   

   Program : ChemSMP v1.0

   Date    : Nov 2015

   Author  : ABHINAV DUBEY
             INDIAN INSTITUTE of SCIENCES, BANGALORE
             INDIA - 560012

This program is freely available ONLY for 'academic' and 'non-proft' purposes

on http://nrc.iisc.ernet.in/hsa/gft.htm


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If you are using our program, please cite the following paper

Chemical Shifts to Metabolic Pathways: Identifying Metabolic Pathways Directly from a Single 2D NMR Spectrum
A Dubey, A Rangarajan, D Pal, HS Atreya - Analytical chemistry, 2015

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INSTRUCTIONS
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0. ChemSMP is Linux compatible

1. (i) Please ENSURE followings files are with the ChemSMP_v1_linux_32.exe present in the folder ChemSMP

   a) HMDB_CS.txt
   b) HMDBID_name.txt
   c) PathwayMetabolites_NMR.txt
   d) MetabolicPathways_Name.txt

   (ii) For demonstration purpose following files are provided along with ReadME
   a) example_INPUT.txt
   b) ChemSMPparameters.txt

2. Please DO NOT change the file names. Keep the files in the same folder as ChemSMP.exe
   Prepare your input file similar to the 'example_INPUT.txt'
   Make desirable changes in the parameter file

3. On executing ChemSMP_v1_linux_32.exe, it asks for input parameter file, input peaklist file. 
   Then it asks for ouput filename. 
   All can be browsed from desired location

4. A paramter file ["ChemSMPparameters.txt'] template is provided. Please make required changes ONLY within '<>'

5. Each line of input file is in FOUR COLUMN FORMAT SEPARATED BY SPACE (see file 'example_INPUT.txt')
   
   sr h1 c1 v

  where sr is the serial number
        h1 is the 1H chemical shift
        c1 is the 13C shemical shift 
	v is the peak volume ( 0 if not available)

  (h1, c1) is a peak in 2D [13C, 1H] HSQC

5. The output is list of metabolic pathways sorted in order of their coverage score
   along with the uniqueness score, statistical significance and metabolitc pathway name. 
   Followed by detailed information about the putative metabolites found through spectra

6. An example input file named'example_INPUT.txt' and corresponding output file named 'example_OUTPUT.txt' 
   is available in this distribution



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A python script ChemSMPBruker.py is avilable to generate ChemSMP compatible input peaklist directly from bruker spectrum
For this you need to install packages "nmrglue", "numpy", "pylab", "tkinter" in Python 3.x and execute the script


1. On executing ChemSMPBruker.py, it asks for directory with 2rr file for processed 2D [13C, 1H] HSQC spectrum

2. Two parameters are to be adjusted iteractively to obtain peaks
   a) Lowest contour level so as to visualize all peaks but not noise
   b) Relative ratio to maximum peak intensity used as cutoff to pick peaks

3. Once staisfied with peak picking it asks for addtional parameters 
   a) Spectral width in 13C and 1H dimension ( in ppm )
   b) Spectral offset in 13C and 1H dimension ( in ppm)

4. Then it asks for the location and filename to save the peaklist

5. With this information it will create and save peaklist at desired location in the required four column format

  

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