bump dependencies

build.gradle

@@ -182,7 +182,7 @@ dependencies {
     implementation 'org.tukaani:xz:1.10'
     implementation 'com.github.luben:zstd-jni:1.5.6-6'
     implementation 'com.github.dpaukov:combinatoricslib3:3.4.0'
-    implementation 'us.ihmc:euclid:0.21.0'
+    implementation 'us.ihmc:euclid:0.22.0'
 
     implementation 'org.slf4j:slf4j-api:2.0.16'
     implementation 'org.slf4j:jul-to-slf4j:2.0.16'         // for netlib logging messages
@@ -202,7 +202,7 @@ dependencies {
 
     implementation fileTree(dir: 'lib', include: '*.jar')
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-engine:5.11.2'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.11.2'
+    testImplementation 'org.junit.jupiter:junit-jupiter-engine:5.11.3'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.11.3'
 
 }

misc/visualization/predict_1fbl_cif/1fbl.pdb_predictions.csv

@@ -0,0 +1,5 @@
+name     ,  rank,   score, probability, sas_points, surf_atoms,   center_x,   center_y,   center_z, residue_ids, surf_atom_ids
+pocket1  ,     1,    9.77,       0.525,         70,         40,    70.5274,    83.4375,   -11.5099, A_103 A_180 A_181 A_182 A_183 A_184 A_186 A_214 A_215 A_218 A_219 A_222 A_226 A_227 A_228 A_238 A_239 A_240, 32 33 651 658 659 664 670 676 679 692 700 929 934 938 942 943 958 959 960 961 962 963 971 972 989 991 992 993 994 1016 1026 1033 1035 1036 1106 1112 1118 1119 1122 1124
+pocket2  ,     2,    3.04,       0.101,         37,         18,    89.2267,    98.6419,    26.7534, A_337 A_339 A_341 A_348 A_357 A_360 A_362 A_366 A_367 A_368 A_400 A_402, 1890 1891 1909 1910 1926 1991 2064 2091 2092 2109 2144 2150 2151 2161 2163 2426 2439 2444
+pocket3  ,     3,    2.94,       0.095,         34,         15,    61.1038,    70.7493,   -13.6472, A_119 A_156 A_160 A_162 A_164 A_168 A_191 A_194 A_196, 171 172 173 472 499 501 514 515 532 560 728 730 746 760 761
+pocket4  ,     4,    1.87,       0.037,         27,         17,    90.8572,    95.9207,    10.7905, A_290 A_291 A_293 A_304 A_320 A_321 A_340 A_353 A_354, 1488 1489 1490 1497 1499 1513 1619 1620 1756 1757 1766 1769 1917 2030 2031 2034 2035

misc/visualization/predict_1fbl_cif/params.txt

@@ -0,0 +1,195 @@
+version: 2.5-dev.12
+git head: aae633f5
+
+Params[
+  apoholo_use_for_eval = false
+  apoholo_use_for_train = false
+  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 = C:\PHD\WORKSPACE\P2RANK\p2rank-private\distro\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
+  fpocket_command = fpocket
+  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 = C:\PHD\WORKSPACE\P2RANK\p2rank-private\distro
+  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
+  loaded_pockets_limit = 0
+  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
+  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 = C:\PHD\WORKSPACE\P2RANK\p2rank-private\distro\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_batch_prediction = true
+  rf_depth = 0
+  rf_ensure_leaves_normalized = false
+  rf_features = 0
+  rf_flatten = false
+  rf_flatten_as_legacy = true
+  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_10_0, DCC_10_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 = 17
+  train_lig_cutoff = 0.0
+  train_pockets = 9
+  train_protein_limit = 0
+  train_random_rotated_copies = 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
+  use_optimized_surface = 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
+]

misc/visualization/predict_1fbl_cif/visualizations/1fbl.pdb.pml

@@ -0,0 +1,75 @@
+
+        from pymol import cmd,stored
+
+        set depth_cue, 1
+        set fog_start, 0.4
+
+        set_color b_col, [36,36,85]
+        set_color t_col, [10,10,10]
+        set bg_rgb_bottom, b_col
+        set bg_rgb_top, t_col      
+        set bg_gradient
+
+        set  spec_power  =  200
+        set  spec_refl   =  0
+
+        load "data/1fbl.pdb", protein
+        create ligands, protein and organic
+        select xlig, protein and organic
+        delete xlig
+
+        hide everything, all
+
+        color white, elem c
+        color bluewhite, protein
+        #show_as cartoon, protein
+        show surface, protein
+        #set transparency, 0.15
+
+        show sticks, ligands
+        set stick_color, magenta
+
+
+
+
+        # SAS points
+
+        load "data/1fbl.pdb_points.pdb.gz", points
+        hide nonbonded, points
+        show nb_spheres, points
+        set sphere_scale, 0.2, points
+        cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
+
+
+        stored.list=[]
+        cmd.iterate("(resn STP)","stored.list.append(resi)")    # read info about residues STP
+        lastSTP=stored.list[-1] # get the index of the last residue
+        hide lines, resn STP
+
+        cmd.select("rest", "resn STP and resi 0")
+
+        for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
+        for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
+        for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
+        for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
+
+
+
+        set_color pcol1 = [0.361,0.576,0.902]
+select surf_pocket1, protein and id [991,992,993,994,1033,1035,1036,1026,664,670,676,971,679,958,959,960,961,962,963,938,942,972,934,929,943,989,1016,32,692,700,33,1118,1119,658,659,1122,1124,651,1112,1106] 
+set surface_color,  pcol1, surf_pocket1 
+set_color pcol2 = [0.490,0.278,0.702]
+select surf_pocket2, protein and id [2109,2144,2091,2092,1991,2150,2151,2161,2163,2444,1891,2426,2439,1910,2064,1909,1890,1926] 
+set surface_color,  pcol2, surf_pocket2 
+set_color pcol3 = [0.902,0.361,0.682]
+select surf_pocket3, protein and id [760,761,730,728,746,173,514,515,171,172,501,472,499,532,560] 
+set surface_color,  pcol3, surf_pocket3 
+set_color pcol4 = [0.702,0.408,0.278]
+select surf_pocket4, protein and id [1488,1497,1513,1619,1620,1769,1490,1756,1757,1489,1766,1917,1499,2030,2031,2034,2035] 
+set surface_color,  pcol4, surf_pocket4 
+
+
+        deselect
+
+        orient
+