File Extension Search

.cml File Extension

Developer: N/A
File type: Chemical Markup Language File
You're here because you have a file that has a file extension ending in .cml. Files with the file extension .cml can only be launched by certain applications. It's possible that .cml files are data files rather than documents or media, which means they're not meant to be viewed at all.

what is a .cml file?

Chemical Markup Language files are affixed with the .cml extension and are integrated with XML-based encoding specifications. These specifications are implemented standards for storing and sharing content integrated with details referring to chemical elements, compounds, analytical work done to experiments using certain chemicals and scientific or mathematical equations used in chemistry. For instance, the data of these CML files may include descriptions of certain molecular structures entered by the authors of those CML files. Files in the CML format are also integrated with DTD specifications stored in associated XSD files. The Avogadro application is a chemical data research and analysis software with different versions for Microsoft Windows-based systems, Mac platforms and Linux, and this program can be used to create, open and edit the content of these CML files. There are other applications that provide support for the CML file format, such as the Open Babel software, which has versions available for these three operating systems.

how to open a .cml file?

Launch a .cml file, or any other file on your PC, by double-clicking it. If your file associations are set up correctly, the application that's meant to open your .cml file will open it. It's possible you may need to download or purchase the correct application. It's also possible that you have the correct application on your PC, but .cml files aren't yet associated with it. In this case, when you try to open a .cml file, you can tell Windows which application is the correct one for that file. From then on, opening a  .cml file will open the correct application. Click here to fix .cml file association errors

applications that open a .cml file

Avogadro for Microsoft Windows

Avogadro for Microsoft Windows

Avogadro is a molecular editor designed for use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It works for different platforms for 3D molecular manipulation and can be easily extended and developed with the use of plugins. In the recent version, developers claimed that bugs have been fixed like the compilation for Windows. It resolved the issue on the new versions of the SIP, can now automatically import Avogadro in the Python terminal, adjustments were made on the new version of Open Babel, issosurface may now align to molecules in all cases, the bugs in the bounds for cubes was already fixed. There is additional picking support in wireframe that enables editing of atoms using this mode, crashes were fixed in drawing with adjust hydrogen on, added the missing entries in the GAMES input dialog, the NWChem input generator was fixed and updates are added when atoms are added, removed or updated. They also fixed the autobonding in animations when rendering in POV-Ray for video, removed old CMaked codes that are no longer needed, and made linguist only optional for Avogadro builds.


The Avogadro software is used in computational chemistry, molecular modeling, bioinformatics, material science and other sciences related to it. With its rendering and plugin architecture, it functions as a molecular editor and provides visualizer designs. This software is free and an open source which is available under GNU GPL. It has international translations, pages can be translated to French, German, Italian, Spanish, Chinese and Russian, the Avogadro team is still working on incorporating more language translations. This program is built for students and advanced researchers and supports computation and multi-threaded rendering. Developers are also welcome, with the program's plugin architecture that includes, tools for rendering and interactivity, commands and Python scripts. Avogadro features an Open Babel, it is a chemical toolbox with all the languages of chemical data. It is a open, collaborative language which means that anyone is welcome to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials and biochemistry. the Open Babel has 110 chemical File formats and has been downloaded for more than 164,000 times.
Bioclipse for Microsoft Windows

Bioclipse for Microsoft Windows

Bioclipse is a program suitable for bio-scientists and researchers. It provides an excellent platform for graphical representation of molecular structures. It functions both for chemoinformatics and bioinformatics with plug-ins that can be added as an additional function for several areas. The latest Java application is needed to run the program, or at least Java 1.6. When accessed, the Bioclipse workbench view is presented, in which molecules are displayed in 3D format. In the editor window, users can edit, copy, paste, save their work, and in the perspective window, a collection of views and editors are presented. Bioclipse also features Pharmacology and Drug Discovery. Quantitative Structure-Activity Relationships (QSAR), is a method that relates responses between multiple chemical structures and a target, it measures the toxicity of drugs and predict if a compound is toxic. Bioclipse contains many features the can work with QSAR and other similar fields, a multi-page is accessible with tabs for selecting chemical structures, choosing mathematical descriptors and other metadata used for performing analysis. Windows users reported that prior to installation, Norton has warned that Bioclipse is unsafe. It is a known problem with Norton, but it can be skipped bu adding an exception. Based on tests done by its developers, Bioclipse is virus-free.
Bioclipse for Mac

Bioclipse for Mac

Based on the Eclipse Rich Client Platform (RCP), Bioclipse is a plug-in architecture and an open source workbench for life sciences. Its interface is based from Eclipse, and has a cross-platform deployment, software updates. help system, preferences and others. Bioclipse uses Cheminformatics which has a framework for management and analyzation of chemical compounds, and it based on the Chemistry Development Kit or (CDK). The software supports 2D editing, processes in tables, collections of molecules in large quantities and calculates several kinds of properties and many other functions of cheminformatics. Bioclipse has an integrated Jmol application that provides interactive 3D visualizations and it functions as an editor in the program. Mainly functioning for analysis and management of biological sequences like DNA, RNA and protein, Bioinformatics is also featured in Bioclipse. This feature heavily relies in BioJava, a graphical editor for sequence alignments and the core of the functions of bioinformatics. Several Web service clients are available for downloading biological sequences and annotations, and bioinformatics analysis. Bioclipse runs within Eclipse on bothe Mac OS X 10.5 (Leopard) and Mac OS X 10.6 (Snowleopard).
Open Babel for Microsoft Windows

Open Babel for Microsoft Windows

The Open Babel for Windows software was also developed by the OpenBabel development team specifically created for and on a Windows operating system. The general OpenBabel software is usually a MAC OS application but it can run on Windows already as a binary installer. While binary files are files that are usually not installed as they are encoded along within a system, OpenBabel for Windows function as a binary installer and it features two programs in one package. First, it comes with the Babel program used to convert file formats and filter them using SMART strings, etc. This program is most especially used for chemistry and molecular data file conversion. Second, OpenBabel for Windows features an OpenBabel GUI program that contributes to the user-friendly functionality of Babel. This feature allows the display of the input and output file content as well as the checkbox presentation of options, and a lot more.

a word of warning

Be careful not to rename the extension on .cml files, or any other files. This will not change the file type. Only special conversion software can change a file from one file type to another.

what is a file extension?

A file extension is the set of three or four characters at the end of a filename; in this case, .cml. File extensions tell you what type of file it is, and tell Windows what programs can open it. Windows often associates a default program to each file extension, so that when you double-click the file, the program launches automatically. When that program is no longer on your PC, you can sometimes get an error when you try to open the associated file.

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