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.
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 $HOME\chemaxon\marvin emplates\functionalgroups.cxsmi (Windows) or$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.cxsmifile 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 amineshould be referred assecondary_aminein Chemical Terms expressions).{primary} Note: from Marvin 5.4
mols.smartsconfiguration file is not used by Chemical Terms. It is replaced byfunctionalgroups.cxsmifile.