DOCK GA Development Goals

Tasks	src	Owner	Complete?
Fix bug that collapsed atom coordinates	everywhere? nowhere?	everyone	I wish
Added Delimeter header	conf_gen_ga	LEP	Yes
Fix xover only feature	conf_gen_ga	LEP	Yes
Put in error messages for mut_rate > 1	conf_gen_ga	LEP	Yes
Manual user-defined mutation type	conf_gen_ga	LEP	Yes
Remove check only option	conf_gen_ga	LEP	Yes

To Do List

1. tanimoto coefficient percent change - might be inaccurate due to tan coef behavior
2. Rotatable bond changes
3. Number of aromatic rings
4. -xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad THIS
5. nonexhaustive xover (pick subset of xover based on probability)
6. 2-3 point xover at once
7. adaptive maintenance ensemble based on ensemble convergence THIS
8. bring in new parents based on convergence
9. Mutations-
   1. adaptive mutation rate THIS
   2. pick location of mutation based on something
   3. pick mutation type based on behavior of ensemble
   4. molecules too large boost deletion
   5. molecules too small, add more groups
   6. change ...boost replace/sub
   7. mutation type selection based on probability vs ensemble
   8. complete x # y mutation so far so less prevalent etc
   9. 3 layer subs do no work so don't do them
   10. replace > 1 segment
10. fitness-
    1. turn on and off niching adaptive/extinction
    2. reduce boost of fragments and all poor mols with niching
    3. pareto/mulitobjective ga
11. selection-
    1. metropolis selection for tournament/roulette
    2. adaptive keep #p and #o
12. extinction-
    1. user defined point vs on-the-fly convergence THIS
13. stop-
    1. convergence
14. which molecules are best-
    1. best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used
    2. geometric diversity using Hingarian and Tan pruning