Logo Search packages:      
Sourcecode: python-biopython version File versions

NOEtools.py

# NOEtools.py: A python module for predicting NOE coordinates from
#                assignment data.  
#
#    The input and output are modelled on nmrview peaklists.
#    This modules is suitable for directly generating an nmrview
#    peaklist with predicted crosspeaks directly from the
#    input assignment peaklist. 

import string
import sys
sys.path=[sys.path,"/usr/people/robert/development/xpktools/"]
import xpktools

def predictNOE(peaklist,originNuc,detectedNuc,originResNum,toResNum):
# Predict the i->j NOE position based on self peak (diagonal) assignments
# 
# example predictNOE(peaklist,"N15","H1",10,12)
#    where peaklist is of the type xpktools.peaklist
#    would generate a .xpk file entry for a crosspeak
#    that originated on N15 of residue 10 and ended up
#    as magnetization detected on the H1 nucleus of
#    residue 12.
# CAVEAT: The initial peaklist is assumed to be diagonal (self peaks only)
#       and currently there is not checking done to insure that this
#       assumption holds true.  Check your peaklist for errors and
#       off diagonal peaks before attempting to use predictNOE.

  returnLine=""   # The modified line to be returned to the caller

  datamap=_data_map(peaklist.datalabels)

  # Construct labels for keying into dictionary
  originAssCol    =  datamap[originNuc+".L"]+1
  originPPMCol    =  datamap[originNuc+".P"]+1
  detectedPPMCol = datamap[detectedNuc+".P"]+1

  # Make a list of the data lines involving the detected
  if (peaklist.residue_dict(detectedNuc).has_key(str(toResNum)) and 
      peaklist.residue_dict(detectedNuc).has_key(str(originResNum))):
    detectedList=peaklist.residue_dict(detectedNuc)[str(toResNum)]
    originList=peaklist.residue_dict(detectedNuc)[str(originResNum)]
    returnLine=detectedList[0]

    for line in detectedList:

      aveDetectedPPM    =_col_ave(detectedList,detectedPPMCol)
      aveOriginPPM      =_col_ave(originList,originPPMCol)
      originAss         =string.splitfields(originList[0])[originAssCol]

    returnLine=xpktools.replace_entry(returnLine,originAssCol+1,originAss)
    returnLine=xpktools.replace_entry(returnLine,originPPMCol+1,aveOriginPPM)

  return returnLine


def _data_map(labelline):
# Generate a map between datalabels and column number
#   based on a labelline
  i=0       # A counter
  datamap={}      # The data map dictionary
  labelList=string.splitfields(labelline) # Get the label line

  # Get the column number for each label
  for i in range(len(labelList)):
    datamap[labelList[i]]=i

  return datamap

def _col_ave(list,col):
# Compute average values from a particular column in a string list
  sum=0; n=0
  for element in list:
    sum=sum+string.atof(string.split(element)[col])
    n=n+1
  return sum/n

Generated by  Doxygen 1.6.0   Back to index