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File formats

BALL INI files

BiochemicalAlgorithms.read_ball_ini_file — Function
read_ball_ini_file(fname::AbstractString, ::Type{T} = Float32) -> BALLIniFile

Read a file in BALL's old Ini file format and return it as a BALLIniFile.

Supported keyword arguments

  • cleanup_keys::Bool = true simplifies colon-separated key names (e.g., ver:version becomes version, key:I becomes I, etc.)
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HyperChem HIN files

BiochemicalAlgorithms.load_hinfile — Function
load_hinfile(io::IO, ::Type{T} = Float32) -> System{T}
load_hinfile(filename::AbstractString, ::Type{T} = Float32) -> System{T}

Read a HyperChem HIN file.

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BiochemicalAlgorithms.write_hinfile — Function
write_hinfile(io::IO, ac::AtomContainer)
write_hinfile(filename::AbstractString, ac::AtomContainer)

Save an atom container as HyperChem HIN file.

Note

HIN files define molecules as connected components in the molecular graph. If the AtomContainer is missing bonds, e.g., after reading a PDB file and not postprocessing it correctly, the HIN file may contain a surprisingly large number of molecules.

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PDB files

BiochemicalAlgorithms.download_pdb — Function
download_pdb(pdb_id::AbstractString; dir = tempdir(), overwrite = false) -> String

Download a PDB structure file from RCSB (https://files.rcsb.org/download/<ID>.pdb) and return the local file path.

pdb_id is the four-character PDB identifier (case-insensitive; normalised to upper case for the URL). The file is written to joinpath(dir, "<ID>.pdb"). If a file already exists at the target path, nothing is re-downloaded unless overwrite = true.

Example

julia> path = download_pdb("2ptc")
"/tmp/2PTC.pdb"

julia> sys = load_pdb(path)
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BiochemicalAlgorithms.load_pdb — Function
load_pdb(io::IO, ::Type{T} = Float32) -> System{T}
load_pdb(filename::AbstractString, ::Type{T} = Float32) -> System{T}

Read a PDB file.

Note

Models are stored as frames, using the model number as frame_id.

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BiochemicalAlgorithms.write_pdb — Function
write_pdb(io::IO, ac::AbstractAtomContainer)
write_pdb(filename::AbstractString, ac::AbstractAtomContainer)

Save an atom container as PDB file.

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PDBx/mmCIF files

BiochemicalAlgorithms.load_mmcif — Function
load_mmcif(io::IO, ::Type{T} = Float32) -> System{T}
load_mmcif(filename::AbstractString, ::Type{T} = Float32) -> System{T}

Read a PDBx/mmCIF file.

Note

Models are stored as frames, using the model number as frame_id.

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BiochemicalAlgorithms.write_mmcif — Function
write_mmcif(io::IO, ac::AbstractAtomContainer)
write_mmcif(filename::AbstractString, ac::AbstractAtomContainer)

Save an atom container as PDBx/mmCIF file.

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PubChem JSON

BiochemicalAlgorithms.load_pubchem_json — Function
load_pubchem_json(io::IO, ::Type{T} = Float32) -> System{T}
load_pubchem_json(filename::AbstractString, ::Type{T} = Float32) -> System{T}

Read a PubChem JSON file.

Note

Conformers are stored as frames.

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Structures data files (SDF, SDFile)

BiochemicalAlgorithms.write_sdfile — Function
write_sdfile(io::IO, ac::AbstractAtomContainer)
write_sdfile(filename::AbstractString, ac::AbstractAtomContainer)

Save a 2D projection of an atom container as SDFile.

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