue a usage hint if called without parameters
#if (len(sys.argv) != 3 ):
# print"Usage: ", sys.argv[0] , "<NMR file> <PDB file>"
# exit()
# read the NMRStar file
nmr_file = NMRStarFile("../../../TEST/data/NMRStarFile_test_1z0r.bmr", File.MODE_IN)
#nmr_file = NMRStarFile(sys.argv[1], File.MODE_IN)
if not nmr_file:
print "Could not open given file, aborting"
exit(-1)
print "File contains ", nmr_file.getNumberOfAtoms(), " chemcial shifts"
# read the corresponding PDB file
p = PDBFile("../../../TEST/data/NMRStarFile_test_1z0r.pdb", File.MODE_IN)
#p = PDBFile(sys.argv[2], File.MODE_IN)
if not p:
print "Could not open given file, aborting"
exit(-1)
S = System()
p.read(S)
# get the sequences to compute an alignment
print Peptides.GetSequence(chains(S)[0])
print nmr_file.getResidueSequence(0)
# get a chemical unit of this file
chem_unit = nmr_file.getMolecularInformation().getChemicalUnit(0).label
print "Label of chemical unit: ", chem_unit
print "Molecular systems name: ", nmr_file.getMolecularInformation().system_name
# create a mapping based on an alignment
mapper = NMRStarFile.BALLToBMRBMapper(chains(S)[0], nmr_file, chem_unit)
mapper.createMapping("MKSTGIVRKVDELGR-VVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMT", "MKSTGIVRKVDELGRVV-IPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMT")
print "Number of mismatches: ", mapper.getNumberOfMismatches()
print "Number of gaps: ", mapper.getNumberOfGaps()
# assign the shifts
nmr_file.assignShifts(mapper)
# get some print outs
for a in atoms(S):
if a.hasProperty("ExperimentalChemicalShift"):
# print a.getProperty("ExperimentalChemicalShift").getFloat()
print a.getProperty(ShiftModule.PROPERTY__EXPERIMENTAL__SHIFT).getFloat()
p.close()
# we are done
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