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version: 2.4.1 |
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git head: f99ac23 |
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Params[ |
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atom_table_feat_keep_sgn = false |
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atom_table_feat_pow = 2.0 |
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atom_table_features = [apRawValids, apRawInvalids, atomicHydrophobicity] |
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average_feat_vectors = false |
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avg_pow = 1.0 |
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avg_weighted = false |
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balance_class_weights = false |
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balance_density = false |
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balance_density_radius = 2.0 |
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cache_datasets = false |
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chains = keep |
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check_vectors = false |
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classifier = FastRandomForest |
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classifier_train_stats = false |
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clear_prim_caches = false |
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clear_sec_caches = false |
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collect_eval_vectors = false |
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collect_only_once = true |
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conserv_cloud_radius = 10.0 |
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conservation_dirs = [] |
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conservation_exponent = 1 |
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crossval_threads = 1 |
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dataset_base_dir = /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_data |
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deep_surrounding = false |
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delete_models = true |
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delete_vectors = true |
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electrostatics_dirs = [] |
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eval_tolerances = [0, 1, 2, 4, 10, 99] |
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extended_pocket_cutoff = 3.5 |
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extra_features = [] |
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fail_fast = false |
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fail_on_conserv_seq_mismatch = false |
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false_positive_cost = 2.0 |
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feat_aa_properties = [] |
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feat_asa_neigh_radius = 6.0 |
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feat_asa_probe_radius = 1.4 |
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feat_asa_probe_radius2 = 3.0 |
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feat_crang_contact_dist = 3.0 |
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feat_csv_columns = [] |
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feat_csv_directories = [] |
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feat_csv_ignore_missing = false |
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feat_pmass_natoms = 70 |
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feat_pmass_nsasp = 40 |
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feat_pmass_radius = 11.0 |
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feat_propensity_tables = SprintT1070 |
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feat_stmotif_motifs = [C2H2, C4, C3H1, E1H2, C2H1, H3, D1H2, C3, D1H1, E1H1, C1H3, C2, H2] |
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feat_stmotif_radius = 4.0 |
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feat_stmotif_useradius = true |
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feature_filters = [] |
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feature_importances = false |
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features = [chem, volsite, protrusion, bfactor] |
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folds = 5 |
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grid_cell_edge = 2.0 |
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grid_cutoff_radius = 3.4 |
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hopt_cache_labeled_points = false |
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hopt_max_iterations = 1000 |
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hopt_objective = DCA_4_0 |
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hopt_optimizer = spearmint |
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hopt_python_command = python |
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hopt_spearmint_dir = |
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hopt_train_only_once = false |
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identify_peptides_by_labeling = false |
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ignore_het_groups = [HOH, DOD, WAT, NAG, MAN, UNK, GLC, ABA, MPD, GOL, SO4, PO4] |
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inner_classifier = FastRandomForest |
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installDir = /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1 |
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label_residues = true |
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ligand_clustering_distance = 1.7 |
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ligand_derived_point_labeling = true |
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ligand_induced_volume_cutoff = 2.5 |
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ligand_protein_contact_distance = 4.0 |
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ligc_prot_dist = 5.5 |
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load_conservation = false |
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log_cases = true |
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log_level = INFO |
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log_scores_to_file = |
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log_to_console = true |
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log_to_file = true |
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loop = 1 |
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max_train_instances = 0 |
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meta_classifier_iterations = 5 |
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min_ligand_atoms = 5 |
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model = default.model |
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neighbourhood_radius = 6.0 |
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neutral_points_margin = 5.5 |
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out_file = <null> |
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out_format = keep |
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out_prefix_date = false |
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out_subdir = <null> |
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output_base_dir = /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output |
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output_only_stats = false |
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pair_hist_bins = 5 |
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pair_hist_deep = true |
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pair_hist_normalize = false |
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pair_hist_radius = 6.0 |
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pair_hist_smooth = false |
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pair_hist_subsample_limit = 0 |
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parallel = true |
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plb_rescorer_atomic = false |
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ploop_delete_runs = false |
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ploop_zip_runs = false |
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point_max_distfrom_pocket = 4.5 |
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point_min_distfrom_protein = 2.5 |
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point_sampler = SurfacePointSampler |
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point_sampling_strategy = surface |
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point_score_pow = 2.0 |
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positive_def_ligtypes = [relevant] |
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positive_point_ligand_distance = 2.6 |
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pred_clustering_dist = 3.0 |
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pred_min_cluster_size = 3 |
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pred_point_threshold = 0.35 |
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pred_protein_surface_cutoff = 3.5 |
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predict_residues = false |
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predictions = true |
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probatp_res_transformer = residue/default_ProbabilityScoreTransformer.json |
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probatp_transformer = default_ProbabilityScoreTransformer.json |
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protr_hist_bins = 5 |
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protr_hist_cumulative = false |
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protr_hist_relative = false |
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protrusion_radius = 10.0 |
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r_generate_plots = true |
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r_plot_stddevs = false |
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r_threads = 2 |
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randomize_seed = false |
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rescorer = ModelBasedRescorer |
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residue_point_score_pow = -1.0 |
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residue_score_extra_dist = 2.0 |
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residue_score_only_exposed = false |
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residue_score_sum_to_avg = 0.0 |
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residue_score_threshold = 1.0 |
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residue_score_transform = NONE |
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residue_table_features = [] |
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rf_bagsize = 100 |
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rf_depth = 0 |
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rf_features = 0 |
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rf_flatten = false |
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rf_threads = 0 |
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rf_trees = 100 |
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sample_negatives_from_decoys = false |
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sampling_multiplier = 3 |
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score_pockets_by = p2rank |
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score_point_limit = 0 |
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seed = 42 |
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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] |
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smooth_representation = false |
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smoothing_radius = 4.5 |
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solvent_radius = 1.6 |
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ss_cloud_radius = 10.0 |
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stats_collect_predictions = true |
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stats_curves = false |
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stdout_timestamp = |
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strict_inner_points = false |
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subsampl_high_protrusion_negatives = false |
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subsample = false |
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supersample = false |
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surface_additional_cutoff = 2.5 |
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target_class_ratio = 0.1 |
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target_class_weight_ratio = 0.1 |
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tessellation = 2 |
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threads = 65 |
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train_lig_cutoff = 0.0 |
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train_pockets = 9 |
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train_protein_limit = 0 |
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train_score_transformers = [] |
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train_score_transformers_for_residues = false |
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train_tessellation = 2 |
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train_tessellation_negatives = 2 |
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use_kdtree_cutout_sphere_thrashold = 150 |
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use_only_positive_score = true |
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vis_all_surface = false |
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vis_copy_proteins = true |
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vis_generate_proteins = true |
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vis_highlight_ligands = false |
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visualizations = true |
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weight_dist_param = 4.5 |
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weight_function = INV |
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weight_power = 2.0 |
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weight_sigma = 2.2 |
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zip_log_file = false |
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zip_visualizations = false |
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zscoretp_res_transformer = residue/default_ZscoreTpTransformer.json |
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zscoretp_transformer = default_ZscoreTpTransformer.json |
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] |
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