CHOMP: Python modules
From SHARPEN
The tutorial scripts show the nitty-gritty aspects of programming SHARPEN in python. See also the video tutorials. Many of these steps can be lumped into useful, modular, routines. By abstracting these routines into a set of topical modules it becomes possible to write very succinct high-level python scripts. Keeping these scripts up to date is a challenge, but a worthy one because the net effect is a very convenient middle layer for using SHARPEN.
| Basic Scripts | |
| chomp_setup.py | basic CHOMP initialization |
| chomp_IO.py | reading and writing to disk |
| chomp_systems.py | merging, renumbering, embedding systems |
| chomp_scoring.py | scoring and energy decomposition |
| chomp_repack.py | shortcuts for repacking and repacking preparation |
| chomp_pdbwizard.py | pdb parsing tools (interactive) |
| chomp_egtools.py | helper routines for applying graph algorithms to optimization |
| pdb_remediation.py | implement atom renaming rules |
| split_pdb_chains.py | decompose a pdb file into component chains |
| Manipulating the backbone | |
| chomp_ramahist.py | a histogram with Ramachandran propensities |
| chomp_phipsi.py | functions for manipulating the backbone dihedrals |
| chomp_dof.py | functions for rotations and translations |
| chomp_reloop.py | loop rebuilding high level functions |
| Hierarchical Optimization | |
| chomp_poses.py | variables needed for routines on discrete backbone blocks and poses |
| chomp_graphs.py | tools for manipulating a hypergraph |
| chomp_sets.py | working with sets |
| Analysis | |
| chomp_metrics.py | functions for quantifying structural deviation |
| Rotamer tools | |
| backbone_independent.py | a set of backbone independent rotamers |
