Development Goals Archive

DOCK_VS - Virtual Screening/Traditional Docking

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

DOCK_DN - De Novo Design

Task	Owner	Notes
When minimizing with descriptor score, make sure fingerprint is turned off	xxx
Speed up fingerprint calculations by saving reference ligand as a permanent object	WJA	yep
Add pre-min conformations to growth trees	WJA	yep
Add verbose flag options	WJA	yep
Put molecular properties (RB, MW, etc) in mol2 header	WJA	yep
Put ensemble properties (RB, MW, etc) output stream at the end of each layer	WJA	yep
Check formal charge prune	BCF	yep
Combination of horizontal pruning metrics (let's consider dropping tanimoto prune and just using hungarian prune)	WJA	yep
Finish implementing growth trees	WJA	yep
Revisit orienting to make sure it is working as intended	WJA	yep
Fixed a bug where we were marking scaffold_this_layer as true for any fragment	WJA	yep
Update random sampling function to use last layer changes in graph function	WJA	yep
Do that same thing for the exhaustive function	WJA	yep
I don't think we ever clear the scaf_link_sid vector, we definitely should do that somewhere	WJA	yep
Update exhaustive to combine all frags into one library, just like graph / random.	WJA	yep
hbond accept/donor descriptor implementation	Lauren
increase orienting verbose statistics for dn	Chris
acceptance based on freq of torsenv	John
secondary torenv check of prune dump molecules and testing	Lauren & John
SMILEs and ZINC script (for dn and ga)	Lauren & John
add dn name with date and counter function	Lauren
Check MGS+(-50)TAN before and after fingerprinting fix for 663 systems	Lauren
determine if random seed is reset for each aps	Lauren
Create testset for each dn function	Lauren
Test simple build function with merged de novo	Lauren
clean make_unique script for release	Lauren & Stephen
merge GA into dock/dn	Lauren
MPI wrapper for 192 processors (8 nodes) for testsets on rizzo cluster	Dwight & Lauren
Create short testsets for denovo frag gen, focused fragment generic for DOCK6.9 release	Lauren
merge parameter files of de novo with DOCK	Dwight & Lauren
add dn_defn file for separate defn with Hydrogens	Lauren
Implement csingleton fix for orienting fragments with less than 3 heavy atoms	Lauren
Test bfochtman fix for rotatable bonds within an user defined anchor	Lauren
Test csingleton fix for orienting fragments with Du	Lauren
Test MGS focused fragment library results with dn paper	Lauren
editting script to calculate SMILE string of de novo molecules in OpenBabel	Stephen
smooth function cutoff for mw	Stephen
Rework VS protocol to integrate de novo protocol more smoothly	Lauren & John
Fix torsion problem for prune_dump molecules	Lauren & John