forward index back metalogo

SEA language

The SEA (Selection, Expression, Action) language is a pattern based language for writing rules about ligand-protein complexes. SEA combines SMARTS with biopolymer features like chain names and residue numbers in the selection part. There is one selection for the ligand and one for the protein. The expression part includes logical combinations of molecular properties and protein-ligand geometry based on the selections. If the expression part evaluates to true, the action part is executed and can be used to mark interactions for further processing, print information, set flags and variables, etc.

# Hbond definitions derived from original smarts from J Bradshaw
define HDon "[$([!#6;+0])]";
define HAcc "[$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv6,Sv4,Sv6]);!$(N[C,S]=O)]";
{smarts("[$HDon]~*")},{chain("A") residue(127) smarts("[$HAcc]~*")}

SEA based rules are used to assign protein-ligand interactions in the program which lays out PLAID diagrams. SEA rules are also used to specify desirable protein-ligand interactions in the Magnet program to be described by Hanneke Jansen in the next talk.