JSpecView as a JCAMP-DX Data Viewer for Windows

History

Authors: D.A.P. Facey, K.A. Bryan and R.J. Lancashire, Department of Chemistry, UWI, Mona Campus, Kingston JAMAICA, JMAAW15 (robert.lancashire@uwimona.edu.jm)
C. Muir and H. Reichgelt, originally from the Department of Computer Science and Mathematics, UWI, Mona, Kgn7 JAMAICA

In 1988, the Department purchased a diskless Perkin Elmer 1605 FTIR. To help in the process of being able to store the IR spectra recorded, two Pascal programs were written. The first to capture the files via the serial port (RS-232) and the second to display the data.

For information on the first program, FTtoPC, and other DOS utilities to convert files obtained from various instruments to JCAMP-DX format, see our JCAMP-DX utility page.

The original display program was totally rewritten in C++ and the code licensed to MDL in 1998 for incorporation into their plugin CHIME. Our contract with MDL has now finished (November 2005) but we will endeavour to be involved with future upgrades to the CHIME plugin. The last release (2.6 SP6) was April 2004 and this is available from the MDL web site..

In March 2006 we released JSpecView as an Open Source project at Sourceforge. A report on this is published in Chemistry Central Journal 2007, 1:31 (07Dec2007). The JAVA applet and application along with source code is being developed with JAVA 1.5+.

In some of the demonstrations and examples we show the use of links between spectra and molecular graphics display such that clicking on peaks in a Mass Spectrum will highlight the relevant FRAGMENTS in the molecule, clicking on peaks in the IR spectrum will highlight the relevant BONDS or animate the vibrational mode and clicking on peaks in the NMR will highlight the appropriate protons or carbon atoms. See below for more details on how to set up these links.

Justification

With the widespread use of the WWW growing so unbelievably fast, the idea of being able to link not only molecular coordinates via MOL (PDB) format to a document, but being able to display various types of spectra seemed a wonderful opportunity to enhance the teaching of spectroscopy. To that end, problem sets can be established of known and unknown samples to view. See a makeup demo of how this might look. The possibility of sub-structure searches returning structures and spectra can now be accomplished.

Information needed to configure a server for use with MDL CHIME

The MIME types posted by our web server for "chemical" type files are:

mime type file extension
chemical/x-mdl-molfile mol
chemical/x-mdl-rxnfile rxn
chemical/x-pdb pdb emb embl
chemical/x-xyz xyz
chemical/x-gaussian-input gau
chemical/x-mopac-input mop
application/x-spt spt
chemical/x-csm csm csml
chemical/x-jcamp-dx jdx dx
application/x-rasmol scr
chemical/x-mdl-tgf tgf skc
chemical/x-gaussian-cube cub cube

To configure the CHIME plugin, all you need to do is run the installer. To test, try out the demo files or sample testdata files.

screen dump of plugin

For the JAVA application, JSVApp.jar, there are several files that need to be available in the same directory as the jar file. See the README.txt file in the file release for details.

The JCAMP-DX data exchange formats and standards are currently the responsibility of the IUPAC Committee on Printed and Electronic Publications (CPEP). The CPEP JCAMP working party is chaired by Antony Davies, ISAS, Germany.

Joint Committee on Atomic and Molecular Physical Data Exchange References.

A copy of some of the following papers is available in Adobe Acrobat (PDF) format from the JCAMP-DX web site (www.jcamp-dx.org).

For an historical account of JCAMP-DX development, see the summary posted on the bionet.structure-nmr news group in January 1996. A local copy has been made available by the author.

The pages on JCAMP-DX by Antony Davies and Bob McDonald are essential reading for anyone interested in learning more about the JCAMP-DX specifications.
(Tony chairs the IUPAC working group on JCAMP-DX and Bob, who was a member, coauthored the original paper describing JCAMP-DX for IR). Both have provided test data for downloading from their web sites.

The method of encoding data, relies on substitution of numbers by ASCII characters. The following gives the compression tables used for this purpose.

Compression Table
ASCII digits 0 1 2 3 4 5 6 7 8 9
Positive SQZ digits @ A B C D E F G H I
Negative SQZ digits   a b c d e f g h i
Positive DIF digits % J K L M N O P Q R
Negative DIF digits   j k l m n o p q r
Positive DUP digits   S T U V W X Y Z s
    
Compression types handled by CHIME/JSpecView
FIX e.g. 99 98 97 96 98 93 fixed format
PAC e.g. 99+98+97+96+98+93 packed
SQZ e.g. 99I8I7I6I8I3 simple compression
DIF e.g 99jjjKn difference
DUP e.g 99jUKn difference and duplicates
CSV e.g 99,98,97,96,98,93 Comma separated values


Creating links between spectra and 3D molecular graphics display

The original mechanism used for CHIME in creating the links was to add new HEADER items to the JCAMP-DX file (##$ASSIGNMENT TYPE= , ##$CHIME TARGET= along with ##$PEAK LINKS= ).

With the release of MDL Chime 2.6SP5 there was no need to edit the JCAMP-DX file and all the links could be controlled via JavaScript code. See a report on "Embedding spectra and structures in your web pages", in Spectroscopy Europe 17(5), 28-30, 2005.

The JavaScript code can be handled as external files and by using an HTML template it is only necessary to change the name of the file containing the data. This can be easily done with a text editor without knowledge of HTML.

The method below shows what was used for the JAVA version of JSpecView
A sample set of JavaScript files are given below. The first establishes the arrays that will hold the link information and includes the setup for IR and both H and C NMR while the second contains the actual FTIR spectral information that is used to link the spectra to the molecular display animations of the vibration modes.

Contents of setup.js
//edit the following lines with caution!

var IRinfo = new Array();
function IRLinks(x,y,w,script,desc) {
  var n=IRinfo.length;
	IRinfo[n] = new Array();
	IRinfo[n].xpos=x;
	IRinfo[n].ypos=y;
	IRinfo[n].width=w;
	IRinfo[n].script=script;
	IRinfo[n].desc=desc;
}

var HNMRinfo=new Array()
function HNMRLinks(x,y,w,script){
 var n=HNMRinfo.length;
 HNMRinfo[n]=new Array();
 HNMRinfo[n].xpos=x;
 HNMRinfo[n].ypos=y;
 HNMRinfo[n].width=w;
 HNMRinfo[n].script=script;
}

var CNMRinfo=new Array();
function CNMRLinks(x,y,w,script){
 var n=CNMRinfo.length;
 CNMRinfo[n]=new Array();
 CNMRinfo[n].xpos=x;
 CNMRinfo[n].ypos=y;
 CNMRinfo[n].width=w;
 CNMRinfo[n].script=script;
}

//you should not need to edit the html files.

Contents of acetoph.js
//edit the following lines with the spectral information

var IRfilName= "acetophenone.jdx";
var MolfilName= "acetophenone.xyz";

IRLinks(3101, 1, 20, 1,"symm stretch of aromatic CH group (~3100 cm-1)");
IRLinks(3086, 1, 15, 2,"asymm stretch of aromatic CH group (~3085 cm-1)");
IRLinks(3062, 1, 15, 3,"asymm stretch of CH group (~3060 cm-1)");
IRLinks(3038, 1, 10, 4,"asymm stretch of CH group (~3040 cm-1)");
IRLinks(3029, 1, 10, 5,"asymm bend of CH3 group (~3030 cm-1)");
IRLinks(3005, 1, 20, 6,"symm stretch of methyl group (~3005 cm-1)");
IRLinks(2969, 1, 30, 7,"asymm stretch of methyl group (~2970 cm-1)");
IRLinks(2921, 1, 30, 8,"symm stretch of CH group (~2920 cm-1)");
IRLinks(1684, 1, 30, 9,"Carbonyl stretching band (~1685 cm-1)");
IRLinks(1599, 1, 30, 12,"C-C of aromatic group (~1600 cm-1)");
IRLinks(1449, 1, 20, 14,"symm stretch of CH3 group (~1450 cm-1)");
IRLinks(1359, 1, 30, 16,"C-H twist of methyl group (~1360 cm-1)");
IRLinks(1265, 1, 20, 21,"scissors of aromatic C-H groups (~1265 cm-1)");
IRLinks(1180, 1, 40, 22,"scissors of CH group (~1180 cm-1)");
IRLinks(1078, 1, 30, 25,"symm stretch of CH3 group (~1080 cm-1)");
IRLinks(1025, 1, 20, 26,"symm stretch of CH group (~1025 cm-1)");
IRLinks(1001, 1, 20, 27,"asymm bend of CH3 group (~1000 cm-1)");
IRLinks(956, 1, 20, 28,"aromatic ring perturbation mode (~955 cm-1)");
IRLinks(760, 1, 20, 31,"aromatic ring perturbation mode (~760 cm-1)");
IRLinks(691, 1, 20, 33,"aromatic ring perturbation mode (~690 cm-1)");
IRLinks(588, 1, 20, 37,"concerted rocking mode of CH groups (~590 cm-1)");

var ShowDesc= "T";

var title= "acetophenone";
var author= "Prof. Robert John Lancashire";
var address1= "Department of Chemistry";
var address2= "University of the West Indies";
var address3= "Mona, Kingston 7, JAMAICA";
var lastMod= "8th March 2006";

//you should not need to edit the html files.

JSpecView (2006) and merged with Jmol 2012

The HTML file (acetophenone.html) that calls these files gives an example of linking IR spectra to molecular display and loads a single animation file (xyz) containing the vibration vectors. When peaks are selected in the JSpecView spectral display the appropriate FRAME in the xyz file is displayed.
Jmol is another Open Source project originally available from Sourceforge. The JSpecView and Jmol applets were merged in early 2012 after collaboration with Prof Bob Hanson at St Olaf College. Bob has made numerous enhancements to the code and taken on the future development since my retirement.

JSmol - from 2013

The open source HTML5/JavaScript package of JSmol incorporating JSpecView and Jmol was first released in October 2013. JSmol is a JavaScript framework that allows web developers to create pages that utilize either Java or HTML5 (no Java), at will. This enables Jmol to display interactive 3D molecular structures on devices that do not have Java installed, or for which Java is not available (such as smart phones and some tablet computers, e.g. iPad) or has not been installed because of concerns for Java being a security threat.
Simulate NMR spectra from name or structure

JSmol is integrated fully with JSME as well and an example that uses all 3 involves the use of the JSmol on a webpage that calls servers in Frederick, Maryland (NIH resolver, for name-to-structure) and Lausanne, Switzerland (nmrdb, for structure-to-spectrum). By drawing a structure in JSME or by simply providing a name of a molecule and submitting the information then within about 10 seconds simulated NMR spectra (H and/or C) are displayed and this allows for changes to the structure to be made and resubmitting so that the spectra can be compared. The H or C atoms in the 2D and 3D molecular structures displayed are linked to the peaks in the spectra. Clicking on an atom or on a peak will highlight both in the displays.
More details are in Spectroscopy Europe 26(5) 15-17, 2014

Sample test files for error checking

A collection of files useful for checking JCAMP-DX programs have been assembled from various sources. Some provide error free information, while others are more of the nature of an "assault course for JCAMP-DX". Some FAQ on scientific data formats (including JCAMP-DX) have been collated by Ilana Stern and posted at a number of sites.
There are several other data formats commonly found in scientific laboratories such as NUTS for NMR and netCDF for MS and chromatography.

A company that for many years specialised in offering not only interfaces to equipment, but converters between data formats was Galactic Industries Corporation now Thermo Fisher Scientific.
Thermo Fisher Scientific logo

Their product, GRAMS, uses .SPC binary files and a number of sites offer spectra in this format. Thermo offer a SPC Developers Kit for programmers to create their own file converters etc. Try their searchable database of IR and Raman spectra.

The following links may be useful for more details of databases and viewers:

KnowItAll Bio-Rad Knowitall download logo from Bio-Rad, originally marketed as ChemWindows and the Sadler Suite, can read and display a wide range of spectral file types, including JCAMP-DX. A handy feature is that it allows you to insert live IR, NMR, MS spectra, and chromatograms into Microsoft applications like Word and Powerpoint.

Another commercial company that has made a large impact on data visualisation and handling is ACD Labs.
ACD Labs

ACD/Spectral Processing Software allows the user to process a range of spectral types: NMR, MS, UV, Visible, IR, NIR and Raman spectra. Supported file formats include the following: ACD (*.esp), Galactic (*.spc), JCAMP-DX (*.jdx, *.dx. *.jxs,*.jx) and ASCII (*.txt).


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Copyright © 1994-2019 by Robert John Lancashire, all rights reserved.

Created and maintained by Prof. Robert J. Lancashire,
The Department of Chemistry, University of the West Indies,
Mona Campus, Kingston 7, Jamaica.
Created Oct 1994. Links checked and/or last modified 24th December 2019.
URL http://wwwchem.uwimona.edu.jm/software/jcampdx.html