SetOption

From BioNetWiki

Contents 1 Name 2 Synopsis 3 Description 4 Examples

Name

setOption - Set global BioNetGen options

Synopsis

setOption( optionName, value)

Description

Sets options that affect the global behavior of methods that operate on objects in BNGModel. So far, only canonical labeling is controlled.

Valid optionNames are

SpeciesLabel - Determines the behavior of the function used in determining uniqueness of generated species. Allowed values are Auto (default), HNauty, and Quasi.

Auto works by generating a quasi-canonical label that includes all information about the Species except the bonds. Only the bond order of each Molecule or Component is used. Because this label is not canonical, if two species share a label, they are checked for isomorphism directly using a variant of the Ullman algorithm. This method is always correct, but may be very slow if the number of identical Molecules or Components in a complex is greater than 10.

HNauty uses a hierarchical version of the Nauty algorithm to generate a canonical label for every Species generated by application of the reaction rules. Isomorphism is checked using string comparison. This method is exact, but slower than Auto except when oligomerization occurs.

Quasi treats the quasi-canonical strings as canonical, introducing the possibility that two Species with different connectivity may be treated as identical. This can speed network generation in cases where the quasi-canonical strings are known to be exact, single chain of oligomers or bivalent ligand bivalent receptor. Equivalent to using generate_network(check_iso=>0), which is now deprecated.

Examples

These commands should be placed at the top of the BNGL file. To use HNauty instead of the default scheme, use the command

setOption(SpeciesLabel,HNauty);

at the top of the BNGL file.