Email comments/bugs to: walthall@stanford.edu

Important: The official site to obtain MW Calc is at PalmGear.com

Be sure to delete the old version before you install the new one.
You now need to install MathLib.  Click here to get it.

Contents:

• What's new in v6.0!
• Reporting bugs.
• Conventions used in this document.
• Features of the Application.
• Grammar Rules.
• Using Caps.
• Amino Acids.
• Using Periods / Spaces.
• Using All Lowercase.
• Using Numbers.
• Using Parenthesis and nested parenthesis.
• Using Both Caps and Periods.
• Looking Up Elements.
• Exact Masses.
• Mass Percents.
• Known Bugs.
• Future Releases.
• History.
• Download the .prc file.

What's new in v6.0!

Someone made the excellent request that I support Amino Acids.  So, after dragging my feet for far too long, I finally got my act together last weekend and implemented it.  (It turned out to be surprisingly easy, so I felt really dumb for not doing it sooner.)
 

What's new in v5.0!

I've had several requests for a new feature since I released this program: isotope patterns.  I finally got around to implementing it!  It unfortunately requires Mathlib since I needed to use pow(...) function [ie a^b].  You will need to install MathLib.  You can get it here.
 
 
 

Reporting Bugs:

Email walthall@leland.stanford.edu with the description of the error and what you entered that caused the error.

• Molecular formulas will appear in fixed font, one per line whenever possible.
• All capitalization and punctuation should be entered exactly as it appears.
• Regular text will appear in this font.

FEATURES OF THE APPLICATION: 

• Calculates masses of molecular formulas.
• Looks up elements: 
• Supports copying (of the formula and the mass) and pasting (of the formula): 
• Supports for isotopes of Hydrogen (D and T).
• Does AMU calculations using the most common isotope for each element.
• Will tell you the Mass Percent for the elements in the formula.
• Calculates Mass Spec. isotope patterns.  (This can be very slow, especially for large numbers of atoms.)
• If an erroneous formula is entered, a copy of the formula appears at the bottom with an asterisk (*) marking the spot of the error. (Note that the actual correction may need to be quite a bit before the error, but the first place that the error was noticed was at the *. Using Caps or Periods helps eliminates this problem.) 

"Grammar" Rules for this program:

CAPS:
One method is to use correct capitalization for the elements. This ensures that the correct element will be looked-up. Note that if any caps are used, then it is required that all of the elements be correctly capitalized.

(There are certain minor variations, such as Hgs will return the same as HgS, but Hgss will return an error. This is a result of the order of checking that is done on the string. I tried to be as relaxed as possible when checking for error while still ensuring that a correctly inputted formula would return the correct value.)

Correct Usage:

NaOH
HHeLiBe
No
NO

(In the case of No, it would return the mass of Nobelium, and in the case of NO, it would return the mass of Nitrogen + Oxygen.)
 
 

AMINO ACIDS:
Amino acids are now supported.  Since there is confusion between elements and amino acids, all amino acids must be contained in curly braces.

Curly Braces:

{ }

Multiple amino acids can be combined into one set of curly braces.  Since both 1 letter codes {AWVG} and 3 letter codes {AlaTrpValGly} are supported, correct capitalization is required for amino acids.  In addition, to make it simple to include atoms inside the amino acid braces, parenthesis can be used.

Example:
{AlaGly(CH3)} corresponds to Alanine + Glycine + carbon + 3hydrogens.

When amino acids masses are handled, they are assumed to have had the HOHremoved.  Thus, {Gly} corresponds to glycine missing an H from one end of the chain and an OH from the other.
 

normal glycine	glycine without the H and OH

So the string {AlaGly} corresponds in this program to:

To get amino acid sequences that are terminated as normal, one can use many different but equivalent ways:

{AlaGly(H2O)}
{(H)AlaGly(OH)}
{AlaGly}H2O

I prefer the first or second because it reads easier, and it is simpler to later change the nuber of the string.  For example, we may want to know what the mass of five alanine-glycine amino acid sequences is.  Using the first two above requires only adding the number.  The third one above, while faster to write initially, requires either multiplying each part separately by 5, or requires combining them into one set of parenthesis and then multiplying by 5.  This is much more prone to error.

{AlaGly(H2O)}5
{(H)AlaGly(OH)}5

{AlaGly}5(H2O)5
({AlaGly}H2O)5
 


PERIODS / Spaces:

Another method of entering a formula is to use period to separate the elements. If any periods are used in the formula, then periods are required after any element that is only one letter (o, s, h, etc.). Periods are not required after double letter elements. Extra periods are ignored. (There is one exception, which is noted later on.)  A space can be used any place that a period can be used.  This was added because it may be more convenient to make a space than double tap the sceen to make a period.

Correct Usage:

na.o.h
h.he.li.br
na....o..h...
.h.f.c.c.o.
na o h
h he li br
 
 

Incorrect Usage, but will give the correct answer:

nao.bis.ca
nao bis ca

I would advise that you use the following instead:

na.o.bi.s.ca
na o bi s ca

Incorrect Usage, resulting in an error:

na.oli
na oli

(This would try to find the element Ol, which does not exist.)

Periods and spaces can be used inside of parenthesis as well as inside of curly braces (amino acids).


 

ALL LOWERCASE:

While this is allowed, it is very discouraged. Unexpected results are likely to occur. For example, attempting to lookup HgS as hgs will lookup H, then try to find G, then try to find Gs. Typing be to lookup beryllium will instead try to find B, then E; (it is better typed as .be or be. or Be).

 

NUMBERS:

Numbers are allowed as they would normally be entered. If used with periods, the number must precede the next period.
Numbers can be any non-negative real number.  (Sorry, negative numbers and imaginary numbers are not allowed.  I had great difficulty in imagining why anyone would use imaginary numbers.  Negative numbers are not too tough to imagine a use for, and probably not too tough to implement, but as there is not demand for them, I won't bother.)

Correct Usage:

h2.s.o4
H2
H2SO4
H2O
Cl2
.cl2

Incorrect Usage:

h.2.o
2h


 

PARENTHESIS AND NESTED PARENTHESIS:

Parenthesis may be used in the molecular formula. This allows for easier entering of formulas. When combined with correct capitalization, it allows one to enter the formula exactly as it would be written (except of course for subscripting). Nested parenthesis are allowed, but all parenthesis must be matched. Only true parenthesis () are allowed, curly braces { } and square braces [ ] will cause an error to be displayed.

[Note that a set of parenthesis can be empty. That is, the following is allowed: Na()OH ]

Correct Usage:

Al(OH)2
.al.(o.h)2
al (o h)2
 


 

USING BOTH CAPS AND PERIODS:

This is perfectly acceptable, but will not increase the accuracy or the speed of the program. It will only be slower to input.

LOOKING UP ELEMENTS:

To lookup an element, enter two periods at the beginning of the formula, followed by the element that you want to lookup. (This is the exception to the rule that extra periods are ignored. A formula beginning with two periods is treated specially.)   A second way to lookup elements is to press the "ELT INFO" button.  This will automatically look up the element.  You can eliminate the ".." that was previously needed.

You can also lookup elements by their atomic number.

Correct Usage using "..":

..al
..h

Incorrect Usage using "..":

..h2co3

EXACT MASSES:

    To use the exact masses, click the "AMUs" button.  This program used the most abundant isotope in its calculation of mass. This feature used the lighest isotope in its calculation of mass.  (This is a change from older versions which did not have include mass spec stuff.)
 

MASS PERCENTS:

    To get mass percents, click the "Mass%" button.  You are limited to ten elements by space constraints of the program.  However, you can copy the extra field "Command:E" or "Copy Field" and paste it into the notepad to see them all, or use the scroll buttons on the side.  (You are acutally limited to about 30 elements by the length of the string, but I don't forsee this as a problem.  If it is, contact me and I can make it larger.  For people that don't have a program that increases the size of thier clipboard, they will be limited by their clipboard anyway.)
 
 

KNOWN BUGS:

• Some formulas display a warning when they should return an error (according to this ReadMe). This is a result of the way that parenthesis were implemented.
• It occurs when a formula has periods in it, but the part in parenthesis is all lowercase, without periods.
• This will NOT be corrected in future versions unless there people want me to correct it. As it is, this rarely occurs, and it does return the right mass (using all lowercase rules).
• Trying to calculate a mass that is too large gives -1.0000 as the answer.  This was done to eliminate a serious bug where the program was in an infinite loop.  It seems to be a decent fix.  To test the mass limit, try writing a formula with thousands of C's in it. (ie C100000 or more!).
• There is no current way to use elements 110 and 111.
• They have 3 letters as their symbol, which this program does not support.
• It is not possible to calculate their masses or to lookup their element number.

FUTURE RELEASES:
The users of this program determine what I will implement. If there are requests for a feature, I'll try to add it.  Right now I am fairly happy with the program, so nothing specific is planned as of yet.

Here are some features that I plan to implement at some time:

• Adding support for user defined amino acid sequences.  Since there are only 20 naturally occuring amino acids, the other six letters can be used for user defined "sets" of elements.  For example, protected amino acids that a research group frequently used could be added used quickly.  The six letters remaining are: B, J, O, U, X, and Z.
• Support for the use of the pageup and pagedown buttons.  Silly of me not to think of it myself, a user pointed out to me that using them would be easier than having my own buttons.

VERSION HISTORY: (b denotes a beta release, not widely distributed.)
 

Version:	Notes about release:
6.0	Added Amino Acids! Fixed a display bug: on nested parenthesis, it did not correctly display the spot of the error
5.0	Added Mass Spec. isotope patterns.  Fixed a minor rounding bug.
4.6	Added single precision calculations (the x.x button). You can now look-up elements by their number or their symbol.
4.0	Added support for fractional coefficients [ie  YBaCuO6.7 ]. Added Mass Percents! Added exact masses (AMUs) for all elements that I could find.  ---->Data from Scientific Instrument Services, Inc. Added MP and BP and much other data for elements. ---->Many thanks to PrEpsilon and Craig Counterman's page for the data.
3.0	Fixed one major bug (the copying of mass/pasting => hard reset bug) and one minor annoyance (field looks like it has the focus, but doesn't).
2.5	Added support for spaces.
2.4	Added support for looking up elements (the CH3Br graphic). Fixed the ..D and ..T bug. Added the element name when looking up elements (as per user suggestion). (Available to registered users only.)
2.3	(First widely available release.) Added element lookup.
2.2b	Added nested parenthesis.  Fixed an error where it wrote directly to low memory.
2.1b	Added periods and numbers.  Fixed problem with display. Added Warning and Errors.
2.0.1b	Added the masses of D and T.
2.0b	Ported for PalmIII. Initial beta release.
1.0	PC version developed. Support for Caps only.