Daylight v4.9
Release Date: 1 February 2008


rubicon - rule-based invention of conformations

Unix Synopsis

rubicon [options]


For a complete description of the Rubicon algorithm and options, see the "Rubicon Reference Manual." The following is an excerpt from its "Introduction" chapter:

"Rubicon" stands for "RUle-Based Invention of CONformations". Rubicon is a distance-geometry method which produces 3-D conformations given chemical structures with only connectivity specified. Distance-geometry methods randomly sample conformations and are particularly powerful for problems dealing with molecular matching and flexibility. The method has three basic parts: establishing geometric constraints in distance-space, sampling a conformation in that space, and embedding it in 3-dimensions while minimizing bounds violations.

One of the fundamental difficulties with most distance distance geometry programs is that they have a very naive view of chemical geometry. Also, the chemical intelligence that they do have is typically hard coded into the program and is very difficult to improve upon. Rubicon addresses this problem by employing a soft, rule-based method for establishing geometric constraints which is based on a powerful language for describing chemical patterns (SMARTS).


-HELP or -help
Show syntax and help instructions
-OPTIONS or -options
Show options summary (this info)
-SETTINGS or -settings
Show options settings in effect
Acceptable RMS of gradient vector for convergence
Acceptable maximum distance violation, Angstroms
Acceptable maximum volume violation, cubic Angstroms
Effective machine accuracy
(Don't) apply VDW bumping to nonbonded 1-4 distances
-RUBE_DEBUG <flag>
QUIET ..... no output on standard error
TERSE ..... only show progress
ERRORS .... also show error messages
WARNINGS .. also show warning messages
NOTES ..... also show notes
DEBUG ..... also show debugging output
VERBOSE ... also show all debugging output
(Don't) enforce chirality in conformation filter.
-RUBE_FILTER_SLOP <tolerance>
Minimum distance between equivalent atoms to consider conformations non-identical, Angstroms (off if 0.0).
SMARTS used for conformation filter atom matching. If "USMILES", unique SMILES is used as target.
ALL ....... include all hydrogens
SOME ...... include specified hydrogens
NONE ...... suppress all normal hydrogens
Limit function evaluations allowed per minimization
-RUBE_NCONFS <nconfs>
Number of conformations generated for each molecule
TDT ....... Write output in TDT format
PDB ....... write output in PDB format
-RUBE_RULES <rulefiles>
Name(s) of Rubicon rule file(s) Rubicon rule file names typically end .rules Quote if multiple, e.g. -RUBE_RULES "a.rules b.rules"
Add $D3DG generation item with runid to TDT output. If set to "NONE", $D3DG item will not be output.
-RUBE_SEED <seed>
Random number seed in range 0 to 900000000
Number of trials per conformation
Add smoothed distance bounds matrix and list of volume bounds to output (TDT output only).

Return Value

Returns status zero if all goes well, or non-zero if a problem is detected.

Related Topics

autorules(1) licensing(5)



Daylight License

programs: rubicon