Mol2db2 Format 2

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Revision as of 17:50, 16 April 2010 by Rgc (talk | contribs) (adding to atom line)
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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

  • T type information (implicitly assumed)
  • M molecule (only 2 lines ever)
  • A atoms
  • B bond
  • X xyz
  • G group
  • D group-conf mapping
  • C conformation
  • S sets
T ## namexxxx (implicitly assumed to be the standard 7)
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.

on the atom line, dt is dock type and co is color.

          1         2         3         4         5         6         7
01234567890123456789012345678901234567890123456789012345678901234567890123456789
T ## typename
M ZINCCODEX PROTCODEX ATO BON XYZXXX GRO CONFSX SETSXXXXX
M +CHA.RGEX +POLAR.SOL +APOLA.SOL SURFA.REA +TOTAL.SOL
A NUM NAME TYPEX DT CO +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

the type lines following are assumed by dock unless overriden:

T  1 positive
T  2 negative
T  3 acceptor
T  4    donor
T  5  ester_o
T  6  amide_o
T  7  neutral

the following are the format statements for python for each line

T %2d %8s\n
M %9s %9s %3d %3d %6d %3d %6d %9d\n
M %+9.4f %+10.3f %+10.3f %9.3f %+10.3f\n