Mol2db2 Format 2: Difference between revisions

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m (working through columns)
m (atoms and bonds)
Line 38: Line 38:
  01234567890123456789012345678901234567890123456789012345678901234567890123456789
  01234567890123456789012345678901234567890123456789012345678901234567890123456789
  M ZINCCODEX PROTCODEX ATO BON XYZXXX GRO CONFSX SETSXXXXX
  M ZINCCODEX PROTCODEX ATO BON XYZXXX GRO CONFSX SETSXXXXX
  M +CHA.RGE +POLAR.SOL +APOLA.SOL SURFA.REA +TOTAL.SOL
  M +CHA.RGEX +POLAR.SOL +APOLA.SOL SURFA.REA +TOTAL.SOL
  A   
  A NUM NAME TYPEX +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA
  B NUM ATO ATO TYPE


[[Category:Wishlists]]
[[Category:Wishlists]]

Revision as of 17:47, 15 April 2010

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 zincname protname #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 #lines #children_total
G groupnum linenum #children childgroup [until column is full]
GC groupnum #lines #confs_total  
GC groupnum linenum #confs confnum [until column is full]
C confnum #lines #children_total
C confnum linenum #children childconf [until column is full]
S #confnums confnum [more] data_about_this_conf

With the above descriptions, here is a description of the columns that are used. Format statements for python/fortran will also appear at some point. If speed/size becomes an issue this might get replaced with a binary file format.

01234567890123456789012345678901234567890123456789012345678901234567890123456789
M ZINCCODEX PROTCODEX ATO BON XYZXXX GRO CONFSX SETSXXXXX
M +CHA.RGEX +POLAR.SOL +APOLA.SOL SURFA.REA +TOTAL.SOL
A NUM NAME TYPEX +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA
B NUM ATO ATO TYPE