Chemical & Biomolecular Formats

The Wolfram Language can import—and often export—standard formats used in chemistry, molecular biology and bioinformatics, routinely handling a full range of molecular types, as well as genome-sized datasets.

Chemical Formats

"XYZ" — XYZ molecule geometry file (.xyz)

"MOL" — MDL MOL format (.mol)

"MOL2" — Tripos MOL2 format (.mol2)

"SDF" — MDL SDF format (.sdf)

"SMILES" — SMILES chemical format (.smi)

"HIN" — HyperChem molecular data format (.hin)

"CML" — Chemical Markup Language (.cml)

"CDX" — ChemDraw Exchange format (.cdx)

"CDXML" — ChemDraw Exchange XML format (.cdxml)

"Cube" — Gaussian Cube file (.cub)

"FCHK" — Formatted Checkpoint file (.fchk)

"GaussianLog" — Gaussian log file (.log)

"JCAMP-DX" — chemical spectroscopy format (.jdx, .dx, .jcm)

Bioinformatics Formats

"GenBank" — NCBI GenBank sequence format (.gb, .gbk)

"FASTA" — DNA, RNA, and amino acid sequence format (.fasta, .fa, .fsa, .mpfa)

"FASTQ" — DNA and RNA sequence format with base qualities (.fastq, .fq)

"NEXUS" — NEXUS phylogenetic data format (.nex, .ndk)

"AgilentMicroarray" — microarray data format (.txt)

"Affymetrix" — microarray data format (.cel, .cdf, .chp, .gin, .psi)

"SFF" — DNA sequence flowgram format (.sff)

Molecular Biology Formats

"PDB" — Protein Data Bank format (.pdb)

"MMCIF" — MMCIF 3D molecular model format (.cif)

"FCS" — flow cytometry data format (.fcs, .lmd)

Common Elements

"Molecule" — a symbolic representation of the molecule model

"StructureDiagram" — chemical structure diagram

"Graphics3D" — 3D molecular graphics

"VertexCoordinates" — 3D coordinates of atoms

"Sequence" — base-pair or amino acid sequence

"Elements" — all available elements