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
• D 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]
D groupnum #lines #confs_total  
D groupnum linenum #confs confnum [until column is full]
C confnum #lines #children_total
C confnum linenum #children childconf [until column is full]
S setnum #lines #confs_total [INPUT|MIX] broken omega_energy
S setnum linenum #confs confs [until full column]

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.

notes: 17 children groups/group per line in current scheme. 9 children confs/group per line. 9 children confs/conf per line. 8 confs/set per line.

          1         2         3         4         5         6         7
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
X ATO CONFNU +XCO.OORD +YCO.ORD +ZCO.ORD
G GRO #LI #CH
G GRO LIN #C CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN
D GRO #LIN #CONFS
D GRO LINE # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS  
C CONFNO #LIN #CONFS
C CONFNO LINE # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS
S SETIDXXXX #LINES #CONFS I C +ENER.GYX
S SETIDXXXX LINENO # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS