Updated documentation and organisation

README.md

@@ -3,34 +3,48 @@
 
 # Match those fragments!
 
-A peptide fragmentation matching library for rust. Split into multiple smaller modules to help keep things organised.
+A peptide fragmentation matching library for Rust.
 
 ## Features
 
  - Read [ProForma](https://github.com/HUPO-PSI/ProForma) sequences (complete specification supported: 'level 2-ProForma + top-down compliant + cross-linking compliant + glycans compliant + mass spectrum compliant')
  - Generate theoretical fragments with control over the fragmentation model from any ProForma peptidoform/proteoform
-   - Generate fragments from satellite ions (w, d, and v)
-   - Generate glycan fragments
-   - Generate theoretical fragments for modifications of unknown position
    - Generate theoretical fragments for chimeric spectra
    - Generate theoretical fragments for cross-links (also disulfides)
- - Integrated with [mzdata](https://crates.io/crates/mzdata) for reading raw data file
+   - Generate theoretical fragments for modifications of unknown position
+   - Generate peptide backbone (a, b, c, x, y, and z) and satellite ion fragments (w, d, and v)
+   - Generate glycan fragments (B, Y, and internal fragments)
+ - Integrated with [mzdata](https://crates.io/crates/mzdata) for reading raw data files
  - Match spectra to the generated fragments
  - [Align peptides based on mass](https://pubs.acs.org/doi/10.1021/acs.jproteome.4c00188)
  - Fast access to the IMGT database of antibody germlines
  - Reading of multiple identified peptide file formats (Fasta, MaxQuant, MSFragger, Novor, OPair, Peaks, and Sage)
  - Exhaustively fuzz tested for reliability (using [cargo-afl](https://crates.io/crates/cargo-afl))
  - Extensive use of [uom](https://docs.rs/uom/latest/uom/) for compile time unit checking
+ - Python bindings are provided to several core components of the rustyms library. Go to the [Python documentation](https://rustyms.readthedocs.io/) for more information.
 
-## Python bindings
+# Folder organisation
 
-Python bindings are provided to several core components of the rustyms library. Go to the
-[Python documentation](https://rustyms.readthedocs.io/) for more information.
+## rustyms
 
-# Contributing
+This is the main library. This contains all source code, databases (Unimod etc) and example data to run the rustyms library.
+
+## examples
+
+Some examples on how to use the rustyms library are provided here, see the readme file in the examples themselves for more details.
+
+## fuzz
 
-Any contribution is welcome (especially adding/fixing documentation as that is very hard to do as main developer).
+The harness to fuzz test the library for increased stability, see the readme for more details.
 
-# IMGT generate
+## rustyms-py
+
+This Rust library provides python bindings (using pyO3) for rustyms.
+
+## rustyms-imgt-generate
+
+Using the `rustyms-imgt-generate` the definitions for the germlines can be updated. Put the imgt.dat.Z file in the `rustyms-imgt-generate/data` directory and unpack it (this can be downloaded from https://www.imgt.org/download/LIGM-DB/imgt.dat.Z). Then run `cargo run --release -p rustyms-imgt-generate` (from the root folder of this repository).
+
+# Contributing
 
-Using the `rustyms-imgt-generate` the definitions for the germlines can be updated. Put the imgt.dat.Z file in the `data` directory and unpack it (this can be downloaded from https://www.imgt.org/download/LIGM-DB/imgt.dat.Z). Then run `cargo run --release -p rustyms-imgt-generate` (from the root folder of this repository).
+Any contribution is welcome (especially adding/fixing documentation as that is very hard to do as main developer).

fuzz/Cargo.toml

@@ -31,9 +31,3 @@ path = "fuzz_targets/peaks.rs"
 test = false
 doc = false
 bench = false
-
-# in root dir
-# cargo afl build --release -p rustyms-fuzz
-# cargo afl fuzz -i fuzz/in_pro_forma -o out_pro_forma target/release/pro_forma
-# open out_pro_forma/default/crashes/* | save crashes.txt -f
-# cat out_pro_forma/default/crashes/* >> crashes.txt

fuzz/README.md

@@ -0,0 +1,17 @@
+# Fuzzing
+
+Uses [cargo-afl](https://crates.io/crates/cargo-afl) for [fuzz testing](https://en.wikipedia.org/wiki/Fuzzing). Note that this only works on Linux.
+
+From root directory
+```
+cargo-afl afl system-config
+cargo afl build --release -p rustyms-fuzz
+cargo afl fuzz -i fuzz/in_pro_forma -o out_pro_forma target/release/pro_forma
+```
+Several fuzz targets are defined: `pro_forma`, `sloppy_pro_forma`, and `peaks`. The two peptide targets share the `in_pro_forma` directory with input examples. The peaks target has `in_peaks` as directory of input examples.
+
+After running the fuzzer the following commands can be used to easily save all crashes into a single file.
+```
+open out_pro_forma/default/crashes/* | save crashes.txt -f (nushell)
+cat out_pro_forma/default/crashes/* >> crashes.txt (bash)
+```

rustyms-imgt-generate/src/main.rs

@@ -21,8 +21,8 @@ use rustyms::*;
 use structs::{Location, SequenceRegion};
 
 fn main() {
-    let file = File::open("data/imgt.dat")
-        .expect("Please provide the 'imgt.dat' file in the 'data' directory in the root.");
+    let file = File::open("rustyms-imgt-generate/data/imgt.dat")
+        .expect("Please provide the 'imgt.dat' file in the 'rustyms-imgt-generate/data' directory in the root.");
     let mut output = BufWriter::new(File::create("rustyms/src/imgt/germlines/mod.rs").unwrap());
     let mut docs = BufWriter::new(File::create("rustyms/src/imgt/germlines/germlines.md").unwrap());
     let mut error = BufWriter::new(File::create("errors.dat").unwrap());

rustyms/src/fragment.rs

@@ -6,7 +6,6 @@ use std::{
 };
 
 use itertools::Itertools;
-use ordered_float::OrderedFloat;
 use serde::{Deserialize, Serialize};
 
 use crate::{