Predefined Functional Groups and Named Molecule Groups

Referring molecules by names is sometimes easier than using explicit SMARTS strings or molecule file paths. For example, you may want to write nitro or carboxyl as query in a match function.

The built-in functional groups file

Frequently used queries are pre-defined in the built-in functional groups file (chemaxon/marvin/templates/functionalgroups.cxsmi within MarvinBeans-templates.jar).

User-defined groups

You can also define your favourite query SMARTS in marvin/config/marvin/templates/functionalgroups.cxsmi file and in $HOME\chemaxon\marvin emplates\functionalgroups.cxsmi (Windows) or$HOME/.chemaxon/marvin/templates/functionalgroups.cxsmi (UNIX / Linux) file where marvin is the Marvin installation directory, $HOME is your user home directory.

{info} However, there are some limitations when choosing the molecule names. Molecule names should be composed of letter, digit characters, and the '' character. This means that molecule names cannot contain special characters, such as '=', '-', etc. with the exception of ''. Molecule name definitions in functionalgroups.cxsmi file can contain whitespace characters (space, tab), but when names are referenced from a Chemical Terms expression the whitespace characters should be replaced with a single '_' character (e.g. secondary amine should be referred as secondary_amine in Chemical Terms expressions).

{primary} Note: from Marvin 5.4 mols.smarts configuration file is not used by Chemical Terms. It is replaced by functionalgroups.cxsmi file.