Chemical & Biomolecular Formats
Mathematica 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.
"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)
"GenBank" — NCBI GenBank sequence format (.gb, .gbk)
"FASTA" — bioinformatics sequence format (.fasta, .fa, .fsa, .mpfa)
"NEXUS" — NEXUS phylogenetic data format (.nex, .ndk)
Molecular Biology Formats
"PDB" — Protein Data Bank format (.pdb)
"MMCIF" — MMCIF 3D molecular model format (.cif)
— chemical structure diagram
— 3D molecular graphics
— 3D coordinates of atoms
— base-pair or amino acid sequence
— all available elements
