NMRpal

NMR calculator and data tables for PalmOS



 


 

NMRpal v1.2

This is the second official release of NMRpal. Since version 1.0.1 (released at ENC 2000), I've had a number of obstacles to doing concentrated work on the program (a new kid (good!), and the death of my development machine (bad!))  Well, the long wait is over!  I have moved all development over to the G4, and into CodeWarrior.  The GCC prc-tools are quite good, and I'd recommend them to anyone, but CW is frankly, just better.
This is to some extent a transitional release, done to some extent to make sure the code is stable on the new development platform, however there are some new features to tempt you to upgrade.

Major features of this version:

ACKNOWLEDGEMENTS:

Steve Smallcombe of Varian was very important in the development of this program, both for a lot of helpful suggestions and for providing most of the actual NMR data (nucleus properties, solvent shifts).

DISCLAIMER:

As is always the case with software licenses, I will claim only that this is software.  Any other claim about usability, warranty, or the like is premature and  irresponsible. You use this software at your own risk - it may crash your machine, erase your data, or kill your dog - I don't know (although I kind of doubt it would do the last one).

That said, I have put in a fair amount of error checking code, and the code has been pretty exhaustively checked out on the emulator (if anyone cares, it has now survived 3.5 million Gremlin events before I got bored and shut it off). When it does fail, it does so gracefully.  I use it daily on my machine, and this version has yet to do anything bad; of course, it is still in active development, and I'm sure I've introduced new bugs that I have yet to see.
 

CONTACT INFORMATION:

It is best to send me email about NMRpal at bbfcmm@rcn.com.  And, of course, you can go to the website to find the latest information and program versions (http://users.rcn.com/bbfcmm/loafpan.html).
 

REGISTRATION AND PRICING:

This program is shareware.  Try it out and see if you like it.  If you find it useful, and use it, please register the program.  If not,  don't keep using it.  I know it can be hard to get the motivation to pay for something that you can use for free, but I did put a lot of work into the program, and heck, it's just not that expensive!

Registration is handled through Kagi.  You can register either by using the Register program included in the distribution, or by going directly to the LoafPan registration page here.  Kagi handles just about every payment method and currency you might want to pay with (and charge me a pretty low fee for doing it).

The price for a license to use NMRpal for whatever you want forever is a paltry 12 USD.  C'mon, $12!  Impress your friends with how your copy doesn't keep bugging you every time you change screens!

There are also two special categories of registration:

DESCRIPTION:

NMRpal was designed for two purposes. The first is to perform NMR calculations such as finding Ernst angles and the like conveniently (as you're sitting in front of the scanner). These are simple calculations, but I find that anything that requires more than 3 or 4 operations on a handheld calculator, I'm likely to mess up.

The other purpose is to consolidate as much specific NMR information as possible in a convenient form (properties and gammas of nuclei, and resonance positions of lines). This is to help with the "conference problem" - you go to ENC or SMR and see lots of talks and papers that make you think about all the cool projects you want to do as soon as you get back to the lab, ("Eureka! If only I had a nitrogen echo planar imaging sequence...), and you can't wait to start doing back of the envelope calculations to see if your brainstorms are practical. But of course, you didn't bring a stack of reference books and papers with you, so you have to try to remember if it's N-14 or N-15 that's the dominant isotope, and which one is spin 1,  blah blah blah, so you have to wait until you get home to decide if your idea is doable.

(Putting this data in electronic form is also useful if your reference books have a tendency to wander into other people's offices...)

One (I think) cool feature of the way this data is stored is that the reference information will be editable and sharable by the user. I did this because I want NMRpal to be useful to as many people as possible. Since I know nothing about many nuclei, it makes more sense that other people can create and share databases tailored to their specific needs. The database editor, unfortunately, is not yet done, so for the time being, you have to use the canned database.
 

REQUIREMENTS:

NMRpal in its current incarnation requires about 80k to install the program itself and the minimal set of databases. NMRpal also requires MathLib, which takes another 55k or so, so the minimum installation is about 135k. This shouldn't be a problem for any but the most RAM starved, and if you've installed a lot of other math intensive programs, you may already have MathLib installed.
 

COMPATIBILITY:

Because NMRpal uses a shared library (MathLib), it requires PalmOS 2.0 or better to run. I have tested the program in the Emulator under PalmOS 3.1, 3.3, 3.5 and 4.0 extensively, and minimally under 2.0. I run it on a Palm IIIx running PalmOS 3.3, and have seen it on Palm V, and even a PalmPilot upgraded to OS3.  It really doesn't use any strange OS features, so I don't have any reason to believe it won't work on any 3Com or licensee devices.

NOTE: This program currently does NOT work under PalmOS 2.0 due to a font problem.  I will fix this when I get around to it (not yet a priority).
 

DOWNLOAD:

Click the following link to download the NMRpal distribution version 1.2.
nmrpal_1_2.zip NOTE: Until I find a free tool to make .sit files, it's only in .zip format.  Since Stuffit for the Mac automatically decompresses .zip files now, this should not be a problem for anybody.  If it is, contact me.

nmrpal_1_0_1.zip The previous release version of the software.  I can't imagine why you'd want it, but you might, so here it is.

INSTALLATION:

To run NMRpal, you must install the application and MathLib on your device.
The zipfile distribution contains: If you are currently using a previous version of NMRpal, you can just install the new version and it will update any databases it needs to.  If you have a registered copy, the upgraded copy will also be registered (that said, it's always a good idea to write down your registration key before upgrading, accidents happen).

Use your palm desktop software to install the two .prc files on your machine. The simplest way to do this is to use the install conduit (the specifics are in the manual that came with your device - I am only familiar with the Macintosh desktop software, so rather than say something wrong, I'll point you to the documentation).

Alternately, if someone already has the program installed on their device, they can just beam you both of these files (DON'T FORGET MATHLIB!  NMRpal won't run without it.).

When running, NMRpal uses a number of external databases.  If none are present NMRpal will create stripped down versions so you'll be able to get some work done.
 

USAGE:

Yup, right about here, you'd think you'd find some kind of a manual.  Sadly, you'd be wrong.  It would be nice if the external documentation were done, but for the time being, you'll have to puzzle it out.  If you are familiar with NMR, it should be obvious what each screen is for (if it isn't, tell me - this is part of the input I want).  In terms of actual use, there is helpful information in the program itself - touch the 'i' in the circle in the upper right corner of any screen to get help (explanation of input and output parameters, etc.)  As of version 1.2, all of the internal documentation is in place.
 

NOTES ON DEVELOPMENT:

For anyone who cares, NMRpal was originally developed using the GNU development system (prctools-0.5.0) on a SparcStation classic running RedHat Linux 6.1.  Why would I choose this development platform?  Because MIT was salvaging out SparcStation Classics for 25 bucks, and I'm a Linux fan, I was wondering if it could be done, and most of all, I was saving my money for a new Mac.  Testing was done on various versions of POSE on the macintosh (originally on a very sad Powermac 6100, and now on a spiffy G4/400 - finally got it!), and on Palm IIIx running PalmOS3.3.  For anyone wanting to try running POSE on a Sparc Linux box, I would say, give up.  Apparantly (and it took me a good week of tearing out my hair to find this out) the Sparc assembler in gcc chokes on the nice, informative long variable names used in the POSE source, so unless you recompile GCC and glibc with new options, it will never work.  Don't say you weren't warned.
As of version 1.1, I moved over to using CodeWarrior for PalmOS 6, and it is just a joy to use.  No disrespect towards the prc-tools - they served me quite well.  But CW is much more polished, and on the Mac it's really the only game in town (yes, I did try porting prc-tools 2.0 to the command line layer of MacOSX PB, but I'd like to spend the tiny amount of computer time that is left over after the slice reserved for two little kids actually programming, not porting programming tools!)
 

CHANGE HISTORY:

Changes in v1.2

Changes in v1.1

Changes in v1.0.1

Changes in Alpha 6:

Changes in Alpha 5:

Changes in Alpha 4:

Changes in Alpha 3:

Changes in Alpha 2.1:

Changes in Alpha 2:



If you have comments or suggestions (or are offering money), email me at:
bbfcmm@rcn.com