File formats
BiochemicalAlgorithms.load_hinfileBiochemicalAlgorithms.load_mmcifBiochemicalAlgorithms.load_pdbBiochemicalAlgorithms.load_pubchem_jsonBiochemicalAlgorithms.load_sdfileBiochemicalAlgorithms.read_ball_ini_fileBiochemicalAlgorithms.write_hinfileBiochemicalAlgorithms.write_mmcifBiochemicalAlgorithms.write_pdbBiochemicalAlgorithms.write_sdfile
BALL INI files
BiochemicalAlgorithms.read_ball_ini_file — Functionread_ball_ini_file(fname::AbstractString, ::Type{T} = Float32) -> BALLIniFileRead a file in BALL's old Ini file format and return it as a BALLIniFile.
Supported keyword arguments
cleanup_keys::Bool = truesimplifies colon-separated key names (e.g.,ver:versionbecomesversion,key:IbecomesI, etc.)
HyperChem HIN files
BiochemicalAlgorithms.load_hinfile — Functionload_hinfile(
fname::AbstractString,
::Type{T} = Float32
) -> System{T}Read a HyperChem HIN file.
BiochemicalAlgorithms.write_hinfile — Functionwrite_hinfile(
fname::AbstractString,
ac::AtomContainer
)Save an atom container as HyperChem HIN file.
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.
PDB files
BiochemicalAlgorithms.load_pdb — Functionload_pdb(fname::AbstractString, ::Type{T} = Float32) -> System{T}Read a PDB file.
Models are stored as frames, using the model number as frame_id.
BiochemicalAlgorithms.write_pdb — Functionwrite_pdb(fname::AbstractString, ac::AbstractAtomContainer)Save an atom container as PDB file.
PDBx/mmCIF files
BiochemicalAlgorithms.load_mmcif — Functionload_mmcif(fname::AbstractString, ::Type{T} = Float32) -> System{T}Read a PDBx/mmCIF file.
Models are stored as frames, using the model number as frame_id.
BiochemicalAlgorithms.write_mmcif — Functionwrite_mmcif(fname::AbstractString, ac::AbstractAtomContainer)Save an atom container as PDBx/mmCIF file.
PubChem JSON
BiochemicalAlgorithms.load_pubchem_json — Functionload_pubchem_json(fname::AbstractString, ::Type{T} = Float32) -> System{T}Read a PubChem JSON file.
Conformers are stored as frames.
Structures data files (SDF, SDFile)
BiochemicalAlgorithms.load_sdfile — Functionload_sdfile(fname::AbstractString, ::Type{T} = Float32) -> System{T}Read an SDFile.
BiochemicalAlgorithms.write_sdfile — Functionwrite_sdfile(fname::AbstractString, ac::AbstractAtomContainer)Save a 2D projection of an atom container as SDFile.