DOCK GA Development Goals

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Revision as of 11:46, 15 February 2019 by Lprentis (talk | contribs)
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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 conf_gen_ga 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