molfile

Molfile is a widely used ASCII format for representing chemical structures, developed by MDL (Molecular Design Limited). It stores molecule-level information and structural data such as atom coordinates, element types, bond connectivity and orders, stereochemistry, isotopes, charges, and certain query information. It is commonly used as a portable representation and as a component of Structure Data Files (SDF), which can store multiple mol blocks along with property data.

A Molfile typically begins with a title line, followed by a program line and a comment line, and then a counts line that reports the number of atoms and bonds (and optional additional fields). The atom block contains one line per atom, specifying the x, y, z coordinates (in angstroms), the atomic symbol, and optional fields for isotope, mass difference, charge, and other properties. The bond block contains one line per bond, indicating the indices of the two bonded atoms and the bond type (single, double, triple, or aromatic) and, in some versions, stereochemical information.

Molfile has evolved into several versions. Molfile V2000 is the long-standing standard that covers basic connectivity and geometry. Molfile V3000 is a more flexible version that can represent larger molecules and expanded atom and bond properties, including more detailed stereochemical and query information.

Usage: The format is supported by many cheminformatics toolkits and software packages, including RDKit, Open Babel, the Chemistry Development Kit (CDK), and ChemDraw. It is commonly used as the backbone of Structure Data Files and is widely supported for data exchange between systems. Limitations include the fixed-column layout of older versions and limited support for some modern features, which V3000 addresses.