Introduction

SEA is a language for specifying selections, expressions and actions (SEA). The current implementation is aimed toward molecular interactions and so the selection clause typically has two sections, a left and right part which are, by convention, used to select the ligand and receptor targets respectively.

A complete SEA rule has the following format:

 {lselection},{rselection}; {expression} {action;action;...}; 

or

 define name "smarts" 

or

 begin {action;action;...}; 

A rules file contains one or more such rules. The define statements must occur before any rules which use the defined name (see below for further information about define statements).

The rules are executed from top to bottom. All the matches for each rule are processed before the next rule in the file is executed.

The selection clauses specify sets of atoms which are then used in the expression and action clauses. The expression clause can compute various geometric properties of the selected atoms and make logical and arithmetic tests. The truth value of the expression clause is tested at completion and the action clause is optionally executed if the expression clause is true (non zero). The actions can print values and/or record them for inclusion in file output.