Update BuildPackagedBindings to stage static and database files.
Adding staging of static files in packaged bindings package directory,
as opposed to module directory. Modifying packaging script to accept
target package directory instead of module directory. Adding
symlink-based staging of database files.
Adding initial nose-based binding tests, to be staged and run as
component of binding package. Adding configuration for nose-based tests.
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Adding peptoids to Rosetta
Despite the short commit title, this commit has been a long time coming. Most of the work was done by myself but it also includes contributions from Tim Craven and from Glenn Butterfoss. It was recently published in JACS (http://pubs.acs.org/doi/abs/10.1021/ja503776z).
**A Rotamer Library to Enable Modeling and Design of Peptoid Foldamers. P. Douglas Renfrew, Timothy W. Craven, Glenn L. Butterfoss, Kent Kirshenbaum, and Richard Bonneau, Journal of the American Chemical Society, Article ASAP
It contains...
-- more 100 residue type parameter files (and various patches) for peptoid side chains (only 2 are enabled by default as they are used in integration tests)
-- 2 peptoid rotamer libraries (there are more but they are large and can be downloaded separately)
-- updates to MM atom types and params to suport peptoids
-- updates to MM atom type names in metal ions
-- code and some basic movers to create score and minimize cyclic peptides and peptoids (this was done independently of the cyclic work Vikram has been doing and the 2 functionalities should be resolved at some point)
-- updated UnfoldedStateEnergyCalculator to work with peptoids and simple sequence profiles rather than only random fragments
-- added unfolded state energies for peptoids
-- updated and basically rewritten MakeRotLib protocol that works peptides and peptoids, and can distribute jobs via the MPI jobdistributors
-- added an assortment of pilot apps to work with peptoids
-- refactoring some of the rotamer library code to separate large classes in to multiple files
-- added a new rotamer library class for peptoid rotamer libraries which are dependent of the preceeding-omega, phi and psi torsion angles
-- some random little code clean ups
Unit tests: All pass
Integration tests:
Expected changes:
cyclization
make_rot_lib
ncaa_fixbb
unfolded_state_energy_calc
number_of_residuetypes
Cosmetic changes:
splice_in
splice_out
fold_and_dock
splice_seq_constraint
Saw some rounding changes on linux/gcc
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Add text parsing to BOND_TYPE lines
Instead of SDF-based numerical values, you can now use text
designations (like ARO or DELOCALIZED) to specify bond types
in params files.
Database files have been updated to use the new scheme, but
molfile_to_params.py will still output the old numeric values.
No substantive test changes expected.
(Standard numeric variablilty with ligand_dock_script encountered.)
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Move packaged binding generation scripts into packaged_bindings submodule.
Moving egg-packaged binding generation scripts into standalone
packaged_bindings submodule to support independant modification of
package-oriented bindings. Updating packaged binding script to support
unix-like platforms.
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Adding new app and integration test that prints the number of ResidueTypes in the default FA_STANDARD and CENTROID ResidueTypeSets.
Integration test status: [1]
The new number_of_residuetypes test will "fail".
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