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#!/usr/bin/env python
# ** What is this code? **
#
# This is an example script for using new biopython modules for
# generating NOE crosspeak peaklists from diagonal peaklist within
# the framework of nmrview.
# nmrview is not required to run this script, only an installed
# version of python.
# ** What's important? **
#
# The xpktools.py and NOEtools.py modules are what I'm trying to
# demonstrate. They provide methods and a data class for performing
# some general analysis on NMR data taken directly from peaklist.
# The code in this script will demonstrate how they are used.
# ** Who wrote this code? **
# Robert Bussell, Jr.
# rgb2003@med.cornell.edu
# ** Running this script **
#
# To run this script on a UNIX/Linux system, make it executable and
# modify the first line of this script to point to python if necessary.
# First try running the code with the peaklist that I provide to get
# the feel of how things work, then you can use your own peaklist if you
# modify the variables under the "INITS" code block to make it work
# with your data. The modules xpktools and NOEtools can be called from
# your own scripts when you have them in place on your computer.
# NOTE: It is very important to have an intact peaklist. If you copy and
# paste mine into a file be prepared to remove inappropriate line breaks.
# ** Output of this script **
#
# This script generates a human readable standard output version of the
# NOE coordinates as well as an nmrview peaklist out_example.xpk.
# ***********************************************************************
# ***** LOAD MODULES *****
from __future__ import print_function
import string
# -- don't need to modify sys.path with the *tools in Biopython
# -- just need Biopython installed somewhere in the PYTHONPATH
# sys.path=[sys.path,"./"]
# sys.path=[sys.path,"/usr/people/robert/development/xpktools"]
from Bio.NMR import xpktools # Contains data classes and functions for .xpk files
from Bio.NMR import NOEtools # A module specific for generate NOE predictions
# * * * * * * * * * * MAIN * * * * * * * * * *
# ***** INITS *****
inc = 1 # The NOE increment (n where i->i+n and i->i-n are noes)
infn = "./noed.xpk" # Input peaklist
outfn = "./out_example.xpk" # Output peaklist
detectatom = "H1" # Directly detected atom
relayatom = "N15" # J-coupling from here to detected atom
fromatom = "15N2" # The other labelled nucleus
# First the peaklist is read into a data class from xpktools
# that contains methods for easily extracting information from
# the peaklist file
peaklist = xpktools.Peaklist(infn) # infn is the name of the xpk file
# The class attribute residue_dict allows the data lines
# to be separated from the header and returned here to
# the dictionary <dict> as a list indexed by the assignment
# of any of the nuclei in the file -- here, the detected atom
# is used
dict = peaklist.residue_dict(detectatom)
# As well as the data, the dictionary contains two other entries,
# corresponding to the maximum and minimum residues indexed
MAXRES = dict["maxres"]
MINRES = dict["minres"]
# ****** CALCULATE AND WRITE CROSSPEAK PEAKLIST *****
# The peaklist class has a method for writing out the header
# information in a format recognizable by nmrview
peaklist.write_header(outfn) # Write the header to the output file
# Predict the i->i+inc and i->i-inc noe positions if possible
# Write each one to the output file as they are calculated
count = 0 # A counter that number the output data lines in order
res = MINRES # minimum residue number in the set
outlist = [] # Holds the output data
while (res <= MAXRES):
# Predicting the NOE positions based on peak assignment data
# is done by supplying the peaklist to and specifying the label
# of the origin and detected atom in the NOE transfer as well as
# the residues between which the NOE transfer takes places.
noe1 = NOEtools.predictNOE(peaklist, "15N2", "H1", res, res + inc)
noe2 = NOEtools.predictNOE(peaklist, "15N2", "H1", res, res - inc)
# The output of predictNOE is in the form of an xpk entry line
# suitable for printing to an output file
# Additionally, it is possible to extract information easily from
# these output lines by using the xpktools.XpkEntry class
entry1 = xpktools.XpkEntry(noe1, peaklist.datalabels)
if noe1 != "":
# Here I'm using the XpkEntry class to gain access to
# specific fields in the that make the information
# more readable and suitable for creating data tables
# This output will be printed to the screen.
# The data table contains the assignment, coordinates and
# intensity of the resonance.
print(string.split(entry1.fields["15N2.L"], ".")[0], "-->",
string.split(entry1.fields["N15.L"], ".")[0], "\t",
entry1.fields["H1.P"], entry1.fields["N15.P"],
entry1.fields["15N2.P"], entry1.fields["int"])
noe1 = noe1 + "\012"
noe1 = xpktools.replace_entry(noe1, 1, count)
outlist.append(noe1)
count += 1
if noe2 != "":
noe2 = noe2 + "\012"
noe2 = xpktools.replace_entry(noe2, 1, count)
outlist.append(noe2)
count += 1
res += 1
# Open the output file and write the data
with open(outfn, 'a') as outfile:
outfile.writelines(outlist) # Write the output lines to the file
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