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

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