All on Input and Output

BiochemicalAlgorithms.jl supports the reading and writing of several common structural data formats.

Protein Data Bank Format (PDB)

The most common format ist the PDB. Have a look at Learning about PDB data if you want to refresh your knowledge about this format. For a deeper understanding you can also read PDB format specifications.

using BiochemicalAlgorithms

# Read PDB file from the BiochemicalAlgorithms.jl repository
pdb_sys = load_pdb(ball_data_path("../test/data/AlaAla.pdb"))

for atom in atoms(pdb_sys)
    if atom.element == Elements.S
        print(atom.number)
    end
end

fdb = FragmentDB()

normalize_names!(pdb_sys,fdb)
reconstruct_fragments!(pdb_sys, fdb)
build_bonds!(pdb_sys, fdb)
write_pdb("Ala_out.pdb", pdb_sys)

PubChem

In addition to PDB, the pubchem data base plays an important role as a source of structural data. Pubchem allows to retrieve data in JSON which is read by BiochemicalAlgorithms.jl as shown below:

pubchem_sys = load_pubchem_json(ball_data_path("../test/data/aspirin_pug.json"))

fdb = FragmentDB()
normalize_names!(pdb_sys,fdb)
reconstruct_fragments!(pdb_sys, fdb)
build_bonds!(pdb_sys, fdb)

for atom in atoms(pdb_sys)
    if atom.element == Elements.S
        println(atom.number)
    end
end

SD file

sd_sys = load_sdfile(ball_data_path("../test/data/rings_test.sdf"))

fdb = FragmentDB()
normalize_names!(sd_sys,fdb)
reconstruct_fragments!(sd_sys, fdb)
build_bonds!(sd_sys, fdb)

for atom in atoms(sd_sys)
    if atom.element == Elements.S
        println(atom.number)
    end
end

write_sdfile(ball_data_path("../test/data/rings_test_out.sdf"), sd_sys)