Daylight Summer School 1998, July 28-30, St. John's College, Santa Fe, NM
Daylight Worksheet - Rubicon
Rubicon, "Rule-Based Invention of
Conformations", generates 3D coordinates for a TDT file using a simple
set of rules, or rules generated from a training set with autorules.
- Generate 3D coordinates to the day1.tdt dataset created in
the PCModels exercise or use the ~mug/data/day1.tdt file.
- List Rubicon options
- List current settings
- Generate 3D coordinates with standard ruleset
rubicon < day1.tdt > day1.3d.tdt
- Generate 3D coordinates using rules generated from a training set and autorules. Obtain the training set from a substructural search of the medchem98demo
database and thorlookup to obtain the $D3D data.
- Open the medchem98demo database in merlin and search for a substructure from
the ~mug/data/day1.tdt dataset.
- Save the search results in a tdt file
- Use thorlookup to find the $D3D data
- generate a rule set
autorules < hitlist.tdt > output.rules
- Generate 3D structures for day1.tdt dataset using the new ruleset
Daylight Chemical Information Systems Inc.