Supported formats

Datagrok supports over 50 file formats, including domain-specific like SDF, FASTA, and others. It also understands how data is structured or represented within those files (e.g., assay plates within an XLSX, SDTM conventions within a CSV, and notations like SMILES and HELM).

Structured and analytical data

Tabular and semi-structured data

Format	Type	Description	Required plugins
.csv	File format	Comma-separated values	--
.tsv	File format	Tab-separated values	--
.txt	File format	Plain text	--
.xlsx	File format	Microsoft Excel	--
.d42	File format	Datagrok [dashboadr]	--
.json	File format	JavaScript Object Notation	--
.xml	File format	Extensible Markup Language	--
.HTML	File format	HyperText Markup Language	--

Statistical and scientific formats

Format	Type	Description	Required plugins
.rds, .rda	File format	R serialized data	--
.mat	File format	MATLAB array and matrix data	--
.h5	File format	Hierarchical data in HDF5	--
.nc, .netcdf	File format	NetCDF scientific data file	--
.sas7bdat	File format	SAS database file	--
.kxl	File format	KeyCreator engineering data format	--

Columnar and database formats

Format	Type	Description	Required plugins
.parquet	File format	Columnar storage format	Arrow
.feather	File format	Arrow-based binary format	Arrow
.sqlite	File format	SQLite database	SQLite

Archives and packaging

Format	Type	Description	Required plugins
.zip	File format	ZIP archive (auto-extracted for supported types)	--
.tar	File format	Tape archive	--
.gz, .gzip	File format	Gzip-compressed files	--

Notebooks and documents

Notebooks and computations

Format	Type	Description	Required plugins
.ipynb	File format	Jupyter Notebook	Notebooks
.ivp	File format	Interactive differential equations	Diff Studio

Docs and reports

Format	Type	Description	Required plugins
.pdf	File format	Portable Document Format	File Editors
.docx	File format	Microsoft Word document	File Editors
.tex	File format	LaTeX Source File	File Editors

Domain-specific formats

Cheminformatics

Molecular structures

Format	Type	Description	Required plugins
.sdf, .sd	File format	Structure-data file	Chem
.mol	File format	MDL Molfile	Chem
.mol2	File format	SYBYL molecule representation	Chem
.smi	File format	SMILES file format	Chem
SMILES	Notation	Linear representation of molecular structure	Chem
SMARTS	Notation	Substructure search patterns	Chem
InChI, InChIKey	Notation	IUPAC identifiers	Chem
SMIRKS	Notation	Reaction transformation notation	Chem

Bioinformatics

Macromolecules and sequences

Format	Type	Description	Required plugins
.fasta	File format	FASTA format (fa, fna, ffn, faa, frn, fa, fst)	Bio
HELM	Notation	Biopolymer notation for peptides and oligonucleotides	Bio
BILN	Notation	Linear notation for complex biopolymers	Bio

Phylogenetic trees

Format	Type	Description	Required plugins
.nwk, .newick	File format	Newick format for phylogenetic trees	PhyloTree Viewer

3D structures and density maps

Macromolecular structure formats

Format	Type	Description	Required plugins
.pdb	File format	Protein structure (coordinates only)	Biostructure Viewer
.pdbqt	File format	PDB with charges and atom types	Biostructure Viewer
.cif	File format	Crystallographic data	Biostructure Viewer
.cifCore	File format	Core crystallographic data	Biostructure Viewer
.mcif	File format	Macromolecular crystallographic data	Biostructure Viewer
.mmcif	File format	Macromolecular crystallographic data	Biostructure Viewer
.mmtf	File format	Compressed macromolecular structure format	Biostructure Viewer
.ent	File format	Legacy PDB structure file	Biostructure Viewer

Electron density and volumetric data

Format	Type	Description	Required plugins
.ccp4	File format	Electron density map	Biostructure Viewer
.brix	File format	Electron density map	Biostructure Viewer
.mrc	File format	Electron density volume	Biostructure Viewer
.xplor	File format	Electron density map	Biostructure Viewer
.cub, .cube	File format	3D orbital or charge density grid	Biostructure Viewer
.dsn6	File format	Ribbons-format electron map	Biostructure Viewer

Simulation and topology formats

Format	Type	Description	Required plugins
.gro	File format	GROMACS structure file	Biostructure Viewer
.top	File format	GROMACS topology definition	Biostructure Viewer
.prmtop	File format	AMBER force field topology	Biostructure Viewer
.parm7	File format	AMBER topology file	Biostructure Viewer
.psf	File format	CHARMM or NAMD structure topology	Biostructure Viewer
.cns	File format	NMR structure description for CNS	Biostructure Viewer

3D mesh formats

Format	Type	Description	Required plugins
.obj	File format	3D mesh geometry	Biostructure Viewer
.ply	File format	Polygon mesh data	Biostructure Viewer
.xyz	File format	Atomic coordinates in XYZ format	Biostructure Viewer

Bioassays and experimental data

Format	Type	Description	Required plugins
.xlsx	Data structure	Assay plate data (auto-detected in file)	Curves

Spectroscopy and NMR

Format	Type	Description	Required plugins
.jdx	File format	Spectroscopy data (JCAMP-DX)	Chem Spectra Viewer
.dx	File format	NMR spectroscopy data (JCAMP-DX variant)	NMRium
.nmrium	File format	NMR experiment data for NMRIum viewer	NMRium

Biosignals

Format	Type	Description	Required plugins
.edf	File format	Multichannel biosignal recordings (e.g., EEG, EMG)	--

Clinical and regulatory data

Format	Type	Description	Required plugins
.csv	Data structure	SDTM-formatted datasets (auto-detected from folder structure)	Clinical Case

Geospatial formats

Format	Type	Description	Required plugins
.kml	File format	Geospatial annotation file (Google Earth)	GIS
.kmz	File format	Compressed geospatial annotation file	GIS
.geojson	File format	Geospatial data encoded in JSON	GIS
.topojson	File format	Compressed topological geospatial data	GIS

Images and diagrams

Format	Type	Description	Required plugins
.jpg, .jpeg	File format	Photo, scan
.png	File format	Screenshot, icon, UI graphic
.svg	File format	Logo, diagram, UI asset
.bmp	File format	Raw pixel data
.excalidraw	Drawing format	JSON-based vector drawings	Excalidraw