Difference between revisions of "DOCK Release Objectives"

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(Created page with "DOCK 6.10 To do list *(1)Update the FMS and FPS test cases *(2)Change variables in the FMS and FPS *(3)Merge all the changes with the latest CVS version for testing *(4)Up...")
 
 
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DOCK 6.10 To do list
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''DOCK 6.10 To do list''
  
 
*(1)Update the FMS and FPS test cases
 
*(1)Update the FMS and FPS test cases
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*(3)Merge all the changes with the latest CVS version for testing
 
*(3)Merge all the changes with the latest CVS version for testing
  
*(4)Update the DOCK 6.8 HTM file
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*(4)Update the DOCK 6.9 HTM file
  
 
*(5)Perform the descriptor tests
 
*(5)Perform the descriptor tests
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# <s>Test Courtney's orienting fixx</s>
 
# <s>Test Courtney's orienting fixx</s>
 
# <s>Test Brian's rotatable bond fix</s>
 
# <s>Test Brian's rotatable bond fix</s>
# HMS = NA vs 9999 and implications on dn generic
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# <s>HMS = NA vs 9999 and implications on dn generic</s>
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# HMS pruning in database filter
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# database filter to charge molecule with gasteiger charge
 
# score molecule = no, internal energy = yes problem
 
# score molecule = no, internal energy = yes problem
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# Ensure that primary vs. secondary has been removed
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 +
POTENTIAL DOCK DESCRIPTORS
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# <s>QED</s>
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# <s>logp</s>
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# <s>logS</s>
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# <s>aromatic rings</s>
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# <s>lipinski alerts/violations</s>
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# <s>ligand SASA</s>
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# ligand desolvation penalty
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# <s>polar surface area</s>
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# Rizzo coefficient
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#
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''POST- DOCK 6.10 release to-dolist''
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 +
RDKIT
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# label in the header of the mol2 that the molecule has a covalent warhead
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# We want to eventually add energy score to the pruned dumped mol2 file during D3N
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# Add more sophisticated code that outputs the reason why molecules are rejected in the header of the mol2.

Latest revision as of 13:39, 16 May 2022

DOCK 6.10 To do list

  • (1)Update the FMS and FPS test cases
  • (2)Change variables in the FMS and FPS
  • (3)Merge all the changes with the latest CVS version for testing
  • (4)Update the DOCK 6.9 HTM file
  • (5)Perform the descriptor tests
  • (6)Check in the changes to DOCK CVS Tree

Developer To Do:

  1. Test Courtney's orienting fixx
  2. Test Brian's rotatable bond fix
  3. HMS = NA vs 9999 and implications on dn generic
  4. HMS pruning in database filter
  5. database filter to charge molecule with gasteiger charge
  6. score molecule = no, internal energy = yes problem
  7. Ensure that primary vs. secondary has been removed

POTENTIAL DOCK DESCRIPTORS

  1. QED
  2. logp
  3. logS
  4. aromatic rings
  5. lipinski alerts/violations
  6. ligand SASA
  7. ligand desolvation penalty
  8. polar surface area
  9. Rizzo coefficient

POST- DOCK 6.10 release to-dolist

RDKIT

  1. label in the header of the mol2 that the molecule has a covalent warhead
  2. We want to eventually add energy score to the pruned dumped mol2 file during D3N
  3. Add more sophisticated code that outputs the reason why molecules are rejected in the header of the mol2.