DOCK VS Development Goals
From Rizzo_Lab
| Tasks | src | Owner | Complete? |
|---|---|---|---|
| SYLVIA Score | LEP | 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 | ||
| put in compiler directives to compile with or without timespec | dock.cpp | GDRM | yes |
| Web server | SMT | No | |
| Consensus score (within descriptor score) | SMT | No | |
| Fix bug that prints out 2/3 sigfigs instead of 6 for MW and FC | library_file, filter, amber_typer | LEP | Yes |
| Clean GNU warnings | LEP | No | |
| 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 |
| 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 | |
| RDKit integration with DOCK | |||
| 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 |
