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).
You can also define your favourite query SMARTS in marvin/config/marvin/templates/functionalgroups.cxsmi file and in $HOME\chemaxon\marvin\templates\functionalgroups.cxsmi (Windows) or$HOME/.chemaxon/marvin/templates/functionalgroups.cxsmi (UNIX / Linux) file where marvin is the Marvin installation directory, $HOME is your user home directory.
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).
Note: from Marvin 5.4 mols.smarts configuration file is not used by Chemical Terms. It is replaced by functionalgroups.cxsmi file.