DOCK VS Development Goals

Tasks	src	Owner	Complete?
Potential minimization error
Check amide bond rotation during sampling
Write out # of HBond Donors and Acceptors	conf_gen_dn, library_file	LEP	yes
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
put in compiler directives to compile with or without timespec	dock.cpp	LEP	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		GDM
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