What is a .SDF file?
An SDF is a stack of Molfiles: one molecule after another, each followed by its own tagged data fields - identifiers, activities, whatever the database wanted to carry - and terminated by a line of four dollar signs. The same extension is also SQL Server Compact’s database file and Autodesk’s spatial data file.
- Did you know
- It is the format chemical databases hand you a search result in, which is why a single SDF can hold a million compounds and still be read one at a time.
- An SDF wraps the MDL Molfile, appending tagged data items after each molecule.
- Records inside an SDF are separated by a line of four dollar signs, $$$$.
- What Analyser reads
- Open chemical structures and see the molecule: MOL and SDF connection tables, MOL2, plain XYZ coordinates, Protein Data Bank entries and mmCIF/CIF crystallographic files, all drawn in an interactive 3D viewer you can rotate, zoom and restyle. Small molecules come up as ball-and-stick with the standard element colours; proteins and nucleic acids get a cartoon instead, drawing each chain as a ribbon along its backbone with helices and sheets picked out and any bound ligand still shown as sticks - which is the only way a structure of tens of thousands of atoms is readable at all. Alongside the picture, the composition is worked out from the atoms actually present rather than from any label in the file: molecular formula in Hill notation, molecular weight, net charge, element counts, and for a macromolecule the chain, residue and secondary-structure counts plus every non-polymer group - bound drugs, cofactors, metal ions and crystallisation buffer. PDB headers give up the entry ID, title, experimental method and resolution; an SDF is stepped through record by record with each molecule's tagged data fields read out.
- Depth of analysis
- .SDF is an identification-grade format: Analyser recognises it from its bytes and decodes the header metadata it carries, rather than opening it in a full viewer. Formats that do get a full viewer are marked "Full" on the formats page.
- Open a .SDF file
- Drag a .SDF file onto the Analyser home page (or tap to pick one). It is identified entirely in your browser - nothing is uploaded, there is no account, and it works offline once installed.