Rubicon

Daylight's 3-D structure generator, available as the program Rubicon and the Rubicon Toolkit

 Applications:

• 3D structure generation from 2D connectivities
• 3D structure generation with contstraints from training set of known 3D structures
• 3D structure generation within a pharmacophore model

• establish geometric constraints in distance-space
• sample a conformation in that space
• embed it in 3-dimensions while minimizing bounds violations

The Rules/Constraints...

• Default Ruleset- $DY_ROOT/data/rubicon.rules
• Generate ruleset from a known set of 3D structures: autorules
• Make up your own, e.g pharamcophore model

RULENAME smarts (atomlist) bounds

DISTANCE c:o (1,2) 1.324 1.402 -Sets the bond length bounds for bonds betwee all aromatic carbon and oxygen to the range (1.324-1.402)

TORSION a1aaaaa1 (1,2,3,4) 0.0 0.0- Keeps aromatic rings planar

-RUBE_LIMITEVAL--Limit function evaluations allowed per minimization   (rubicon)
-RUBE_NCONFS --Number of conformations generated for each molecule   (rubicon)
-RUBE_OUTPUT_FORMAT-TDT ....... Write output in TDT format,PDB format

• default rule set, default options

rubicon [options] < input.tdt > output.tdt
 
• generate rule set from molecular training set

autorules [options] < input.tdt > output.rules
rubicon -RUBE_RULES output.rules <input.tdt>output.tdt