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	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

-xover- -guided based on score

1. good v good
2. bad v good
3. bad v bad
4. nonexhaustive xover (pick subset of xover based on probability)
5. 2-3 point xover at once
6. adaptive maintenance ensemble based on ensemble convergence
7. bring in new parents based on convergence
8. Mutations-
9. adaptive mutation rate
10. pick location of mutation based on something
11. pick mutation type based on behavior of esemble
12. too large boost deletion
13. too small more add
14. change ...boost replace/sub
15. mutation type selection based on probability vs ensemble
16. complete x # y mutation so far so less prevalent etc
17. 3 layer subs do no work so don't do them
18. replace > 1 segment
19. fitness-
20. turn on and off niching adaptive/extinction
21. reduce boost of fragments and all poor mols with niching
22. pareto/mulitobjective ga
23. selection-
24. metropolis selection for tournament/roulette
25. adaptive keep #p and #o
26. extinction-
27. automated vs on convergence
28. stop-
29. convergence
30. which molecules are best-
31. best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used