Difference between revisions of "DOCK VS Development Goals"
From Rizzo_Lab
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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 | ||
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| + | |HMS Islands || Use HMS to determine clusters of best overlaid congeneric poses || Open || No || JDB | | ||
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Revision as of 08:47, 7 April 2022
| Tasks | src | Owner | Complete? | |
|---|---|---|---|---|
| put in warning flag for missing flex defn type instead of segfaulting | 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 | SMT | No | ||
| Consensus score (within descriptor score) | SMT | 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 |
| 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 |
