View source for DB2 File Format

This page explains the DB2 file format used in DOCK37.

= Nomenclature Definitions =

* Conf - one set of atoms that moves together with a single position per atom.
* Set - a group of conformations that completely defines one position for each atom in a ligand.
* Cluster - Not yet implamented in DOCK3.7
* Cloud - Not yet implamented in DOCK3.7

= Record Types =
*T type information (implicitly assumed)
*M molecule (4 lines req'd, after that they are optional, 24 lines max)
*A atoms
*B bond
*X xyz 
*R rigid xyz for matching (can actually be any xyzs) 
*C conformation
*S sets
*D clusters
*E end of molecule

 T ## namexxxx (implicitly assumed to be the standard 7)
 M zincname protname #atoms #bonds #xyz #confs #sets #rigid #Mlines #clusters
 M charge polar_solv apolar_solv total_solv surface_area
 M smiles
 M longname
 [M arbitrary information preserved for writing out]
 A stuff about each atom, 1 per line 
 B stuff about each bond, 1 per line
 X coordnum atomnum confnum x y z 
 R rigidnum color x y z
 C confnum coordstart coordend
 S setnum #lines #confs_total broken hydrogens omega_energy
 S setnum linenum #confs confs [until full column]
 D clusternum setstart setend matchstart matchend #additionalmatching
 D matchnum color x y z
 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 ZINCCODEXXXXXXXX PROTCODEX ATO BON XYZXXX CONFSX SETSXX RIGIDX MLINES NUMCLU
 M +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA
 M SMILESXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
 M LONGNAMEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
 [M ARBITRARY_INFORMATION_PRESERVEDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]
 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
 R NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX
 C CONFNO COORDSTAR COORDENDX
 S SETIDX #LINES #CO C H +ENERGY.XXX
 S SETIDX LINENO # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS
 D CLUSID STASET ENDSET MST MEN ADD
 D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX
 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 %16s %9s %3d %3d %6d %6d %6d %6d &6d %6d\n
 M %+9.4f %+10.3f %+10.3f %+10.3f %9.3f\n
 M %77s\n
 M %77s\n
 M %77s\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
 R %3d %2d %+9.4f %+9.4f %+9.4f\n
 C %6d %9d %9d\n
 S %6d %6d %3d %1d %1d %+11.3f\n
 S %6d %6d %1d %6d %6d %6d %6d %6d %6d %6d %6d\n 
 D %6d %6d %6d %3d %3d %3d\n
 D %3d %2d %+9.4f %+9.4f %+9.4f\n
 E\n

The following are the fortran77 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 #rigid #mlines #clusters
 2000 format(2x,a16,1x,a9,1x,i3,1x,i3,1x,i6,1x,i6,1x,i6,x,i6,x,i6,x,i6,x,i6)
 !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)
 !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,x,f9.4,1x,f9.4,1x,f9.4)
 !R rigidnum color x y z
 6000 format(2x,i3,x,i2,x,f9.4,1x,f9.4,1x,f9.4)
 !C confnum #startcoord #endcoord
 7000 format(2x,i6,1x,i9,1x,i9)
 !S setnum #lines #confs_total broken hydrogens omega_energy
 8000 format(2x,i6,1x,i6,1x,i3,1x,i1,1x,i1,1x,f11.3)
 !S setnum linenum #confs confs [until full column]
 8100 format(2x,i6,1x,i6,1x,i1,1x,i6,1x,i6,1x,i6,1x,i6,
     &       1x,i6,1x,i6,1x,i6,1x,i6)
 !D CLUSID STARTSETX ENDSETXXX ADD MST MEN
 9000 format(2x,i6,x,i6,x,i6,x,i3,x,i3,x,i3)
 !D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX
 !re-use 6000
 !E
 !E does not get a format line

The following are Fortran95 format statements:

 !T ## namexxxx (implicitly assumed to be the standard 7)
       character (len=*), parameter :: DB2NAME = '(2x,i2,x,a8)' !1000
 !M zincname protname #atoms #bonds #xyz #confs #sets #rigid #maxmlines #clusters
       character (len=*), parameter :: DB2M1 =
      &    '(2x,a16,x,a9,x,i3,x,i3,x,i6,x,i6,x,i6,x,i6,x,i6,x,i6)' !2000
 !M charge polar_solv apolar_solv total_solv surface_area
       character (len=*), parameter :: DB2M2 =
      &    '(2x,f9.4,x,f10.3,x,f10.3,x,f10.3,x,f9.3)' !2100
 !M smiles/longname/arbitrary
       character (len=*), parameter :: DB2M3 = '(2x,a78)' !2200
 !A stuff about each atom, 1 per line
       character (len=*), parameter :: DB2ATOM =
      &    '(2x,i3,x,a4,x,a5,x,i2,x,i2,x,f9.4,x,f10.3,x,
      &    f10.3,x,f10.3,x,f9.3)' !3000
 !B stuff about each bond, 1 per line
      character (len=*), parameter :: DB2BOND =
      &    '(2x,i3,x,i3,x,i3,x,a2)' !4000
 !X coordnumx atomnum confnum x y z
       character (len=*), parameter :: DB2COORD =
      &    '(2x,i9,x,i3,x,i6,x,f9.4,x,f9.4,x,f9.4)' !5000
 !R rigidnum color x y z
       character (len=*), parameter :: DB2RIGID =
      &    '(2x,i6,x,i2,x,f9.4,x,f9.4,x,f9.4)' !6000
 !C confnum coordstart coordend
       character (len=*), parameter :: DB2CONF = '(2x,i6,x,i9,x,i9)' !7000
 !S setnum #lines #confs_total broken hydrogens omega_energy 
       character (len=*), parameter :: DB2SET1 =
      &    '(2x,i6,x,i6,x,i3,x,i1,x,i1,x,f11.3)' !8000
 !S setnum linenum #confs confs [until full column]
       character (len=*), parameter :: DB2SET2 =
      &    '(2x,i6,x,i6,x,i1,x,i6,x,i6,x,i6,x,i6,
      &    1x,i6,x,i6,x,i6,x,i6)' !8100
 !D CLUSID STASET ENDSET ADD(ittional matching spheres count) MST(art) MEN(d)
       character (len=*), parameter :: DB2CLUSTER =
      &    '(2x,i6,x,i6,x,i6,x,i3,x,i3,x,i3)' !9000
 !D NUM CO x y z
 !reuse DB2RIGID
 !E
 !E does not get a format line 

[[Category:Formats]]