Difference between revisions of "DOCK VS Development Goals"

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|Fix bug that prints out 2/3 sigfigs instead of 6 for MW and FC || library_file, filter, amber_typer || LEP || Yes
+
| put in warning flag for missing flex defn type instead of segfaulting || amber_typer.cpp probably || evan || no
 +
|-
 +
| make a single point calculation mode for rescoring exlucisvely (rigid no orientation/minimization) || dock.cpp and another probably || evan (?) || 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 || || Pak || 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
 
|-
 
|-
−
|<strike>Roulette function to Random and Graph as an option</strike> || LEP ||  
+
|HMS Islands || Use HMS to determine clusters of best overlaid congeneric poses || Open || No
 
|-
 
|-
−
|<strike>Overhaul the simple build function</strike> || LEP ||  
+
|Anchor names || Output anchor names alongside molecule number when writing out conformers || Brock || No
 
|-
 
|-
−
|When minimizing with descriptor score, make sure fingerprint is turned off || xxx ||
+
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<br>
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{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
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|- style="background:lightblue"
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! style="width:75%" !|Tasks
 +
! style="width:25%" !|src
 +
! style="width:13%" !|Owner
 +
! style="width:10%" !|Complete?
 
|-
 
|-
−
|Speed up fingerprint calculations by saving reference ligand as a permanent object || WJA || yep
+
| verbose ==2 option in dock6 beta || utils.cpp|| LEP || yes
 
|-
 
|-
−
|Add pre-min conformations to growth trees || WJA || yep
+
| Add total conformers samples || || ||  
 
|-
 
|-
−
|Add verbose flag options || WJA || yep
+
| Check amide bond rotation during sampling - it's nto a bug it was fixed back in 2014 || || LEP||yes
 
|-
 
|-
−
|Put molecular properties (RB, MW, etc) in mol2 header || WJA || yep
+
| Write out # of HBond Donors and Acceptors || conf_gen_dn, library_file || LEP || yes
 
|-
 
|-
−
|Put ensemble properties (RB, MW, etc) output stream at the end of each layer || WJA || yep
+
|put in compiler directives to compile with or without timespec || dock.cpp || LEP || yes
 
|-
 
|-
−
|Check formal charge prune || BCF || yep
+
|Fix bug that prints out 2/3 sigfigs instead of 6 for MW and FC  || library_file, filter, amber_typer || LEP || Yes
 
|-
 
|-
−
|Combination of horizontal pruning metrics (let's consider dropping tanimoto prune and just using hungarian prune) || WJA  || yep
+
|Fix nano/micro/milisecond timer  || dock.cpp || GDRM || Yes
 
|-
 
|-
−
|Finish implementing growth trees || WJA || yep
+
|ga flag and verbose == 2 for premin_mol in simplex  || simplex.cpp || LEP || Yes
 
|-
 
|-
−
|Revisit orienting to make sure it is working as intended || WJA || yep
+
|Merge Hackathon changes to beta for clean faster code  || pow/memcpy/mpi pointers everywhere || LEP || Yes
 
|-
 
|-
−
|Fixed a bug where we were marking scaffold_this_layer as true for any fragment || WJA || yep
+
|Add Tip3p atom type to dock ||vdw.defn fingerprint || LEP || Yes
 
|-
 
|-
−
|Update random sampling function to use last layer changes in graph function || WJA || yep
+
|Hide secondary scoring function permanently ||lots || LEP || Yes
 
|-
 
|-
−
|Do that same thing for the exhaustive function || WJA || yep
+
|Merge GIST into latest dock ||grid, master_score, score_descriptor, score_gist || LEP || Yes
 
|-
 
|-
−
|I don't think we ever clear the scaf_link_sid vector, we definitely should do that somewhere || WJA || yep
+
|Add second layer of verbosity ||  utils, conf_gen_dn so far || LEP || Yes
 
|-
 
|-
−
|Update exhaustive to combine all frags into one library, just like graph / random. || WJA || yep
+
|RDKit integration with DOCK || || GDM || Yes
 
|-
 
|-
 +
|Modify Grid to show error on nonintegrality || || BTB || Yes
 
|}
 
|}
 
<br>
 
<br>

Latest revision as of 10:29, 1 August 2024

Tasks src Owner Complete?
put in warning flag for missing flex defn type instead of segfaulting amber_typer.cpp probably evan no
make a single point calculation mode for rescoring exlucisvely (rigid no orientation/minimization) dock.cpp and another probably evan (?) 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 Pak 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


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