Difference between revisions of "DOCK VS Development Goals"
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! style="width:10%" !|Complete? | ! style="width:10%" !|Complete? | ||
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| − | | put in warning flag for missing flex defn type instead of segfaulting || || | + | | fix segfaulting when fp_ref_mol and fp_ref_mol are both set to no for multigrid_score_primary || || open || no |
| + | |- | ||
| + | | put in warning flag for missing flex defn type instead of segfaulting || amber_typer.cpp probably || evan || no | ||
| + | |- | ||
| + | | make a single point calculation mode for rescoring exlucisvely (rigid no orientation/minimization) || dock.cpp and another probably || evan (?) || no | ||
|- | |- | ||
| update torenv in dock6 beta || fraglib_torenv.dat || JDB || no | | update torenv in dock6 beta || fraglib_torenv.dat || JDB || no | ||
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|put in best first clustering option for database filter || || ||no | |put in best first clustering option for database filter || || ||no | ||
|- | |- | ||
| − | |Web server || || | + | |Web server || || Pak || no |
|- | |- | ||
| − | |Consensus score (within descriptor score)|| || | + | |Consensus score (within descriptor score)|| || Open || No |
|- | |- | ||
|Clean GNU warnings || || || No | |Clean GNU warnings || || || No | ||
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|Fix minimization issue with perfectly linear (alkyne) compounds|| Add dummy atom 90* as in other codes so dihedral is defined, treat the hydrogen as a part of the carbon or heavy atom (united atom) approach, flag dihedrals that are undefined or close to 180* as non rotatable|| Open || No | |Fix minimization issue with perfectly linear (alkyne) compounds|| Add dummy atom 90* as in other codes so dihedral is defined, treat the hydrogen as a part of the carbon or heavy atom (united atom) approach, flag dihedrals that are undefined or close to 180* as non rotatable|| Open || No | ||
|- | |- | ||
| − | |HMS Islands || Use HMS to determine clusters of best overlaid congeneric poses || Open || No || | + | |HMS Islands || Use HMS to determine clusters of best overlaid congeneric poses || Open || No |
| + | |- | ||
| + | |Anchor names || Output anchor names alongside molecule number when writing out conformers || Brock || No | ||
| + | |- | ||
|} | |} | ||
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|- | |- | ||
|RDKit integration with DOCK || || GDM || Yes | |RDKit integration with DOCK || || GDM || Yes | ||
| + | |- | ||
| + | |Modify Grid to show error on nonintegrality || || BTB || Yes | ||
|} | |} | ||
<br> | <br> | ||
Latest revision as of 16:02, 9 July 2025
| Tasks | src | Owner | Complete? |
|---|---|---|---|
| fix segfaulting when fp_ref_mol and fp_ref_mol are both set to no for multigrid_score_primary | open | no | |
| put in warning flag for missing flex defn type instead of segfaulting | amber_typer.cpp probably | evan | no |
| make a single point calculation mode for rescoring exlucisvely (rigid no orientation/minimization) | dock.cpp and another probably | evan (?) | no |
| update torenv in dock6 beta | fraglib_torenv.dat | JDB | no |
| Add total conformers samples | |||
| Put minimize = 0 in flex.defn is a depricated feature in manual | manual | LEP | no |
| input checks in the vs protocol scripts to check whether the step before finalized mpi routines | no | ||
| SYLVIA Score | no | ||
| determine which library generation outputs are appended rather than overwritten, and change to overwrite | no | ||
| put in best first clustering option for database filter | no | ||
| Web server | Pak | no | |
| Consensus score (within descriptor score) | Open | No | |
| Clean GNU warnings | No | ||
| Multigrid footprint text file formatting needs adjustment | LEP | No | |
| Add the DUDE systems created by Jiaye, Brian, and Yuchen to the standard DOCK test set | No | ||
| Create an RNA test set using systems suggested by Al-Hashimi | Rodger, John | No | |
| Fix minimization issue with perfectly linear (alkyne) compounds | Add dummy atom 90* as in other codes so dihedral is defined, treat the hydrogen as a part of the carbon or heavy atom (united atom) approach, flag dihedrals that are undefined or close to 180* as non rotatable | Open | No |
| HMS Islands | Use HMS to determine clusters of best overlaid congeneric poses | Open | No |
| Anchor names | Output anchor names alongside molecule number when writing out conformers | Brock | No |
| 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 |
