Mol2db2 Format 2

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