Welcome to BiochemicalAlgorithms.jl

In this tutorial, you will learn about the basic concepts of the BiochemicalAlgorithms.jl-library (sometimes shortened to BALL.jl) – a complete rewrite of the C++-framework BALL in Julia.

To use BiochemicalAlgorithms.jl in your code, add it to your project

import Pkg
Pkg.add(url="https://github.com/hildebrandtlab/BiochemicalAlgorithms.jl")

and use it in your code:

using BiochemicalAlgorithms

Representing molecular systems

In BiochemicalAlgorithms.jl, all molecules are stored in so-called Systems. While a System can be created from scratch and filled programmatically, it is commonly created by reading a molecular file, such as a PDB-file:

s = load_pdb("data/5PTI.pdb")

System with 1087 atoms (5PTI.pdb)

You can then run methods on this system, e.g.

println("The system $(s.name) contains $(natoms(s)) atoms.")

The system 5PTI.pdb contains 1087 atoms.

Common preparation steps

The data stored in many molecular file formats is incomplete, or needs to be normalized in certain ways. PDB-files, for instance, often omit hydrogen atoms, and don’t usually store bonds that can be inferred otherwise. BiochemicalAlgorithms.jl offers a number of methods that perform preparation steps that are common to most molecular modelling applications, such as normalizing atom- and fragment names, computing bonds, adding missing atoms from a library of templates (such as amino acids), or saturating a molecule with hydrogen atoms. The template information used by these methods is stored in the so-called FragmentDB. A common series of operations to prepare a system for further processing is as follows:

fdb = FragmentDB()

normalize_names!(s, fdb)
reconstruct_fragments!(s, fdb)
build_bonds!(s, fdb)

[ Info: reconstruct_fragments!(): added 109 atoms.
[ Info: build_bonds!(): built 912 bonds