Mol2db2 Format 2: Difference between revisions
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m (mmm's suggestion) |
(preliminary file format) |
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Line 10: | Line 10: | ||
*specified rigid component override (and better rules for finding non-ring rigid components) | *specified rigid component override (and better rules for finding non-ring rigid components) | ||
*per molecule pKa | *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 | |||
*C conformation | |||
*S sets | |||
M name #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 #children childgroup [more] #confs confnum [more confnums] | |||
C confnum #children childconf [more] | |||
S #confnums confnum [more] data_about_this_conf | |||
[[Category:Wishlists]] | [[Category:Wishlists]] |
Revision as of 00:36, 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
- C conformation
- S sets
M name #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 #children childgroup [more] #confs confnum [more confnums] C confnum #children childconf [more] S #confnums confnum [more] data_about_this_conf