Files in momeara/RosettaFeatures
Tools for analyzing macromolecular feature distributions with Rosetta

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/analysis_support/align_features.py
R/compare_sample_sources.R R/features_analysis.R R/output_formats.R R/support-comparison_statistics.R R/support-coordinate_normalizations.R R/support-density_estimation.R R/support-ggplot2_geom_indicator.R R/support-instancer.R R/support-locate_rosetta_application.R R/support-polynomial_methods.R R/support-primary_modes.R R/support-query_sample_sources.R R/support-save_plots.R R/support-save_tables.R R/support-save_trees.R R/support-summary_statistics.R R/support-vector_math.R
R/sysdata.rda
R/utils.R README.md data-raw/output_formats.R
data-raw/output_formats.tsv
inst/scripts/analysis/instances/hbonds/AHdist_bbbb.R inst/scripts/analysis/instances/hbonds/AHdist_bbbb_seq_sep_2.R inst/scripts/analysis/instances/hbonds/AHdist_bbbb_seq_sep_m2.R inst/scripts/analysis/instances/hbonds/dAMOaPBA.R inst/scripts/analysis/instances/hbonds/hbond_AHD_pole.R inst/scripts/analysis/instances/hbonds/hbond_BB-BB_a-helix_seq_sep_3_chi_270_BAH_45.R inst/scripts/analysis/instances/hbonds/hbond_BB-BB_a-helix_seq_sep_3_chi_270_BAH_65.R inst/scripts/analysis/instances/hbonds/hbond_BB-BB_seq_sep_3_cosBAH_-0.2_to_0.1_AHdist_2.5_to_3.R inst/scripts/analysis/instances/hbonds/hbond_aSER_dBB_seq_sep_-1_chi_170_190.R inst/scripts/analysis/instances/residues/tyr.R inst/scripts/analysis/instances/rotamer_recovery/not_recovered.R inst/scripts/analysis/instances/rotamer_recovery/weird_salt_bridges.R inst/scripts/analysis/plots/EXAMPLE_PLOT.R inst/scripts/analysis/plots/backbone_geometry/bond_angles.R inst/scripts/analysis/plots/backbone_geometry/omega_angle.R inst/scripts/analysis/plots/backbone_geometry/on_grid.R inst/scripts/analysis/plots/backbone_geometry/rama_by_chi1.R inst/scripts/analysis/plots/backbone_geometry/rama_tight_kernel.R inst/scripts/analysis/plots/backbone_geometry/rama_zoom_THR.R inst/scripts/analysis/plots/backbone_geometry/rama_zoom_all_beta.R inst/scripts/analysis/plots/backbone_geometry/rama_zoom_helix_LEU_chi1-60.R inst/scripts/analysis/plots/backbone_geometry/ramachandran_by_residue_type_and_secondary_structure.R inst/scripts/analysis/plots/backbone_geometry/ramachandran_by_residue_type_and_secondary_structure_tight_kernel.R inst/scripts/analysis/plots/charge_charge_pairs/charge_charge_distances.R inst/scripts/analysis/plots/charge_charge_pairs/charge_charge_energies.R inst/scripts/analysis/plots/hbonds/AHdist_CXL_ARG_bfac20.R inst/scripts/analysis/plots/hbonds/SSdists_Sheet_O_HA.R inst/scripts/analysis/plots/hbonds/abnormalities/AHchi_AHD_pole_bump.R inst/scripts/analysis/plots/hbonds/abnormalities/fade_bump.R inst/scripts/analysis/plots/hbonds/bifurcated_at_acceptor.R inst/scripts/analysis/plots/hbonds/bifurcated_at_donor.R inst/scripts/analysis/plots/hbonds/chi_sinBAH_polar_scatter_AHdis2p0_by_chem_type_dcut.R inst/scripts/analysis/plots/hbonds/chi_sinBAH_polar_scatter_bb_by_ss.R inst/scripts/analysis/plots/hbonds/chi_sinBAH_polar_scatter_by_chem_type.R inst/scripts/analysis/plots/hbonds/chi_sinBAH_polar_scatter_by_chem_type_long_range.R inst/scripts/analysis/plots/hbonds/energy_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/ADdist_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/AHD_cdf_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/AHD_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/AHD_chem_type_comparison.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/AHchi_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/AHdist_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/AHdist_chem_type_with_rosetta_model.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/BAchi_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/DHdist_don_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/chi_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/chi_chem_type_long_range.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosAHD_acc_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosAHD_bbbb.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosAHD_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosAHD_chem_type_with_rosetta_model.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosAHD_don_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosAHD_qq_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosBAH_acc_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosBAH_bbbb.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosBAH_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosBAH_chem_type_AHcut2p4.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosBAH_chem_type_with_rosetta_model.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosBAH_dAH2p4cut_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/hdist_out_of_sp2plane.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/his_inplane.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/out_of_plane_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/quarter_BAchi_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d/quarter_chi_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_1d_conditional/ADdist_backbone_backbone_by_sequence_separation.R inst/scripts/analysis/plots/hbonds/geo_dim_1d_conditional/AHdist_backbone_backbone_by_sequence_separation.R inst/scripts/analysis/plots/hbonds/geo_dim_1d_conditional/AHdist_by_environmental_weight.R inst/scripts/analysis/plots/hbonds/geo_dim_1d_conditional/AHdist_by_rank.R inst/scripts/analysis/plots/hbonds/geo_dim_1d_conditional/AHdist_by_resolution.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/AHchi_AHD_eq_polar_density_PBAtoPBA.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/AHchi_AHD_eq_polar_density_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/angle_dependence_on_AHdist.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/chi_BAH_eq_polar_density.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/chi_BAH_eq_polar_density_HXLtoCXL.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/chi_BAH_eq_polar_density_HXLtoCXL_low_resolution.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/chi_BAH_eq_polar_density_PBAtoAMO_by_resolution.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/chi_BAH_eq_polar_density_PBAtoPBA.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/chi_BAH_eq_polar_density_PBAtoPBA_low_resolution.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/geo_dim_pairs.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/geo_dim_pairs_scatter_chem_type_by_sample_source.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/geo_dim_pairs_scatter_sample_source_by_chem_type.R inst/scripts/analysis/plots/hbonds/geo_dim_2d/hbond_backbone_correlation.R inst/scripts/analysis/plots/hbonds/geo_dim_2d_conditional/AHchi_AHD_eq_polar_density_salt_bridge_geometries.R inst/scripts/analysis/plots/hbonds/geo_dim_2d_conditional/chi_BAH_eq_polar_density_bb_by_ss.R inst/scripts/analysis/plots/hbonds/geo_dim_2d_conditional/sp2_BAH_chi_polar_density_beta_sheet.R inst/scripts/analysis/plots/hbonds/geo_dim_2d_conditional/sp2_BAH_chi_polar_density_by_seq_sep_dssp.R inst/scripts/analysis/plots/hbonds/geo_dim_3d/AHdist_sp2_dPBA_aPBA.R inst/scripts/analysis/plots/hbonds/hbond_geo_dim_scales.R
inst/scripts/analysis/plots/hbonds/hbond_plots.README
inst/scripts/analysis/plots/hbonds/hydroxyl_sites/HAHangle_HXL_as_acceptor.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/HAHangle_HXL_as_acceptor_and_donor.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/HXL_as_donor_hbond_chi.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/OHacceptor_chi.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/OHdonor.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/OHdonor_ADdist.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/OHdonor_AHdist.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/OHdonor_AHdist_morse_fit.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/RealBAH_HXL_as_acceptor.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/VBAH_VBchi_equal_area.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/cosB2AH_chem_type.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/cosB2AH_sp3_acceptors.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/cosBAH_hbacc_HXLAXL.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/cosBAH_hbacc_HXLAXL_hist.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/hydroxyl_overview.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/hydroxyl_proton_chi.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/sp3_acceptor_angle_geometry.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/tyr_as_donor_hbond_chi.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/tyr_hbond_chi.R inst/scripts/analysis/plots/hbonds/hydroxyl_sites/vBAH_chem_type.R inst/scripts/analysis/plots/hbonds/motif/scbb_bbbb_motifs_by_seq_sep.R inst/scripts/analysis/plots/hbonds/parametric_model/angle_kernels.R inst/scripts/analysis/plots/hbonds/parametric_model/cosAHD_beta_regression.R inst/scripts/analysis/plots/hbonds/parametric_model/cosBAH_regression.R inst/scripts/analysis/plots/hbonds/parametric_model/hbond_AHdist_cosAHD_regression.R inst/scripts/analysis/plots/hbonds/parametric_model/hbond_AHdist_regression.R inst/scripts/analysis/plots/hbonds/parametric_model/hbond_cosAHD_regression.R inst/scripts/analysis/plots/hbonds/parametric_model/hbond_null.R inst/scripts/analysis/plots/hbonds/parametric_model/hbond_regression.R inst/scripts/analysis/plots/hbonds/pilot/backbone_backbone_hbond.R inst/scripts/analysis/plots/hbonds/pilot/backbone_backbone_hbond_AHdist.R inst/scripts/analysis/plots/hbonds/pilot/backbone_backbone_hbond_chi.R inst/scripts/analysis/plots/hbonds/pilot/backbone_backbone_hbond_cosAHD.R inst/scripts/analysis/plots/hbonds/pilot/backbone_backbone_hbond_cosBAH.R inst/scripts/analysis/plots/hbonds/pilot/cosBAH_by_resolution.R inst/scripts/analysis/plots/hbonds/pilot/kmeans_cluster.R inst/scripts/analysis/plots/hbonds/summary/Sp2_character.R inst/scripts/analysis/plots/hbonds/summary/compute_heavy_atom_satisfaction.R inst/scripts/analysis/plots/hbonds/summary/hbond_site_propensity_to_donate_or_accept_hbonds.R inst/scripts/analysis/plots/hbonds/summary/num_hbonds.R inst/scripts/analysis/plots/hbonds/summary/num_hbonds_by_neighbor_count.R inst/scripts/analysis/plots/hbonds/summary/num_hbonds_normalized.R inst/scripts/analysis/plots/hbonds/summary/sidechain_propensity_to_donate_or_accept_hbonds.R inst/scripts/analysis/plots/loops/anchor_transform_correlation.R inst/scripts/analysis/plots/loops/single_dof_density_estimates.R inst/scripts/analysis/plots/loops/tau_angles.R inst/scripts/analysis/plots/loops/tau_qq_plot.R inst/scripts/analysis/plots/orbitals/eqpoldens/anion_pi_eqpoldens_scOrbOp_Haro_chiBDHO_cosDHO.R inst/scripts/analysis/plots/orbitals/eqpoldens/anion_pi_eqpoldens_scOrbOsp2_Haro_chiBAOH_cosAOH.R inst/scripts/analysis/plots/orbitals/eqpoldens/cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_.R inst/scripts/analysis/plots/orbitals/eqpoldens/cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH.R inst/scripts/analysis/plots/orbitals/eqpoldens/cation_pi_eqpoldens_scOrbCpi_Hpol_chiBDHO_cosDHO.R inst/scripts/analysis/plots/orbitals/eqpoldens/cation_pi_eqpoldens_scOrbCpi_scOrbNpi_chiBAOO_cosAOO.R inst/scripts/analysis/plots/orbitals/eqpoldens/pi_pi_eqpoldens_scOrbCpi_Haro_chiBAHD_AHD.R inst/scripts/analysis/plots/orbitals/eqpoldens/pi_pi_eqpoldens_scOrbCpi_Haro_chiBAOH_cosAOH.R inst/scripts/analysis/plots/orbitals/eqpoldens/pi_pi_eqpoldens_scOrbCpi_Haro_chiBDHO_cosDHO.R inst/scripts/analysis/plots/orbitals/eqpoldens/salt_bridge_eqpoldens_scOrbOsp2_Hpol_chiBAOH_cosAOH.R inst/scripts/analysis/plots/orbitals/eqpoldens/salt_bridge_eqpoldens_scOrbOsp2_Hpol_chiBDHO_cosDHO.R inst/scripts/analysis/plots/orbitals/heatmaps/cation_pi_heatmap_scOrbCpi_Hpol_by_angle_dist.R inst/scripts/analysis/plots/orbitals/heatmaps/cation_pi_heatmap_scOrbCpi_scOrbNpi_by_angle_dist.R inst/scripts/analysis/plots/orbitals/heatmaps/pi_pi_heatmap_scOrbCpi_Haro_by_angle_dist.R inst/scripts/analysis/plots/orbitals/heatmaps/pi_pi_heatmap_scOrbCpi_scOrbCpi_by_angle_dist.R inst/scripts/analysis/plots/orbitals/heatmaps/salt_bridge_heatmap_scOrbOsp2_Hpol_by_angle_dist.R inst/scripts/analysis/plots/orbitals/histograms/cation_pi_hist_scOrbCpi_Hpol_by_angle.R inst/scripts/analysis/plots/orbitals/histograms/cation_pi_hist_scOrbCpi_scOrbNpi_by_angle.R inst/scripts/analysis/plots/orbitals/histograms/pi_pi_hist_scOrbCpi_Haro_by_angle.R inst/scripts/analysis/plots/orbitals/histograms/pi_pi_hist_scOrbCpi_scOrbCpi_by_angle.R inst/scripts/analysis/plots/orbitals/histograms/salt_bridge_hist_scOrb_Hpol_by_angle.R inst/scripts/analysis/plots/orbitals/scatter_plots/geo_dim_orbitals.R inst/scripts/analysis/plots/pair_distances/residue_pair_distance_vs_num_neighbors_scatter.R inst/scripts/analysis/plots/pair_distances/residue_pair_distances_vs_neighbors.R inst/scripts/analysis/plots/rmsd/hbond_AHdist_vs_rmsd.R inst/scripts/analysis/plots/rmsd/score_vs_rmsd.R inst/scripts/analysis/plots/rotamer_geometry/ASN_conditional_on_short_range_backbone_hbond_formation.R inst/scripts/analysis/plots/rotamer_geometry/ASP_salt_bridge_in_helices.R inst/scripts/analysis/plots/rotamer_geometry/DENQ_by_secondary_structure.R inst/scripts/analysis/plots/rotamer_geometry/DN_by_dssp_lower_chi_tight_kernel.R inst/scripts/analysis/plots/rotamer_geometry/DN_by_lower_chi.R inst/scripts/analysis/plots/rotamer_geometry/DN_by_lower_chi_tight_kernel.R inst/scripts/analysis/plots/rotamer_geometry/DN_in_helix_by_lower_chi_tight_kernel.R inst/scripts/analysis/plots/rotamer_geometry/EQ_by_dssp_lower_chi_tight_kernel.R inst/scripts/analysis/plots/rotamer_geometry/EQ_by_lower_chi.R inst/scripts/analysis/plots/rotamer_geometry/EQ_by_lower_chi_tight_kernel.R inst/scripts/analysis/plots/rotamer_geometry/HTFY_by_dssp_lower_chi_tight_kernel.R inst/scripts/analysis/plots/rotamer_geometry/fa_dun_scores.R inst/scripts/analysis/plots/rotamer_geometry/rotamer_angles.R inst/scripts/analysis/plots/rotamer_geometry/rotamer_bins.R inst/scripts/analysis/plots/rotamer_geometry/rotamer_bins_ASN_psi-120_phi110.R inst/scripts/analysis/plots/rotamer_geometry/rotamer_chi_deviation.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_by_HBChemType.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_by_res_type.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_by_salt_bridge_geometry.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_by_secondary_structure.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_chi_by_secondary_structure.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_difference_by_res_type.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_differences_by_secondary_structure.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_hbond_geometry.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_hbond_geometry_2d_scatter.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_salt_bridge.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_salt_bridge_lys_CLX_psi_rho.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_summary.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_vs_dunbrack.R inst/scripts/analysis/plots/rotamer_recovery/rotamer_recovery_vs_score.R inst/scripts/analysis/plots/rotamer_recovery/salt_bridge_recovery.R inst/scripts/analysis/plots/rotamer_recovery/salt_bridge_recovery_rot_bin.R inst/scripts/analysis/plots/salt_bridges/bidentite_energy_gap.R inst/scripts/analysis/plots/salt_bridges/bidentite_hbond_asymmetry.R inst/scripts/analysis/plots/salt_bridges/bidentite_hbond_geometry.R inst/scripts/analysis/plots/salt_bridges/geo_dim_1d.R inst/scripts/analysis/plots/salt_bridges/geo_dim_2d.R inst/scripts/analysis/plots/salt_bridges/hbond_geo_dim_2d_by_salt_bridge_clusters.R inst/scripts/analysis/plots/salt_bridges/hbond_geo_dim_2d_dARG_aCXL_by_salt_bridge_clusters.R inst/scripts/analysis/plots/salt_bridges/lys_rotamer_hbond_interaction.R inst/scripts/analysis/plots/salt_bridges/psi_by_chemical_type.R inst/scripts/analysis/plots/salt_bridges/psi_rho_dARG_aCXL.R inst/scripts/analysis/plots/salt_bridges/salt_bridge_clusters.R inst/scripts/analysis/plots/salt_bridges/salt_bridge_psi_rho_dARG_aCXL.R inst/scripts/analysis/plots/salt_bridges/salt_bridge_scales.R inst/scripts/analysis/plots/sample_source_summary/bfactors.R inst/scripts/analysis/plots/sample_source_summary/residue_type_counts.R inst/scripts/analysis/plots/scores/component_scores.R inst/scripts/analysis/plots/scores/component_scores_one_body.R inst/scripts/analysis/plots/scores/component_scores_one_body_by_radius_of_gyration.R inst/scripts/analysis/plots/scores/component_scores_one_body_differences.R inst/scripts/analysis/plots/scores/hbond_score_vs_score.R inst/scripts/analysis/plots/scores/hbond_score_vs_score_bb_seqsep.R inst/scripts/analysis/plots/scores/hbond_scores.R inst/scripts/analysis/plots/scores/hbond_scores_by_chem_type.R inst/scripts/analysis/plots/scores/pro_close.R inst/scripts/analysis/plots/scores/rama_score.R inst/scripts/analysis/plots/scores/relative_score_in_environment.R inst/scripts/analysis/plots/scores/respair_sweep/respair_energies_sweep_AHdist.R inst/scripts/analysis/plots/scores/structure_component_scores.R inst/scripts/analysis/plots/scores/structure_scores.R inst/scripts/analysis/plots/scores/zero_score_cusp.R inst/scripts/analysis/plots/secondary_structure/SSDist_Sheet_AHdist.R inst/scripts/analysis/plots/secondary_structure/SSDist_Sheet_cosBAH.R inst/scripts/analysis/plots/secondary_structure/SSDists_Helix.R inst/scripts/analysis/plots/secondary_structure/SSDists_Helix_gt2bonds.R inst/scripts/analysis/plots/secondary_structure/SSDists_Sheet.R inst/scripts/analysis/plots/secondary_structure/SSDists_Sheet_O_CA.R inst/scripts/analysis/plots/secondary_structure/SSDists_Sheet_O_HA.R inst/scripts/analysis/plots/secondary_structure/SSDists_Sheet_O_N.R inst/scripts/analysis/plots/secondary_structure/SSDists_Sheet_O_O.R inst/scripts/analysis/plots/secondary_structure/SSDists_Sheet_gt2bonds.R inst/scripts/analysis/plots/secondary_structure/alpha_helices.R inst/scripts/analysis/plots/secondary_structure/apsa_summary.R inst/scripts/analysis/plots/secondary_structure/bb_by_pos_seq_sep.R inst/scripts/analysis/plots/secondary_structure/beta_mediated_hbonds.R inst/scripts/analysis/plots/secondary_structure/dssp_content.R inst/scripts/analysis/plots/secondary_structure/helical_i_p3.R inst/scripts/analysis/plots/secondary_structure/pi_helices.R inst/scripts/analysis/plots/sequence_recovery/sequence_recovery.R inst/scripts/analysis/plots/sequence_recovery/sequence_recovery_precision_vs_recall.R inst/scripts/analysis/plots/sequence_recovery/sequence_recovery_summary.R inst/scripts/analysis/plots/solvation/burial_of_secondary_structure_elements.R inst/scripts/analysis/plots/solvation/buried_unsatisfied.R inst/scripts/analysis/plots/solvation/dehydron.R inst/scripts/analysis/plots/solvation/number_of_neighbors.R inst/scripts/analysis/plots/solvation/radius_of_gyration.R inst/scripts/analysis/plots/solvation/solvation_vs_hbonding.R inst/scripts/analysis/plots/solvation/solvation_vs_hbonding_scatter.R inst/scripts/analysis/plots/structure_confidence/polar_site_temperature_factors_by_chem_type.R inst/scripts/analysis/statistics/hbonds/ADdist_chem_type_comparison.R inst/scripts/analysis/statistics/hbonds/ADdist_chem_type_solvent_exposure_comparison.R inst/scripts/analysis/statistics/hbonds/AHD_cdf_75.R inst/scripts/analysis/statistics/hbonds/AHD_chem_type_comparison.R inst/scripts/analysis/statistics/hbonds/AHD_chem_type_solvent_exposure_comparison.R inst/scripts/analysis/statistics/hbonds/AHdist_by_chem_type_signal.R inst/scripts/analysis/statistics/hbonds/AHdist_chem_type_comparison.R inst/scripts/analysis/statistics/hbonds/AHdist_chem_type_solvent_exposure_comparison.R inst/scripts/analysis/statistics/hbonds/AHdist_min_chem_type_with_params.R inst/scripts/analysis/statistics/hbonds/BAH_chem_type_comparison.R inst/scripts/analysis/statistics/hbonds/BAH_chem_type_solvent_exposure_comparison.R inst/scripts/analysis/statistics/hbonds/average_deviation.R inst/scripts/analysis/statistics/hbonds/chi_chem_type_comparison.R inst/scripts/analysis/statistics/hbonds/chi_chem_type_solvent_exposure_comparison.R inst/scripts/analysis/statistics/hbonds/geodim_mrf.R inst/scripts/analysis/statistics/hbonds/main_geom_conditional_comparisons.R inst/scripts/analysis/statistics/hbonds/main_geom_conditional_comparisons_minimal.R inst/scripts/analysis/statistics/hbonds/main_geom_conditional_statistics.R inst/scripts/analysis/statistics/hbonds/main_geom_dendrogram.R inst/scripts/analysis/statistics/hbonds/rosetta_sample_depth.R inst/scripts/analysis/statistics/rotamer_recovery/rotamer_recovery_summary.R
inst/scripts/benchmark/cache_features_db_into_testing_server_db.py
inst/scripts/benchmark/extract_features_db_from_testing_server_db.py
inst/scripts/benchmark/one_sample_source_general_analysis.json.TEMPLATE
inst/scripts/parameter_analysis/hbonds/methods/methods.R inst/scripts/parameter_analysis/hbonds/methods/rcpp_hbond_evaluation.R inst/scripts/parameter_analysis/hbonds/plot_hbond_contours.R inst/scripts/parameter_analysis/hbonds/plot_hbond_evaluation.R inst/scripts/parameter_analysis/hbonds/plot_hbond_projections.R inst/scripts/parameter_analysis/hbonds/plot_potential_function.R
inst/scripts/parameter_analysis/hbonds/poly_fit.py
inst/scripts/parameter_analysis/hbonds/refit_hbond_polynomials.py
inst/scripts/parameter_analysis/hbonds/shift_hbond_polynomial.py
inst/scripts/parameter_analysis/methods/methods.R man/compute_quantiles.Rd man/cross_validate_statistics.Rd man/date_code.Rd man/estimate_primary_modes_1d.Rd man/find_modes_in_density.Rd man/kolmogorov_smirnov_test.Rd man/major_long_coords.Rd man/prepare_feature_instances.Rd man/save_tables.Rd man/save_trees.Rd man/sliding_windows.Rd man/smooth_comparison_statistics.Rd man/smooth_kl_divergence.Rd man/spherical_normalization.Rd man/vector_crossprod.Rd man/vector_dihedral.Rd man/vector_distance.Rd man/vector_dotprod.Rd man/vector_normalize.Rd tests/testthat.R tests/testthat/test-config_file.R
tests/testthat/test-config_file__analysis_configuration.json
tests/testthat/test-geom_indicator.R
momeara/RosettaFeatures documentation built on May 22, 2017, 12:04 p.m.