Mol2db2 Format 2

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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. mol2db2 format features that are actually implemented so far are marked [x]

New Features

implemented

  • Real Atom Types and Bond Information [x]
  • 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]
  • support for clusters of conformations [x]
  • arbitrary information to be written into output mol2 file (5th and above M lines) [x]

wished

  • Per-conformation per-atom partial charge & solvation information to support internal energies
  • Aliphatic ring movements?
  • 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
  • valence for each atom

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

File Format

current plan for the file format

  • 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