Chemical file format
A chemical file format is a type of data file which is used specifically for depicting molecular data. One of the most widely used is the chemical table file format, which is similar to Structure Data Format (SDF) files. They are text files that represent multiple chemical structure records and associated data fields. 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 and cartesian coordinates. The Protein Data Bank Format is commonly used for proteins but is also used for other types of molecules. There are many other types which are detailed below. Various software systems are available to convert from one format to another.
Distinguishing formats
Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format is indicated in three ways:file extension. This is widely used, but fragile as common suffixes such as.mol and .dat are used by many systems, including non-chemical ones.self-describing files where the format information is included in the file. Examples are CIF and CML.chemical/MIME type added by a chemically aware server.Chemical Markup Language
Chemical Markup Language is an open standard for representing molecular and other chemical data. The open source project includes XML Schema, source code for parsing and working with CML data, and an active community. The articles Tools for Working with Chemical Markup Language and XML for Chemistry and Biosciences discusses CML in more detail. CML data files are accepted by many tools, including JChemPaint, Jmol, XDrawChem and MarvinView.Protein Data Bank Format
The Protein Data Bank Format is an obsolete format for protein structures developed in 1972. It is a fixed-width format and thus limited to a maximum number of atoms, residues, and chains; this resulted in splitting very large structures such as ribosomes into multiple files. For example, the E. coli 70S was represented as 4 PDB files in 2009:,, 3I1O, and 3I1P. In 2014, they were consolidated into a single file, .In 2014, the PDB format was officially replaced with mmCIF, and newer PDB structures may not have PDB files available.
Some PDB files contained an optional section describing atom connectivity as well as position. Because these files were sometimes used to describe macromolecular assemblies or molecules represented in explicit solvent, they could grow very large and were often compressed. Some tools, such as Jmol and KiNG, could read PDB files in gzipped format. The wwPDB maintained the specifications of the PDB file format and its XML alternative, PDBML. There was a fairly major change in PDB format specification in August 2007, and a remediation of many file problems in the existing database. The typical file extension for a PDB file was
.pdb, although some older files used .ent or .brk. Some molecular modeling tools wrote nonstandard PDB-style files that adapted the basic format to their own needs.GROMACS format
The GROMACS file format family was created for use with the molecular simulation software package GROMACS. It closely resembles the PDB format but was designed for storing output from molecular dynamics simulations, so it allows for additional numerical precision and optionally retains information about particle velocity as well as position at a given point in the simulation trajectory. It does not allow for the storage of connectivity information, which in GROMACS is obtained from separate molecule and system topology files. The typical file extension for a GROMACS file is.gro.CHARMM format
The CHARMM molecular dynamics package can read and write a number of standard chemical and biochemical file formats; however, the CARD and PSF are largely unique to CHARMM. The CARD format is fixed-column-width, resembles the PDB format, and is used exclusively for storing atomic coordinates. The PSF file contains atomic connectivity information and is required before beginning a simulation. The typical file extensions used are.crd and .psf respectively.GSD format
The General Simulation Data file format created for efficient reading / writing of generic particle simulations, primarily - but not restricted to - those from HOOMD-blue. The package also contains a python module that reads and writes HOOMD schema gsd files with an easy to use syntax.Ghemical file format
The Ghemical software can use OpenBabel to import and export a number of file formats. However, by default, it uses the GPR format. This file is composed of several parts, separated by a tag.The proposed MIME type for this format is application/x-ghemical.
SYBYL Line Notation
SYBYL Line Notation 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.SMILES
The simplified molecular input line entry system, or 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 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 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 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. 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.
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.For example, to convert the file epinephrine.sdf in SDF to CML use the command
The resulting file is epinephrine.cml.
is a free and open-source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane-wave density-functional-theory software programs. It also supports a flexible framework for generating input files for various software packages. For a complete list of supported formats, please go to https://iodata.readthedocs.io/en/latest/formats.html.
A number of tools intended for viewing and editing molecular structures are able to read in files in a number of formats and write them out in other formats. The tools JChemPaint, XDrawChem, Chime, Jmol, Mol2mol and Discovery Studio fit into this category.
The Chemical MIME Project
"Chemical MIME" is a de facto approach for adding MIME types to chemical streams.
This project started in January 1994, and was first announced during the Chemistry workshop at the First WWW International Conference, held at CERN in May 1994.... The first version of an Internet draft was published during May–October 1994, and the second revised version during April–September 1995. A paper presented to the CPEP at the IUPAC meeting in August 1996 is available for discussion.
In 1998 the work was formally published in the JCIM.