Mol2db2 Format 2: Difference between revisions
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S setnum #lines #confs_total broken hydrogens omega_energy | S setnum #lines #confs_total broken hydrogens omega_energy | ||
S setnum linenum #confs confs [until full column] | S setnum linenum #confs confs [until full column] | ||
D clusternum setstart setend #additionalmatching | D clusternum setstart setend matchstart matchend #additionalmatching | ||
D matchnum color x y z | D matchnum color x y z | ||
E | E | ||
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S SETIDX #LINES #CO C H +ENERGY.XXX | S SETIDX #LINES #CO C H +ENERGY.XXX | ||
S SETIDX LINENO # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS | S SETIDX LINENO # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS | ||
D CLUSID STASET ENDSET ADD | D CLUSID STASET ENDSET MST MEN ADD | ||
D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX | D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX | ||
E | E | ||
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S %6d %6d %3d %1d %1d %+11.3f\n | S %6d %6d %3d %1d %1d %+11.3f\n | ||
S %6d %6d %1d %6d %6d %6d %6d %6d %6d %6d %6d\n | S %6d %6d %1d %6d %6d %6d %6d %6d %6d %6d %6d\n | ||
D %6d %6d %6d %3d\n | D %6d %6d %6d %3d %3d %3d\n | ||
D %3d %2d %+9.4f %+9.4f %+9.4f\n | D %3d %2d %+9.4f %+9.4f %+9.4f\n | ||
E\n | E\n | ||
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& 1x,i6,1x,i6,1x,i6,1x,i6) | & 1x,i6,1x,i6,1x,i6,1x,i6) | ||
!D CLUSID STARTSETX ENDSETXXX ADD | !D CLUSID STARTSETX ENDSETXXX ADD | ||
9000 format(2x,i6,x,i6,x,i6,x,i3) | 9000 format(2x,i6,x,i6,x,i6,x,i3,x,i3,x,i3) | ||
!D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX | !D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX | ||
!re-use 6000 | !re-use 6000 |
Revision as of 20:06, 24 May 2011
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]
- 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]
- 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
- arbitrary information to be written into output mol2 file (5th and above M lines) [x]
the following represents the 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 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 #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 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