DOCK GA Development Goals
From Rizzo_Lab
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-
- 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