DOCK GA Development Goals

Tasks	src	Owner	Complete?
Fix bug that collapsed atom coordinates	everywhere? nowhere?	everyone	No
Added Delimeter header	conf_gen_ga	LEP	Yes
Fix xover only feature	conf_gen_ga	LEP	No
Put in error messages for mut_rate > 1	LEP	Yes
Manual user-defined mutation type	conf_gen_ga	LEP	No

To Do List

-xover- guided based on score 1. good v good 2. bad v good 3. bad v bad nonexhaustive xover (pick subset of xover based on probability) 2-3 point xover at once adaptive maintenance ensemble based on ensemble convergence bring in new parents based on convergence -Mutations- adaptive mutation rate pick location of mutation based on something pick mutation type based on behavior of esemble

  too large boost deletion
  too small more add
  change ...boost replace/sub

mutation type selection based on probability vs ensemble

  complete x # y mutation so far so less prevalent etc
  3 layer subs do no work so don't do them

replace > 1 segment -fitness- turn on and off niching adaptive/extinction reduce boost of fragments and all poor mols with niching pareto/mulitobjective ga -selection- metropolis selection for tournament/roulette adaptive keep #p and #o -extinction- automated vs on convergence -stop- convergence -which molecules are best- -best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used