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== Attendees & Time==
== Attendees & Time==


Date: ???, 2010, ? - ?
Date: April 2nd, 2010. 105 pm.
 
== Slides ==
 
#Philosophy
*deleted unused things
*cleaned up code
*streamlined call graph
*single mode gone (use version 3.5.54.70)
*contact scoring gone
 
#DOCK 3.5.54.72 improvements
*distmap bumping instead of contact bumping
*new hierarchy code (should eliminate some broken)
*no more out of bounds molecules
*no more clashing molecules
*deprecated unused keywords
*64bit/32bit builds (dock.csh instead of calling directly)
*speedups (3-5x)
 
#Deprecated keywords
*write_coordinates
*standard_pdb
*focus_ratio
*normalize_save
*restart_interval
*mirror_ligands
*scoring_option
*mode
*ligand_type
*restart
*output_hydrogens
*recombine_fragments
*interpolate
*ligand_sphere_file
*write_coordinates
*standard_pdb
*focus_ratio
 
#New keywords
*keyword                            default  suggested
*remove_positive_solvation no          YES
*check_clashes                    yes        YES


== Hardware updates==
== Hardware updates==

Revision as of 00:05, 2 April 2010

Attendees & Time

Date: April 2nd, 2010. 105 pm.

Slides

  1. Philosophy
  • deleted unused things
  • cleaned up code
  • streamlined call graph
  • single mode gone (use version 3.5.54.70)
  • contact scoring gone
  1. DOCK 3.5.54.72 improvements
  • distmap bumping instead of contact bumping
  • new hierarchy code (should eliminate some broken)
  • no more out of bounds molecules
  • no more clashing molecules
  • deprecated unused keywords
  • 64bit/32bit builds (dock.csh instead of calling directly)
  • speedups (3-5x)
  1. Deprecated keywords
  • write_coordinates
  • standard_pdb
  • focus_ratio
  • normalize_save
  • restart_interval
  • mirror_ligands
  • scoring_option
  • mode
  • ligand_type
  • restart
  • output_hydrogens
  • recombine_fragments
  • interpolate
  • ligand_sphere_file
  • write_coordinates
  • standard_pdb
  • focus_ratio
  1. New keywords
  • keyword default suggested
  • remove_positive_solvation no YES
  • check_clashes yes YES

Hardware updates

Software updates

Requests/Improvements

Database updates

Varia

Errata

Action Items

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