version: 2.4.1 git head: f99ac23 Params[ atom_table_feat_keep_sgn = false atom_table_feat_pow = 2.0 atom_table_features = [apRawValids, apRawInvalids, atomicHydrophobicity] average_feat_vectors = false avg_pow = 1.0 avg_weighted = false balance_class_weights = false balance_density = false balance_density_radius = 2.0 cache_datasets = false chains = keep check_vectors = false classifier = FastRandomForest classifier_train_stats = false clear_prim_caches = false clear_sec_caches = false collect_eval_vectors = false collect_only_once = true conserv_cloud_radius = 10.0 conservation_dirs = [] conservation_exponent = 1 crossval_threads = 1 dataset_base_dir = /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_data deep_surrounding = false delete_models = true delete_vectors = true electrostatics_dirs = [] eval_tolerances = [0, 1, 2, 4, 10, 99] extended_pocket_cutoff = 3.5 extra_features = [] fail_fast = false fail_on_conserv_seq_mismatch = false false_positive_cost = 2.0 feat_aa_properties = [] feat_asa_neigh_radius = 6.0 feat_asa_probe_radius = 1.4 feat_asa_probe_radius2 = 3.0 feat_crang_contact_dist = 3.0 feat_csv_columns = [] feat_csv_directories = [] feat_csv_ignore_missing = false feat_pmass_natoms = 70 feat_pmass_nsasp = 40 feat_pmass_radius = 11.0 feat_propensity_tables = SprintT1070 feat_stmotif_motifs = [C2H2, C4, C3H1, E1H2, C2H1, H3, D1H2, C3, D1H1, E1H1, C1H3, C2, H2] feat_stmotif_radius = 4.0 feat_stmotif_useradius = true feature_filters = [] feature_importances = false features = [chem, volsite, protrusion, bfactor] folds = 5 grid_cell_edge = 2.0 grid_cutoff_radius = 3.4 hopt_cache_labeled_points = false hopt_max_iterations = 1000 hopt_objective = DCA_4_0 hopt_optimizer = spearmint hopt_python_command = python hopt_spearmint_dir = hopt_train_only_once = false identify_peptides_by_labeling = false ignore_het_groups = [HOH, DOD, WAT, NAG, MAN, UNK, GLC, ABA, MPD, GOL, SO4, PO4] inner_classifier = FastRandomForest installDir = /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1 label_residues = true ligand_clustering_distance = 1.7 ligand_derived_point_labeling = true ligand_induced_volume_cutoff = 2.5 ligand_protein_contact_distance = 4.0 ligc_prot_dist = 5.5 load_conservation = false log_cases = true log_level = INFO log_scores_to_file = log_to_console = true log_to_file = true loop = 1 max_train_instances = 0 meta_classifier_iterations = 5 min_ligand_atoms = 5 model = default.model neighbourhood_radius = 6.0 neutral_points_margin = 5.5 out_file = out_format = keep out_prefix_date = false out_subdir = output_base_dir = /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output output_only_stats = false pair_hist_bins = 5 pair_hist_deep = true pair_hist_normalize = false pair_hist_radius = 6.0 pair_hist_smooth = false pair_hist_subsample_limit = 0 parallel = true plb_rescorer_atomic = false ploop_delete_runs = false ploop_zip_runs = false point_max_distfrom_pocket = 4.5 point_min_distfrom_protein = 2.5 point_sampler = SurfacePointSampler point_sampling_strategy = surface point_score_pow = 2.0 positive_def_ligtypes = [relevant] positive_point_ligand_distance = 2.6 pred_clustering_dist = 3.0 pred_min_cluster_size = 3 pred_point_threshold = 0.35 pred_protein_surface_cutoff = 3.5 predict_residues = false predictions = true probatp_res_transformer = residue/default_ProbabilityScoreTransformer.json probatp_transformer = default_ProbabilityScoreTransformer.json protr_hist_bins = 5 protr_hist_cumulative = false protr_hist_relative = false protrusion_radius = 10.0 r_generate_plots = true r_plot_stddevs = false r_threads = 2 randomize_seed = false rescorer = ModelBasedRescorer residue_point_score_pow = -1.0 residue_score_extra_dist = 2.0 residue_score_only_exposed = false residue_score_sum_to_avg = 0.0 residue_score_threshold = 1.0 residue_score_transform = NONE residue_table_features = [] rf_bagsize = 100 rf_depth = 0 rf_features = 0 rf_flatten = false rf_threads = 0 rf_trees = 100 sample_negatives_from_decoys = false sampling_multiplier = 3 score_pockets_by = p2rank score_point_limit = 0 seed = 42 selected_stats = [DCA_4_0, DCA_4_2, DCA_4_4, DCC_5_0, DCC_5_2, DSOR_02_0, DSOR_02_2, DSWO_05_0, DSWO_05_2, point_MCC, point_TPX, point_LOG_LOSS, AVG_DSO_SUCC, AVG_LIGCOV_SUCC, AVG_POCKETS, AVG_POCKET_SAS_POINTS, AVG_POCKET_SAS_POINTS_TRUE_POCKETS, TIME_MINUTES] smooth_representation = false smoothing_radius = 4.5 solvent_radius = 1.6 ss_cloud_radius = 10.0 stats_collect_predictions = true stats_curves = false stdout_timestamp = strict_inner_points = false subsampl_high_protrusion_negatives = false subsample = false supersample = false surface_additional_cutoff = 2.5 target_class_ratio = 0.1 target_class_weight_ratio = 0.1 tessellation = 2 threads = 4 train_lig_cutoff = 0.0 train_pockets = 9 train_protein_limit = 0 train_score_transformers = [] train_score_transformers_for_residues = false train_tessellation = 2 train_tessellation_negatives = 2 use_kdtree_cutout_sphere_thrashold = 150 use_only_positive_score = true vis_all_surface = false vis_copy_proteins = true vis_generate_proteins = true vis_highlight_ligands = false visualizations = true weight_dist_param = 4.5 weight_function = INV weight_power = 2.0 weight_sigma = 2.2 zip_log_file = false zip_visualizations = false zscoretp_res_transformer = residue/default_ZscoreTpTransformer.json zscoretp_transformer = default_ZscoreTpTransformer.json ]