Difference between revisions of "DOCK VS Development Goals"

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! style="width:13%" !|Owner
 
! style="width:13%" !|Owner
 
! style="width:10%" !|Complete?
 
! style="width:10%" !|Complete?
 +
|-
 +
| put in warning flag for missing flex defn type instead of segfaulting || ||  || no
 +
|-
 +
| update torenv in dock6 beta || fraglib_torenv.dat || JDB || no
 +
|-
 +
| verbose ==2 option in dock6 beta || utils.cpp|| LEP || yes
 +
|-
 +
| Add total conformers samples || || ||
 +
|-
 +
| Put minimize = 0 in flex.defn is a depricated feature in manual ||manual ||LEP || no
 +
|-
 +
| 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
 +
|-
 +
|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
 
|Fix bug that prints out 2/3 sigfigs instead of 6 for MW and FC  || library_file, filter, amber_typer || LEP || Yes
 
|-
 
|-
|Hide secondary scoring function permanently ||a shit ton || LEP || Yes
+
|Clean GNU warnings  ||  ||  || 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
 
|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 || 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
 
|}
 
|}
 
<br>
 
<br>

Latest revision as of 15:46, 20 October 2020

Tasks src Owner Complete?
put in warning flag for missing flex defn type instead of segfaulting no
update torenv in dock6 beta fraglib_torenv.dat JDB no
verbose ==2 option in dock6 beta utils.cpp LEP yes
Add total conformers samples
Put minimize = 0 in flex.defn is a depricated feature in manual manual LEP no
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
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 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 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