Difference between revisions of "DOCK GA Development Goals"
From Rizzo_Lab
BrockBoysan (talk | contribs) |
BrockBoysan (talk | contribs) |
||
| Line 36: | Line 36: | ||
| user defined point vs on-the-fly convergence || confgen_ga.cpp || BTB || no | | user defined point vs on-the-fly convergence || confgen_ga.cpp || BTB || no | ||
|- | |- | ||
| − | + | | metropolis selection for tournament/roulette || conf_gen_ga.cpp || BTB || no | |
| − | + | |- | |
|} | |} | ||
<br> | <br> | ||
| Line 67: | Line 67: | ||
##pareto/mulitobjective ga | ##pareto/mulitobjective ga | ||
#selection- | #selection- | ||
| − | + | ##adaptive keep #p and #o (parents, offspring) | |
| − | ##adaptive keep #p and #o | ||
#extinction- | #extinction- | ||
##user defined point vs on-the-fly convergence THIS | ##user defined point vs on-the-fly convergence THIS | ||
Revision as of 10:52, 17 October 2022
| 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 |
| 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 |
| Compute delta slope of fitness score | congen_ga.cpp | BTB | no |
| slow down molecular evolution so there are less drastic canges between each successive generation | congen_ga.cpp | BTB | no |
| bring in new parents (e.g. from a pool of molecules) based on convergence | confgen_ga.cpp | BTB | no |
| user defined point vs on-the-fly convergence | confgen_ga.cpp | BTB | no |
| metropolis selection for tournament/roulette | conf_gen_ga.cpp | BTB | no |
To Do List
- tanimoto coefficient percent change - might be inaccurate due to tan coef behavior
- Rotatable bond changes
- Number of aromatic rings
- -xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad THIS
- nonexhaustive xover (pick subset of xover based on probability)
- nonexhaustive xover for each pair of parents - have a set number of bonds for xover
- 2-3 point xover at once
- adaptive maintenance ensemble based on ensemble convergence THIS
- Mutations-
- adaptive mutation rate THIS
- pick location of mutation based on something
- pick mutation type based on behavior of ensemble
- molecules too large boost deletion
- molecules too small, add more groups
- 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-
- adaptive keep #p and #o (parents, offspring)
- extinction-
- user defined point vs on-the-fly convergence THIS
- stop-
- convergence
- which molecules are best-
- best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used
- geometric diversity using Hingarian and Tan pruning
- Determine whether the dummy vdw file is necessary for all DN (including GA) or just DN.
Known Bugs
- Molecules Processed bug (dock.cpp)
- verbose mol stats (amber typer)
- molecule being renamed when going into repl even tho it's the same molecule
