Difference between revisions of "DOCK GA Development Goals"

From Rizzo_Lab
Jump to: navigation, search
(→‎To Do List)
 
(20 intermediate revisions by 2 users not shown)
Line 6: Line 6:
 
! style="width:10%" !|Complete?
 
! style="width:10%" !|Complete?
 
|-
 
|-
−
|Fix bug that collapsed atom coordinates  || everywhere? nowhere? || everyone || No
+
|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
 
|Added Delimeter header ||conf_gen_ga || LEP || Yes
Line 18: Line 20:
 
|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 ||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
 
|}
 
|}
 
<br>
 
<br>
Line 23: Line 34:
  
 
==To Do List==
 
==To Do List==
−
#-xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad
+
# 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 (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
 
#2-3 point xover at once
−
#adaptive maintenance ensemble based on ensemble convergence
+
#adaptive maintenance ensemble based on ensemble convergence THIS
 
#bring in new parents based on convergence
 
#bring in new parents based on convergence
 
#Mutations-
 
#Mutations-
−
##adaptive mutation rate
+
##adaptive mutation rate THIS
 
##pick location of mutation based on something
 
##pick location of mutation based on something
 
##pick mutation type based on behavior of ensemble
 
##pick mutation type based on behavior of ensemble
−
##too large boost deletion
+
##molecules too large boost deletion
−
##too small more add
+
##molecules too small, add more groups
 
##change ...boost replace/sub
 
##change ...boost replace/sub
 
##mutation type selection based on probability vs ensemble
 
##mutation type selection based on probability vs ensemble
Line 47: Line 63:
 
##adaptive keep #p and #o
 
##adaptive keep #p and #o
 
#extinction-  
 
#extinction-  
−
##automated vs on convergence
+
##user defined point vs on-the-fly convergence THIS
 
#stop-
 
#stop-
 
##convergence
 
##convergence
 
#which molecules are best-
 
#which molecules are best-
 
##best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used
 
##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

Latest revision as of 16:13, 15 April 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
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 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
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=DOCK_GA_Development_Goals&oldid=15000"