This is the library creation module of a much larger project. 
The basic idea is to generate peptides from artificially digested 
proteins. 

Simply type 'Make' and then 'make run' to run the supplied fasta file, 
test.fasta. Make generates an executable called 'main'. To digest other 
fasta files simply type:  ./main test.fasta

The premise of the program is simple, given a protein:

LLHSLKIHNNTASQKTALMEQYDRYLIVENLYYRGLVSQDINIMQNVFYKELLAHVDTIP

If cleaved at all K's and R's (trypsin), this protein would generate fragments like this:
691.438 LLHSLK
993.499 IHNNTASQK
1107.5  TALMEQYDR
1326.7  YLIVENLYYR
1684.94 LLHSLKIHNNTASQK
1849.94 GLVSQDINIMQNVFYK
2101    IHNNTASQKTALMEQYDR
2434.2  TALMEQYDRYLIVENLYYR
3176.64 YLIVENLYYRGLVSQDINIMQNVFYK

Where the first column correspond to the neutral mass of the 
fragments. Amino acid masses are defined in AminoAcidMasses.h.

It is also possible that trypsin might not digest everything perfectly. 
There are two types of imperfect digestion, missed cleaveage and semi-tryptic. 
A missed cleaveage would correspond to a simple concatenation of two adjacent 
fully tryptic peptides:

LLHSLK + IHNNTASQK = LLHSLKIHNNTASQK

Semi-tryptic means that only one end of the peptide has a tryptic termini, 
all semi tryptic peptides of GLVSQDINIMQNVFYK:
G LVSQDINIMQNVFYK
GL VSQDINIMQNVFYK
GLV SQDINIMQNVFYK
GLVS QDINIMQNVFYK
GLVSQ DINIMQNVFYK
GLVSQD INIMQNVFYK
GLVSQDI NIMQNVFYK
GLVSQDIN IMQNVFYK
GLVSQDINI MQNVFYK
GLVSQDINIM QNVFYK
GLVSQDINIMQ NVFYK
GLVSQDINIMQN VFYK
GLVSQDINIMQNV FYK
GLVSQDINIMQNVF YK
GLVSQDINIMQNVFY K