mass-spec Files

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Installation:
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Uncompress the .tgz archive file in an appropriate location:

  (sudo) tar xvfz MassSpec.tgz

The sudo command is required if you are aiming to install this code in a
system directory rather than a user directory.

Change into the newly created MassSpec subdirectory, and ensure that the 
generate_peaks.py code is executable:

  chmod +x generate_peaks.py

You can check the install directory at this point by typing:

  pwd

Set up your path so the newly installed code can be found without having
to specify the full path name at execution time. On a Mac, this can be achieved 
for all users by editing /etc/paths and then restarting terminal/X-term. On
a Linux machine, each user should edit their ~/.bashrc or ~/.profile (depending 
on which shell is being used to interface with the operating system), and then 
typing "source ~/.bashrc" or "source ~/.profile", respectively.

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Usage:
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generate_peaks.py *max_fragment_size *input_file_name > *output_file_name

The * symbol denotes variables that must be specified by the user:

  *max_fragment_size : an integer denoting the number of indivisible units that 
                       are combined to form mass-spec fragments
  *input_file_name   : a string that specifies the input file that must be in the  
                       current working directory, ideally given an informative name
  *output_file_name  : a string that specifies the name of the output file that 
                       will be created in the current working directory

The input file must contain list of atoms/indivisible fragments and maximum 
number of atoms/indivisible fragments of each type, as per the example files: 
example_atom.input & example_fragment.input

Further information on how to specify sub-fragments and use this code 
efficiently are provided in the user manual in the docs directory.

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Licensing
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This code is released on an all-care no-responsibility basis under the 
MIT open-source license. A copy of this license and its conditions can
be found in the docs directory.