Difference between revisions of "Development Goals Archive"

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(→‎DOCK_DN - De Novo Design)
(→‎DOCK_DN - De Novo Design)
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|Update exhaustive to combine all frags into one library, just like graph / random. || WJA || yep
 
|Update exhaustive to combine all frags into one library, just like graph / random. || WJA || yep
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|hbond accept/donor descriptor implementation || Lauren ||
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|increase orienting verbose statistics for dn || Chris ||
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|acceptance based on freq of torsenv || John ||
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|secondary torenv check of prune dump molecules and testing || Lauren & John ||
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|SMILEs and ZINC script (for dn and ga) || Lauren & John ||
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|add dn name with date and counter function || Lauren ||
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|Check MGS+(-50)TAN before and after fingerprinting fix for 663 systems || Lauren ||
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|determine if random seed is reset for each aps || Lauren ||
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|Create testset for each dn function || Lauren ||
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|Test simple build function with merged de novo || Lauren ||
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|clean make_unique script for release || Lauren & Stephen ||
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|merge GA into dock/dn || Lauren ||
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|MPI wrapper for 192 processors (8 nodes) for testsets on rizzo cluster || Dwight & Lauren ||
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|Create short testsets for denovo frag gen, focused fragment generic for DOCK6.9 release || Lauren ||
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|merge parameter files of de novo with DOCK || Dwight & Lauren ||
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|add dn_defn file for separate defn with Hydrogens || Lauren ||
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|Implement csingleton fix for orienting fragments with less than 3 heavy atoms || Lauren ||
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|Test bfochtman fix for rotatable bonds within an user defined anchor || Lauren ||
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|Test csingleton fix for orienting fragments with Du || Lauren ||
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|Test MGS focused fragment library results with dn paper || Lauren ||
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|editting script to calculate SMILE string of de novo molecules in OpenBabel || Stephen ||
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|smooth function cutoff for mw || Stephen ||
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|Rework VS protocol to integrate de novo protocol more smoothly || Lauren & John ||
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|Fix torsion problem for prune_dump molecules || Lauren & John ||
 
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Revision as of 13:52, 22 October 2022

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


DOCK_GA - Genetic Algorithm

DOCK_CV - Covalent Docking

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