BioShell v.4

What is BioShell?

BioShell project, started in 2006, has been a command line toolkit for structural bioinformatics. Over time, it has also provided Coarse Grained simulations of proteins

WARNING

The fourth version of the BioShell package is still in the very early stage of development. Many important features are still missing and APIs can and will change. Documentation is sparse. If you are looking for a stable package, ypu might consider using the BioShell v.3 package.

Project structure

Curretnly the BioShell v.4 project has been divided into the following crates:

• bioshell-seq: works with biological sequences
• bioshell-pdb: a library to work on with crystallographic Protein DataBank files. It can parse PDB files and perform calculations on macromolecular structures.
• bioshell-cif: reads CIF files
• bioshell-statistics: statistical utilities
• bioshell-clustering: clustering methods, such as K-means and OPTICS
• bioshell-io: I/O utilities

Building

You need to install rust toolchain to compile the package. You can:

• compile the whole project, i.e. all its libraries (called crates) by executing the following command in the root folder of the project:

cargo build --release

This will compile also all the executables (currently the surpass_alfa application)

• compile all examples:

cargo build --examples --release

• compile a selected example:

cargo build --example polymer_perm --release

All the above commands compile the release (i.e. optimized) version. To obtain the debug build, just remove the --release flag.

Documentation has to be built separately for each crate. Enter the crate folder (e.g. bioshell-statistics) and execute the following:

RUSTDOCFLAGS="--html-in-header katex-header.html" cargo doc --no-deps --open

To run all tests (for all the crates of the project), run the:

cargo test

command in the root folder. Alternatively, you can test a single crate by running that command in a respective subfolder.