Mol2db2 Format 2

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Revision as of 22:24, 23 November 2010 by Rgc (talk | contribs) (adding more stuff to db2 file including dud energy placeholder)
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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) [x]
  • A place to store an internal energy for each possible conformation [x]
  • Terminal hydrogen rotations?? [x]
  • 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 5 lines ever)
  • A atoms
  • B bond
  • X xyz
  • G group
  • D group-conf mapping
  • C conformation
  • S sets
  • E end of molecule
T ## namexxxx (implicitly assumed to be the standard 7)
M zincname protname #atoms #bonds #xyz #groups #confs #sets 
M charge polar_solv apolar_solv total_solv surface_area
M smiles
M longname
M best_dud_energy
A stuff about each atom, 1 per line 
B stuff about each bond, 1 per line
X coordnum 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 coordstart coordend
C confnum linenum #children childconf [until column is full]
S setnum #lines #confs_total [INPUT|MIX] broken hydrogens omega_energy
S setnum linenum #confs confs [until full column]
E

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. groups/confs with no children are written out.

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 +TOTAL.SOL SURFA.REA
M SMILESXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
M LONGNAMEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
M +BEST.DUD
A NUM NAME TYPEX DT CO +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA
B NUM ATO ATO TY
X COORDNUMX ATO CONFNU +XCO.ORDX +YCO.ORDX +ZCO.ORDX
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 COORDSTAR COORDENDX
C CONFNO LINE # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS
S SETIDXXXX #LINES #CO I C H +ENERGY.XXX
S SETIDXXXX LINENO # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS
E

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 %+10.3f %9.3f\n
M %77s\n
M %77s\n
M %+10.4f\n
A %3d %-4s %-5s %2d %2d %+9.4f %+10.3f %+10.3f %+10.3f %9.3f\n
B %3d %3d %3d %-2s\n
X %9d %3d %6d %+9.4f %+9.4f %+9.4f\n
G %3d %3d %3d\n
G %3d %3d %2d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d %3d\n
D %3d %4d %6d\n
D %3d %4d %1d %6d %6d %6d %6d %6d %6d %6d %6d %6d\n
C %6d %4d %6d %9d %9d\n
C %6d %4d %1d %6d %6d %6d %6d %6d %6d %6d %6d %6d\n
S %9d %6d %3d %1d %1d %1d %+11.3f\n
S %9d %6d %1d %6d %6d %6d %6d %6d %6d %6d %6d\n 
E\n

The following are the fortran format statements 

!T ## namexxxx (implicitly assumed to be the standard 7)
1000 format(2x,i2,1x,a8)
!M zincname protname #atoms #bonds #xyz #groups #confs #sets
2000 format(2x,a9,1x,a9,1x,i3,1x,i3,1x,i6,1x,i3,1x,i6,1x,i9)
!M charge polar_solv apolar_solv total_solv surface_area
2100 format(2x,f9.4,1x,f10.3,1x,f10.3,1x,f10.3,1x,f9.3)
!M smiles or longname
2200 format(2x,a77)
!M best dud energy (from old version of dock)
2300 format(2x,f10.4)
!A stuff about each atom, 1 per line
3000 format(2x,i3,1x,a4,1x,a5,1x,i2,1x,i2,1x,f9.4,1x,f10.3,1x,
    &       f10.3,1x,f10.3,1x,f9.3)
!B stuff about each bond, 1 per line
4000 format(2x,i3,1x,i3,1x,i3,1x,a2)
!X atomnum confnum x y z
5000 format(2x,i9,1x,i3,1x,i6,f9.4,1x,f9.4,1x,f9.4)
!G groupnum #lines #children_total
6000 format(2x,i3,1x,i3,1x,i3)
!G groupnum linenum #children childgroup [until column is full]
6100 format(2x,i3,1x,i3,1x,i2,1x,i3,1x,i3,1x,i3,1x,i3,1x,i3,
    &       1x,i3,1x,i3,1x,i3,1x,i3,1x,i3,1x,i3,1x,i3,
    &       1x,i3,1x,i3,1x,i3,1x,i3,1x,i3,1x,i3,1x,i3)
!D groupnum #lines #confs_total
7000 format(2x,i3,1x,i4,1x,i6)
!D groupnum linenum #confs confnum [until column is full]
7100 format(2x,i3,1x,i4,1x,i1,1x,i6,1x,i6,1x,i6,1x,i6,1x,i6,
    &       1x,i6,1x,i6,1x,i6,1x,i6)
!C confnum #lines #children_total
8000 format(2x,i6,1x,i4,1x,i6,1x,i9,1x,i9)
!C confnum linenum #children childconf [until column is full]
8100 format(2x,i6,1x,i4,1x,i1,1x,i6,1x,i6,1x,i6,1x,i6,1x,i6,
    &       1x,i6,1x,i6,1x,i6,1x,i6)
!S setnum #lines #confs_total [INPUT|MIX] broken omega_energy
9000 format(2x,i9,1x,i6,1x,i3,1x,i1,1x,i1,1x,i1,1x,f11.3)
!S setnum linenum #confs confs [until full column]
9100 format(2x,i9,1x,i6,1x,i1,1x,i6,1x,i6,1x,i6,1x,i6,
    &       1x,i6,1x,i6,1x,i6,1x,i6)
!E
!E does not get a format line
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