cache

A Cache is used to keep in memory some sub-structures that have already been generated to reduce redundant processing. It is generally attached to a backtrack fragment generator. It is possible to reduce the number of cache-saved structures by eliminating any new structure that is too similar to the previously generated ones. This allows one to avoid generating plenty of equivalent models and greatly facilitates results analysis. The selection algorithm performs Root Mean Square (RMS) alignment of any new structure with all cache-saved models and for each comparison, it returns the RMS deviation. Any value smaller than a user-set RMSD bound will cause the new model to be rejected. The basic idea behind this algorithm is to minimize the differences between the coordinates of corresponding atoms by doing a set of translations and rotations of the ``fit'' set.

Typical values of the RMSD bound are in the range [ 0.0, 5.0 ].

Extensive use of cache objects while modeling large molecules causes the memory needed by the program to grow very rapidly. It is advisable to limit excessive cache growth by an appropriate RMSD bound. This will avoid unecessary virtual memory swapping (or even overflow) and will considerably decrease the execution time.

<name1> = cache (<name><filter function>)

	<filter function>	=	rmsd ( <bound> [align] [ <atomset>] [no_hydrogen])
	<atomset>	=	all | base_only | backbone_only | pse_only

bound

the rmsd lower bound;

align

If this options is chosen, any new structure to be added to the cache will be first aligned to the most similar structure already in the cache;

atomset

One can choose the atoms on which the RMSD comparison algorithm will be applied. The following mutually exclusive options are available: all, base_only, backbone_only and pse_only (the PSE atoms are artificial atoms arbitrarily placed on each base for computational purposes). One can also add the useful no_hydrogen option.

Example:

 hairpin_cache = cache
                 ( 
                   hairpin
                   rmsd (1.0 base_only no_hydrogen)
                 )