========= EXAMPLES: ========= (A) #By default -shapovalov_lib_fixes_enable is off; it disables all my modifications and Rosetta runs the way it did before. -relax:fast -shapovalov_lib_fixes_enable (B) #The least smooth libraries: -relax:fast -shapovalov_lib_fixes_enable true -shap_rama_smooth_level 1 -shap_dun10_smooth_level 1 -shap_p_aa_pp_smooth_level 1 (C) #The least smooth libraries: -relax:fast -shapovalov_lib_fixes_enable -shap_rama_smooth_level lowest_smooth -shap_dun10_smooth_level lowest_smooth -shap_p_aa_pp_smooth_level low_smooth (D) #The most smooth libraries: -relax:fast -shapovalov_lib_fixes_enable -shap_rama_smooth_level 4 -shap_dun10_smooth_level 6 -shap_p_aa_pp_smooth_level 2 (E) #The most smooth libraries: -relax:fast -shapovalov_lib_fixes_enable -shap_rama_smooth_level highest_smooth -shap_dun10_smooth_level highest_smooth -shap_p_aa_pp_smooth_level high_smooth ===== MISC: ===== This work is in progress. No optimization was done for the weight parameters in front of each score term. I tested few fast relaxes, they proved to lower RMSD to natives. More significant testing, benchmarking and optimization is required. More possible bugs should be found. Rosetta community should benefit from making these new statistical potentials available and having several smoothness options. ======== DETAILS: ======== There is a global flag to introduce the new statistical potentials and bug fixes in the 'corrections' namespace: -shapovalov_lib_fixes_enable true. By default it is off: shapovalov_lib_fixes_enable is false. The shapovalov_lib_fixes_enable flag triggers activation of the following arguments in the 'corrections::shapovalov_lib' namespace and sets their default values: -shap_rama_enable -shap_rama_smooth_level -shap_rama_map -shap_rama_nogridshift -shap_dun10_enable -shap_dun10_smooth_level -shap_dun10_dir -shap_dun10_use_minus_log_P_ignore_P -shap_p_aa_pp_enable -shap_p_aa_pp_smooth_level -shap_p_aa_pp Once -shapovalov_lib_fixes_enable is true, there are 3 additional flags which are on by default and enforced. These flags enable/disable the new statistical potentials and their fixes in three categories: (1) New backbone-dependent Ramachandran map: -shap_rama_enable true (2) New backbone-dependent Rotamer Library, dun10: -shap_dun10_enable true (3) New backbone-dependent propensity map or P_aa_pp, -shap_p_aa_pp_enable true Some of these new libraries are based on newer, larger protein datasets. Some libraries might include enhauncements like what parameters they are based on and how they are reported such as scientific notation for decimal-point numbers and log values. For each of the three categories, a subset of libraries is available. There are default values. There are user-friendly argument values in interger format and user-friendly values in string, keyword format. (1) -shap_rama_smooth_level 4 (default) [1, 2, 3, 4] or -shap_rama_smooth_level highest_smooth (default) [lowest_smooth, lower_smooth, higher_smooth, highest_smooth] 1 <=> lowest_smooth 2 <=> lower_smooth 3 <=> higher_smooth 4 <=> highest_smooth (default) -shap_rama_smooth_level sets -shap_rama_map flag, as follows: 1 <=> lowest_smooth <=> -shap_rama_map scoring/score_functions/rama/shapovalov/kappa75/all.ramaProb 2 <=> lower_smooth <=> -shap_rama_map scoring/score_functions/rama/shapovalov/kappa50/all.ramaProb 3 <=> higher_smooth <=> -shap_rama_map scoring/score_functions/rama/shapovalov/kappa37.5/all.ramaProb 4 <=> highest_smooth <=> -shap_rama_map scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb (default) (2) -shap_dun10_smooth_level 3 (default) [1, 2, 3, 4, 5, 6] or -shap_dun10_smooth_level low_smooth (default) [lowest_smooth, lower_smooth, low_smooth, average_smooth, higher_smooth, highest_smooth] 1 <=> lowest_smooth 2 <=> lower_smooth 3 <=> low_smooth (default) 4 <=> average_smooth 5 <=> higher_smooth 6 <=> highest_smooth -shap_dun10_smooth_level sets -shap_dun10_dir flag, as follows: 1 <=> lowest_smooth <=> -shap_dun10_dir rotamer/shapovalov/StpDwn_0-0-0 2 <=> lower_smooth <=> -shap_dun10_dir rotamer/shapovalov/StpDwn_2-2-2 3 <=> low_smooth <=> -shap_dun10_dir rotamer/shapovalov/StpDwn_5-5-5 (default) 4 <=> average_smooth <=> -shap_dun10_dir rotamer/shapovalov/StpDwn_10-10-10 5 <=> higher_smooth <=> -shap_dun10_dir rotamer/shapovalov/StpDwn_20-20-20 6 <=> highest_smooth <=> -shap_dun10_dir rotamer/shapovalov/StpDwn_25-25-25 (3) -shap_p_aa_pp_smooth_level 2 (default) [1, 2] or -shap_p_aa_pp_smooth_level high_smooth (default) [low_smooth, high_smooth] 1 <=> low_smooth 2 <=> high_smooth (default) -shap_rama_smooth_level sets -shap_rama_map flag, as follows: 1 <=> low_smooth <=> -shap_p_aa_pp scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop 2 <=> high_smooth <=> -shap_p_aa_pp scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa50/a20.prop (default) In addition the user can specify a custom path to one of three library categories with: -shap_rama_map or -shap_dun10_dir or -shap_p_aa_pp, for example: -shap_rama_map scoring/score_functions/rama/shapovalov/kappa75/all.ramaProb -shap_dun10_dir rotamer/shapovalov/StpDwn_10-10-10 -shap_p_aa_pp scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop These settings will override -shap_rama_smooth_level or -shap_dun10_smooth_level or -shap_p_aa_pp_smooth_level argument values. March 11, 2015 April 27, 2015 Maxim Shapovalov