CHOMP: Documentation

From SHARPEN

• Tutorial scripts
• Overall CHOMP organization
• Original PyCHOMP API For SHARPEN versions < 1.3
• Old PyCHOMP API walkthrough
• PyCHOMP API For SHARPEN versions >= 1.3
• Autogenerated Doxygen Documentation SHARPEN 1.5

READMEs

• Planned PyCHOMP API changes
• Optimization classes
• Code generation README
• Updating the CHOMP python wrapper
• Hypergraph implementation
• Backbone remodeling
• dunbrack.bbdep

Energy Function Related

• Energy function README
• New Energy Functions organization page
• CHOMP energy function tables
• Adding an individual energy term
• CHOMP tables introduction
• Rosetta hydrogen bonding potential
• Non-pairwise aspects of the Rosetta energy function

Expanding SHARPEN with new residues

Amino Acid Variants

• Understanding the residue description py file
• New Amino Acids
• Updating Intra-residue-vdw tables

Small Molecules

• Parameterize a new molecule for the Rosetta force field
• Current SmallMol Limitations
• Small Molecule List

An entirely new class of molecule (e.g. a new polymer)

• Nucleic Acids
• Adding a new molecule to CHOMP