Notation (SLN) is a chemical line notation. Based on SMILES, it incorporates a complete syntax for specifying relative stereochemistry. SLN has a rich query syntax that allows for the specification of Markush structure queries. The syntax also supports the specification of combinatorial libraries of ChemDraw. Example SLNs SMILES The Simplified Molecular Input Line Entry System (SMILES) is a line notation for molecules. SMILES strings include connectivity but do not include 2D or 3D coordinates. Hydrogen atoms are not represented. Other atoms are represented by their element symbols B, C, N, O, F, P, S, Cl, Br, and I. The symbol "=" represents double bonds and "#" represents triple bonds. Branching is indicated by (). Rings are indicated by pairs of digits. Some examples are XYZ The XYZ file format is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates. MDL number The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number. Other common formats One of the most widely used industry standards are chemical table file formats, like the Structure Data Format (SDF) files. They are text files that adhere to a strict format for representing multiple chemical structure records and associated data fields. The format was originally developed and published by Molecular Design Limited (MDL). MOL is another file format from MDL. It is documented in Chapter 4 of CTfile Formats. PubChem also has XML and ASN1 file formats, which are export options from the PubChem online database. They are both text based (ASN1 is most often a binary format). There are a large number of other formats listed in the table below Converting between formats OpenBabel and JOELib are freely available open source tools specifically designed for converting between file formats. Their chemical expert systems support a large atom type conversion tables. obabel -i input_format input_file -o output_format output_file For example, to convert the file epinephrine.sdf in SDF to CML use the command obabel -i sdf epinephrine.sdf -o cml epinephrine.cml The resulting file is epinephrine.cml. IOData is a free and open-source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry,