Mol2db2 Format 2: Difference between revisions
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m (atoms and bonds) |
m (more) |
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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. | ||
notes: 17 children groups per line in current scheme. | |||
01234567890123456789012345678901234567890123456789012345678901234567890123456789 | 01234567890123456789012345678901234567890123456789012345678901234567890123456789 | ||
Line 40: | Line 42: | ||
M +CHA.RGEX +POLAR.SOL +APOLA.SOL SURFA.REA +TOTAL.SOL | 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 | A NUM NAME TYPEX +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA | ||
B NUM ATO ATO TYPE | B NUM ATO ATO TYPE | ||
X ATO CONFNU +XCO.OORD +YCO.ORD +ZCO.ORD | |||
G GRO #LIN #CH | |||
G GRO LIN #C CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN | |||
[[Category:Wishlists]] | [[Category:Wishlists]] |
Revision as of 17:51, 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
- GC 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] GC groupnum #lines #confs_total GC groupnum linenum #confs confnum [until column is full] C confnum #lines #children_total C confnum linenum #children childconf [until column is full] S #confnums confnum [more] data_about_this_conf
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 per line in current scheme.
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 #LIN #CH G GRO LIN #C CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN CGN