DOCK VS Development Goals
From Rizzo_Lab
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 | Open | 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 |