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.
- 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