| 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 = <null> |
| out_format = keep |
| out_prefix_date = false |
| out_subdir = <null> |
| 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 |
| ] |
|
|
