Difference between revisions of "Development Goals Archive"
From Rizzo_Lab
(→DOCK_VS - Virtual Screening/Traditional Docking) |
(→DOCK_DN - De Novo Design) |
||
| Line 40: | Line 40: | ||
=DOCK_DN - De Novo Design= | =DOCK_DN - De Novo Design= | ||
| − | + | {| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%" | |
| + | |- style="background:lightblue" | ||
| + | ! style="width:50%" !|Task | ||
| + | ! style="width:10%" !|Owner | ||
| + | ! style="width:30%" !|Notes | ||
| + | |- | ||
| + | |When minimizing with descriptor score, make sure fingerprint is turned off || xxx || | ||
| + | |- | ||
| + | |Speed up fingerprint calculations by saving reference ligand as a permanent object || WJA || yep | ||
| + | |- | ||
| + | |Add pre-min conformations to growth trees || WJA || yep | ||
| + | |- | ||
| + | |Add verbose flag options || WJA || yep | ||
| + | |- | ||
| + | |Put molecular properties (RB, MW, etc) in mol2 header || WJA || yep | ||
| + | |- | ||
| + | |Put ensemble properties (RB, MW, etc) output stream at the end of each layer || WJA || yep | ||
| + | |- | ||
| + | |Check formal charge prune || BCF || yep | ||
| + | |- | ||
| + | |Combination of horizontal pruning metrics (let's consider dropping tanimoto prune and just using hungarian prune) || WJA || yep | ||
| + | |- | ||
| + | |Finish implementing growth trees || WJA || yep | ||
| + | |- | ||
| + | |Revisit orienting to make sure it is working as intended || WJA || yep | ||
| + | |- | ||
| + | |Fixed a bug where we were marking scaffold_this_layer as true for any fragment || WJA || yep | ||
| + | |- | ||
| + | |Update random sampling function to use last layer changes in graph function || WJA || yep | ||
| + | |- | ||
| + | |Do that same thing for the exhaustive function || WJA || yep | ||
| + | |- | ||
| + | |I don't think we ever clear the scaf_link_sid vector, we definitely should do that somewhere || WJA || yep | ||
| + | |- | ||
| + | |Update exhaustive to combine all frags into one library, just like graph / random. || WJA || yep | ||
| + | |- | ||
| + | |} | ||
| + | <br> | ||
=DOCK_GA - Genetic Algorithm= | =DOCK_GA - Genetic Algorithm= | ||
Revision as of 13:43, 22 October 2022
Contents
DOCK_VS - Virtual Screening/Traditional Docking
| Tasks | src | Owner | Complete? |
|---|---|---|---|
| verbose ==2 option in dock6 beta | utils.cpp | LEP | yes |
| Add total conformers samples | |||
| Check amide bond rotation during sampling - it's nto a bug it was fixed back in 2014 | LEP | yes | |
| Write out # of HBond Donors and Acceptors | conf_gen_dn, library_file | LEP | yes |
| put in compiler directives to compile with or without timespec | dock.cpp | LEP | yes |
| Fix bug that prints out 2/3 sigfigs instead of 6 for MW and FC | library_file, filter, amber_typer | LEP | Yes |
| Fix nano/micro/milisecond timer | dock.cpp | GDRM | Yes |
| ga flag and verbose == 2 for premin_mol in simplex | simplex.cpp | LEP | Yes |
| Merge Hackathon changes to beta for clean faster code | pow/memcpy/mpi pointers everywhere | LEP | Yes |
| Add Tip3p atom type to dock | vdw.defn fingerprint | LEP | Yes |
| Hide secondary scoring function permanently | lots | LEP | Yes |
| Merge GIST into latest dock | grid, master_score, score_descriptor, score_gist | LEP | Yes |
| Add second layer of verbosity | utils, conf_gen_dn so far | LEP | Yes |
| RDKit integration with DOCK | GDM | Yes | |
| Modify Grid to show error on nonintegrality | BTB | Yes |
DOCK_DN - De Novo Design
| Task | Owner | Notes |
|---|---|---|
| When minimizing with descriptor score, make sure fingerprint is turned off | xxx | |
| Speed up fingerprint calculations by saving reference ligand as a permanent object | WJA | yep |
| Add pre-min conformations to growth trees | WJA | yep |
| Add verbose flag options | WJA | yep |
| Put molecular properties (RB, MW, etc) in mol2 header | WJA | yep |
| Put ensemble properties (RB, MW, etc) output stream at the end of each layer | WJA | yep |
| Check formal charge prune | BCF | yep |
| Combination of horizontal pruning metrics (let's consider dropping tanimoto prune and just using hungarian prune) | WJA | yep |
| Finish implementing growth trees | WJA | yep |
| Revisit orienting to make sure it is working as intended | WJA | yep |
| Fixed a bug where we were marking scaffold_this_layer as true for any fragment | WJA | yep |
| Update random sampling function to use last layer changes in graph function | WJA | yep |
| Do that same thing for the exhaustive function | WJA | yep |
| I don't think we ever clear the scaf_link_sid vector, we definitely should do that somewhere | WJA | yep |
| Update exhaustive to combine all frags into one library, just like graph / random. | WJA | yep |
