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Chemistry & Materials Data Types & File Formats
Chemistry and materials science use a wide range of data formats — from molecular structure representations and spectroscopic data to crystallographic files and simulation outputs. This page provides an overview of the most important formats you will encounter.
Molecular Structure Representations
SMILES (Simplified Molecular-Input Line-Entry System)
A line notation for encoding molecular structures as ASCII strings. Compact and widely supported by cheminformatics tools.
- Example:
c1ccccc1(benzene),CC(=O)O(acetic acid) - Use: Database queries, molecular property prediction, ML model input
- Tools: RDKit, Open Babel, CDK
- Spec: OpenSMILES
InChI (International Chemical Identifier)
A non-proprietary, textual identifier for chemical substances developed by IUPAC. Designed for unique identification rather than human readability.
- Example:
InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H - Use: Cross-database linking, deduplication, unique substance identification
- Spec: IUPAC InChI
MOL / SDF (.mol, .sdf)
MDL Molfile and Structure-Data File — widely used formats for 2D and 3D molecular structures. SDF extends MOL to store multiple molecules with associated data fields.
- Use: Chemical databases, structure exchange, property storage
- Tools: RDKit, Open Babel, Marvin, Avogadro
- Spec: CTfile Formats (Dassault)
PDB (.pdb)
Protein Data Bank format — stores 3D coordinates of atoms in macromolecules. Also used for small molecules in some workflows.
- Use: Protein structures, molecular docking, visualization
- Tools: PyMOL, VMD, Chimera, Biopython
- Spec: wwPDB Format Guide
XYZ (.xyz)
A minimal plain-text format listing atom types and Cartesian coordinates. Simple and widely supported, but carries no bonding or metadata information.
- Use: Quick structure exchange, QM calculation input/output
- Tools: Avogadro, ASE (Python), Jmol
CIF (Crystallographic Information File, .cif)
The standard format for crystallographic data, including unit cell parameters, symmetry, and atomic coordinates.
- Use: Crystal structures from X-ray or neutron diffraction
- Tools: Mercury (CCDC), VESTA, Olex2, pymatgen
- Spec: IUCr CIF
Spectroscopic Data
JCAMP-DX (.jdx, .dx)
Joint Committee on Atomic and Molecular Physical Data — Data Exchange format. A vendor-neutral text format for spectroscopic data.
- Use: IR, Raman, UV-Vis, NMR, mass spectra
- Tools: Various spectroscopy software, jcamp (Python)
- Spec: IUPAC JCAMP-DX
mzML (.mzML)
An open XML-based format for mass spectrometry data, replacing proprietary vendor formats.
- Use: LC-MS, GC-MS, metabolomics, proteomics
- Tools: OpenMS, MZmine, ProteoWizard
- Spec: HUPO-PSI mzML
NMReDATA (.nmredata.sdf)
An extension of the SDF format to include NMR spectral assignments linked to molecular structures.
- Use: NMR data sharing with structure-spectrum assignments
- Spec: NMReDATA Initiative
Bruker / Varian / JEOL (vendor-specific)
Proprietary binary formats from instrument manufacturers. Typically require vendor software or conversion tools.
- Use: Raw instrument data
- Tools: MestReNova, TopSpin, nmrglue (Python)
Simulation and Computation Data
Gaussian Output (.log, .chk, .fchk)
Output files from Gaussian quantum chemistry calculations, containing energies, geometries, molecular orbitals, and vibrational frequencies.
- Use: DFT and ab initio calculations
- Tools: GaussView, cclib (Python), Avogadro
VASP Files (POSCAR, CONTCAR, OUTCAR, vasprun.xml)
A set of files used by the Vienna Ab initio Simulation Package for solid-state DFT calculations.
- Use: Periodic DFT calculations, materials properties
- Tools: pymatgen (Python), ASE, VESTA
Trajectory Files (.xtc, .trr, .dcd, .nc)
Binary formats storing atomic positions (and optionally velocities/forces) at each time step of a molecular dynamics simulation.
- Use: Molecular dynamics analysis
- Tools: MDAnalysis (Python), GROMACS tools, VMD
NOMAD Archive Format
A standardized format used by the NOMAD repository for computational materials science data.
- Use: Archiving and sharing simulation data
- Spec: NOMAD
Reaction and Process Data
RXN / RD Files (.rxn, .rdf)
Extensions of the MOL/SDF format family for storing chemical reactions, including reactants, products, and agents.
- Use: Reaction databases, retrosynthesis
- Tools: RDKit, MarvinSketch
AnIML (Analytical Information Markup Language, .animl)
An XML-based format for analytical chemistry data, supporting multiple technique types.
- Use: Multi-technique analytical data
- Spec: ASTM E1947
Format Selection Guide
| Use Case | Recommended Format |
|---|---|
| Molecular structures (2D/3D) | MOL/SDF or SMILES |
| Unique substance identification | InChI |
| Crystal structures | CIF |
| Protein/macromolecule structures | PDB / mmCIF |
| Spectroscopic data (vendor-neutral) | JCAMP-DX |
| Mass spectrometry | mzML |
| QM calculation results | Gaussian/ORCA output, VASP files |
| MD trajectories | XTC, TRR, or DCD |
| Archiving computational data | NOMAD Archive |