Difference between revisions of "DOCK VS Development Goals"

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! style="width:10%" !|Complete?
 
! style="width:10%" !|Complete?
 
|-
 
|-
−
|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 || || ||  
 
|-
 
|-
−
|Clean GNU warnings  || || LEP || No
+
| Put minimize = 0 in flex.defn is a depricated feature in manual ||manual ||LEP || no
 
|-
 
|-
−
|Fix nano/micro/milisecond timer  || || GDRM || No
+
|input checks in the vs protocol scripts to check whether the step before finalized mpi routines || || || no
 
|-
 
|-
−
|ga flag and verbose == 2 for premin_mol in simplex  || simplex.cpp || LEP || Yes
+
|SYLVIA Score || || ||no
 
|-
 
|-
−
|Merge Hackathon changes to beta for clean faster code  || pow/memcpy/mpi pointers everywhere || LEP || Nooo...
+
|determine which library generation outputs are appended rather than overwritten, and change to overwrite || || ||no
 
|-
 
|-
−
|Add Tip3p atom type to dock ||vdw.defn fingerprint || LEP || Yes
+
|put in best first clustering option for database filter || || ||no
 
|-
 
|-
−
|Hide secondary scoring function permanently ||lots || LEP || Yes
+
|Web server || || Pak || no
 
|-
 
|-
−
|Merge GIST into latest dock ||grid, master_score, score_descriptor, score_gist || LEP || Yes
+
|Consensus score (within descriptor score)|| || Open || No
 
|-
 
|-
−
|Add second layer of verbosity ||  utils, conf_gen_dn so far || LEP || Yes
+
|Clean GNU warnings  ||  || || No
 
|-
 
|-
 
|Multigrid footprint text file formatting needs adjustment || || LEP || No
 
|Multigrid footprint text file formatting needs adjustment || || LEP || No
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|Create an RNA test set using systems suggested by Al-Hashimi|| || Rodger, John || 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
 +
|-
 +
|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
 +
|-
 +
|}
 +
 
 +
<br>
 +
 
 +
 
 +
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
 +
|- style="background:lightblue"
 +
! style="width:75%" !|Tasks
 +
! style="width:25%" !|src
 +
! style="width:13%" !|Owner
 +
! style="width:10%" !|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 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
+
|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
 
|}
 
|}
 
<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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