README

Note that this program has only been tested on linux (Debian Testing/Wheezy) and Windows XP in a virtual machine. 

###  Set up the Python environment ###
First you need to set up yyour python environment and install numpy and matplotlib.
On Debian Testing/Wheezy the command would be
sudo apt-get install python2.7 python-numpy python-matplotlib

Other flavours of linux would have similar packages.

On Windows 
You'll need python, which you can download from here
http://www.python.org/ftp/python/2.7.3/python-2.7.3.msi

You'll also need matplotlib:
http://matplotlib.org/downloads.html

and numpy:
http://sourceforge.net/projects/numpy/files/latest/download?source=files

Once you've installed the three binaries above, go to Control Panel/System/Advanced/Environment Variables.
Under System Variables, edit Path and append 
;C:\Python27
Or whatever the installation directory was.

On Mac you will probably find the necessary files on the same site as the windows binaries above. Note that the python 
provided by Apple may not work, so that you will most likely have to install python from python.org.

### Installation of pyisocalc###
Linux:
Download the pyisocalc.py file and change the permissions to make it executable:
chmod +x pyisocalc.py
A more convenient alternative is to rename the file and put it into /usr/local/bin
sudo mv pyisocalc.py /usr/local/bin/pysisocalc
sudo chmod +x /usr/local/bin/pysisocalc

Assuming that /usr/local/bin is in $PATH you can now call the executable using e.g.
pysisocalc --help

Windows/Mac:
Run cmd.exe, and change directory to where your pyisocalc.py file is, and you should be able to run it using e.g.
python pyisocalc.py -f "CaCl2" -p y

I may write an interactive shell at some later point.

Note that you will most likely need to convert the file from linux 
to Mac/Windows text format e.g. here: http://www.cometdocs.com/unix2dos.htm

### Usage ###
The input format has been extensively rewritten in version 0.8. 
In general, do
./pyisocalc.py --help 
to get a list over acceptable syntax.
-f  --formula     String enclosed in apostrophes, e.g. 'Al2(NO3)6'
-c  --charge      Integer. Can be negative or positive, e.g. -2. By default the charge is calculated based on 
                  a set of default oxidation states defined in pyisocalc.py
-o  --ouput       String. File to save calculated pattern to, e.g. mydata.dat. By default nothing is saved.
-p  --plot        Char/string. Whether to plot the spectrum or not. Use y, Y, yes, Yes, YES. By default no plotting is done.
-g  --gauss       Float. Gaussian broadening factor (essentially sigma). Higher value means lower resolution. 
                  Adjust to simulate spectrometer resolution. Default 0.35.
-r  --resolution  Integer. Number of points in the m/z axis. The actual resolution will depend on the m/z
                  range covered by the isotopic envelope. Default 500.

Example:
./pysisocalc.py -f 'Ru(NO3)6' -c -3 -o rutheniumnitrate.dat -p y -g 0.2 -r 175