Mol2db2 Format 2: Difference between revisions
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m (sets changed) |
m (done for now) |
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Line 17: | Line 17: | ||
*X xyz | *X xyz | ||
*G group | *G group | ||
* | *D group-conf mapping | ||
*C conformation | *C conformation | ||
*S sets | *S sets | ||
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G groupnum #lines #children_total | G groupnum #lines #children_total | ||
G groupnum linenum #children childgroup [until column is full] | 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 #lines #children_total | ||
C confnum linenum #children childconf [until column is full] | C confnum linenum #children childconf [until column is full] | ||
S setnum #lines # | S setnum #lines #confs_total [INPUT|MIX] broken omega_energy | ||
S setnum linenum # | 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. | 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. | ||
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8 confs/set per line. | 8 confs/set per line. | ||
1 2 3 4 5 6 7 | |||
01234567890123456789012345678901234567890123456789012345678901234567890123456789 | 01234567890123456789012345678901234567890123456789012345678901234567890123456789 | ||
M ZINCCODEX PROTCODEX ATO BON XYZXXX GRO CONFSX SETSXXXXX | M ZINCCODEX PROTCODEX ATO BON XYZXXX GRO CONFSX SETSXXXXX | ||
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G GRO #LI #CH | 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 | 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 #LIN #CONFS | ||
C CONFNO LINE # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS | C CONFNO LINE # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS | ||
S SETIDXXXX #LINES #CONFS | S SETIDXXXX #LINES #CONFS I C +ENER.GYX | ||
S SETIDXXXX LINENO # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS | S SETIDXXXX LINENO # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS | ||
[[Category:Wishlists]] | [[Category:Wishlists]] |
Revision as of 18:08, 15 April 2010
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
- M molecule (only 2 lines ever)
- A atoms
- B bond
- X xyz
- G group
- D group-conf mapping
- C conformation
- S sets
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.
1 2 3 4 5 6 7 01234567890123456789012345678901234567890123456789012345678901234567890123456789 M ZINCCODEX PROTCODEX ATO BON XYZXXX GRO CONFSX SETSXXXXX M +CHA.RGEX +POLAR.SOL +APOLA.SOL SURFA.REA +TOTAL.SOL A NUM NAME TYPEX +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