Mol2db2 Format 2

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Revision as of 16:47, 15 April 2010 by Rgc (talk | contribs) (reworking file format)
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This page is a wishlist for features that would be nice for a new version of the flexibase file format to support.

  • Real Atom Types and Bond Information
  • Way to determine which mix-and-match conformations have clashes (and avoid trying them)
  • A place to store an internal energy for each possible conformation
  • Terminal hydrogen rotations??
  • Aliphatic ring movements?
  • support for clusters of conformations
  • group tagging (needed for covalent docking) and basic set of covalent groups
  • specified rigid component override (and better rules for finding non-ring rigid components)
  • per molecule pKa

the following represents the current plan for the file format

  • M molecule (only 2 lines ever)
  • A atoms
  • B bond
  • X xyz
  • G group
  • GC group-conf mapping
  • C conformation
  • S sets
M name #atoms #bonds #xyz #groups #confs #sets 
M charge polar_solv apolar_solv surface_area total_solv
A stuff about each atom, 1 per line 
B stuff about each bond, 1 per line
X atomnum confnum x y z 
G groupnum linenum #children childgroup [until column is full]  
GC #confs confnum [more confnums]
C confnum linenum #children childconf [until column is full]
S #confnums confnum [more] data_about_this_conf