Difference between revisions of "DOCK GA Development Goals"
From Rizzo_Lab
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! style="width:13%" !|Owner | ! style="width:13%" !|Owner | ||
! style="width:10%" !|Complete? | ! style="width:10%" !|Complete? | ||
| + | |- | ||
| + | |Horizontal pruning issue not catching chemically identical molecules || LEP || no | ||
|- | |- | ||
|Fix bug that collapsed atom coordinates || everywhere? nowhere? somewhere. || LEP || YES MUAHAHAHAHA! | |Fix bug that collapsed atom coordinates || everywhere? nowhere? somewhere. || LEP || YES MUAHAHAHAHA! | ||
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|Remove check only option || 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 || | + | |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 | |Compute delta slope of fitness score || congen_ga.cpp || LEP ||no | ||
Revision as of 10:06, 12 August 2021
| 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 |
To Do List
- slow down molecular evolution so there are less drastic canges between each successive generation
- 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
- bring in new parents based on convergence
- 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-
- metropolis selection for tournament/roulette
- adaptive keep #p and #o
- 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
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
