DOCK GA Development Goals

Tasks	src	Owner	Complete?
Horizontal pruning issue not catching chemically identical molecules	LEP	no
Fix bug that collapsed atom coordinates	everywhere? nowhere? somewhere.	LEP	YES MUAHAHAHAHA!
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
Add single molecule evolution in testcase in install dir.	install/test/genetic	LEP	yes
Compute delta slope of fitness score	congen_ga.cpp	LEP	no
Add leading 0's to xover output filenames	conf_gen_ga.cpp	JDB	no
DNM replacement unable to build list?	conf_gen_ga.cpp	JDB	no
Multi-layer replacement for Amides	conf_gen_ga.cpp	JDB	no

To Do List

1. slow down molecular evolution so there are less drastic canges between each successive generation
2. tanimoto coefficient percent change - might be inaccurate due to tan coef behavior
3. Rotatable bond changes
4. Number of aromatic rings
5. -xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad THIS
6. nonexhaustive xover (pick subset of xover based on probability)
7. nonexhaustive xover for each pair of parents - have a set number of bonds for xover
8. 2-3 point xover at once
9. adaptive maintenance ensemble based on ensemble convergence THIS
10. bring in new parents (e.g. from a pool of molecules) based on convergence
11. 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
12. fitness-
    1. turn on and off niching adaptive/extinction
    2. reduce boost of fragments and all poor mols with niching
    3. pareto/mulitobjective ga
13. selection-
    1. metropolis selection for tournament/roulette
    2. adaptive keep #p and #o
14. extinction-
    1. user defined point vs on-the-fly convergence THIS
15. stop-
    1. convergence
16. 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
17. Determine whether the dummy vdw file is necessary for all DN (including GA) or just DN.

Known Bugs

1. Molecules Processed bug (dock.cpp)
2. verbose mol stats (amber typer)
3. molecule being renamed when going into repl even tho it's the same molecule