DUMM6: Difference between revisions

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#Philosophy
#Philosophy
*deleted unused things
**deleted unused things
*cleaned up code
**cleaned up code
*streamlined call graph
**streamlined call graph
**single mode gone (use version 3.5.54.70)
***single mode gone (use version 3.5.54.70)
**contact scoring gone
***contact scoring gone
**precalculate various grid terms
***precalculate various grid terms


#DOCK 3.5.54.72 improvements
#DOCK 3.5.54.72 improvements
*distmap bumping instead of contact bumping
**distmap bumping instead of contact bumping
*new hierarchy code (should eliminate some broken)
**new hierarchy code (should eliminate some broken)
*no more out of bounds molecules
**no more out of bounds molecules
*no more clashing molecules
**no more clashing molecules
*deprecated unused keywords (more later)
**deprecated unused keywords (more later)
*vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
**vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
*64bit/32bit builds (dock.csh instead of calling directly)
**64bit/32bit builds (dock.csh instead of calling directly)
*speedups (3-5x)
**speedups (3-5x)


#Deprecated keywords
#Deprecated keywords
*write_coordinates
**write_coordinates
*standard_pdb
**standard_pdb
*focus_ratio
**focus_ratio
*normalize_save
**normalize_save
*restart_interval
**restart_interval
*mirror_ligands
**mirror_ligands
*scoring_option
**scoring_option
*mode
**mode
*ligand_type
**ligand_type
*restart
**restart
*output_hydrogens
**output_hydrogens
*recombine_fragments
**recombine_fragments
*interpolate
**interpolate
*ligand_sphere_file
**ligand_sphere_file
*write_coordinates
**write_coordinates
*standard_pdb
**standard_pdb
*focus_ratio
**focus_ratio


#New keywords
#New keywords
*keyword                            default  suggested
**keyword                            default  suggested
*remove_positive_solvation no          YES
**remove_positive_solvation no          YES
*check_clashes                    yes        YES
**check_clashes                    yes        YES


#DISI
#DISI
*it is great
**it is great


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

Revision as of 16:19, 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
      • precalculate various grid terms
  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 (more later)
    • vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
    • 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
  1. DISI
    • it is great

Hardware updates

Software updates

Requests/Improvements

Database updates

Varia

Errata

Action Items

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