Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation.
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.
[1] 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.
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.
There was a fairly major change in PDB format specification (to version 3.0) in August 2007, and a remediation of many file problems in the existing database.
Some molecular modeling tools wrote nonstandard PDB-style files that adapted the basic format to their own needs.
It does not allow for the storage of connectivity information, which in GROMACS is obtained from separate molecule and system topology files.
The package also contains a python module that reads and writes HOOMD schema gsd files with an easy to use syntax.
This file is composed of several parts, separated by a tag (!Header, !Info, !Atoms, !Bonds, !Coord, !PartialCharges and !End).
They are text files that adhere to a strict format for representing multiple chemical structure records and associated data fields.
IOData 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.
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.
A paper presented to the CPEP (Committee on Printed and Electronic Publications) at the IUPAC meeting in August 1996 is available for discussion.
[9] For Linux/Unix, configuration files are available as a "chemical-mime-data" package in .deb, RPM and tar.gz formats to register chemical MIME types on a web server.
[10][11] Programs can then register as viewer, editor or processor for these formats so that full support for chemical MIME types is available.