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Welcome to BiochemicalAlgorithms.jl

In this tutorial, you will learn about the basic concepts of the BiochemicalAlgorithms.jl library, a complete rewrite of the C++ framework BALL in Julia.

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

using Pkg
Pkg.add("BiochemicalAlgorithms")

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(ball_data_path("../test/data/2ptc.pdb"))
System{Float32}: COMPLEX (PROTEINASE/INHIBITOR)
  2241 atoms
     9 bonds
     1 molecules
     4 chains
    12 secondary structures
   439 fragments

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

println("The system $(s.name) contains $(natoms(s)) atoms.")
The system COMPLEX (PROTEINASE/INHIBITOR) contains 2241 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)
┌ Warning: reconstruct_fragments!(): could not find reference fragment for  CA:462
└ @ BiochemicalAlgorithms ~/local/BiochemicalAlgorithms.jl/src/preprocessing/reconstruct_fragments.jl:177
[ Info: reconstruct_fragments!(): added 2346 atoms.
┌ Warning: build_bonds!(): could not find reference fragment for  CA.
└ @ BiochemicalAlgorithms ~/local/BiochemicalAlgorithms.jl/src/preprocessing/build_bonds.jl:14
[ Info: build_bonds!(): built 4471 bonds

How to go on?

For an in depth view on the components forming the core of BiochemicalAlgorithms, we highly recommend taking a look at the next section core_components.md which forms a basis for the remaining tutorials dealing with different topics: