diff --git a/tests/fixtures/test_pdb.json b/tests/fixtures/test_pdb.json index 1bead08b..30684669 100644 --- a/tests/fixtures/test_pdb.json +++ b/tests/fixtures/test_pdb.json @@ -163,7 +163,7 @@ "kind": "Global Symmetry" } ], - "rcsb_struct_symmetry_provenance_code": "biojava-7.0.1", + "rcsb_struct_symmetry_provenance_code": "biojava-structure-6.0.5", "rcsb_struct_symmetry_lineage": [ { "id": "Global Symmetry.Cyclic.C3", @@ -188,7 +188,7 @@ ], "rcsb_latest_revision": { "major_revision": 1, - "minor_revision": 4 + "minor_revision": 3 } } }, @@ -701,6 +701,7 @@ "name": "Mogul bond angle outlier", "ordinal": 3, "provenance_source": "PDB", + "reference_scheme": "PDB entity", "type": "MOGUL_ANGLE_OUTLIER", "feature_value": [ { @@ -728,6 +729,7 @@ "name": "Mogul bond distance outlier", "ordinal": 4, "provenance_source": "PDB", + "reference_scheme": "PDB entity", "type": "MOGUL_BOND_OUTLIER", "feature_value": [ { @@ -1000,18 +1002,86 @@ "assignment_version": "V1.0", "comp_id": "Y3P", "description": "Mogul bond angle outlier in Y3P instance J model 1", - "feature_id": "MOGUL_BOND_OUTLIER_1", + "feature_id": "MOGUL_ANGLE_OUTLIER_1", + "name": "Mogul bond angle outlier", + "ordinal": 49, + "provenance_source": "PDB", + "type": "MOGUL_ANGLE_OUTLIER", + "feature_value": [ + { + "comp_id": "Y3P", + "details": "O2,C1,C2 angle=117.31 Z=-2.41", + "reference": 120.08, + "reported": 117.31, + "uncertainty_estimate": -2.41, + "uncertainty_estimate_type": "Z-Score" + }, + { + "comp_id": "Y3P", + "details": "O3,C2,C1 angle=115.41 Z=2.31", + "reference": 114.01, + "reported": 115.41, + "uncertainty_estimate": 2.31, + "uncertainty_estimate_type": "Z-Score" + }, + { + "comp_id": "Y3P", + "details": "O4,C4,C3 angle=116.13 Z=-2.44", + "reference": 123.89, + "reported": 116.13, + "uncertainty_estimate": -2.44, + "uncertainty_estimate_type": "Z-Score" + } + ] + }, + { + "assignment_version": "V1.0", + "comp_id": "Y3P", + "description": "Mogul bond distance outlier in Y3P instance J model 1", + "feature_id": "MOGUL_BOND_OUTLIER_2", "name": "Mogul bond distance outlier", - "ordinal": 51, + "ordinal": 50, "provenance_source": "PDB", "type": "MOGUL_BOND_OUTLIER", "feature_value": [ { "comp_id": "Y3P", - "details": "O3,C2 angle=1.39 Z=3.43", - "reference": 1.32, + "details": "O1,C1 angle=1.24 Z=-2.01", + "reference": 1.3, + "reported": 1.24, + "uncertainty_estimate": -2.01, + "uncertainty_estimate_type": "Z-Score" + }, + { + "comp_id": "Y3P", + "details": "C2,C1 angle=1.55 Z=5.59", + "reference": 1.48, + "reported": 1.55, + "uncertainty_estimate": 5.59, + "uncertainty_estimate_type": "Z-Score" + }, + { + "comp_id": "Y3P", + "details": "O2,C1 angle=1.31 Z=3.39", + "reference": 1.22, + "reported": 1.31, + "uncertainty_estimate": 3.39, + "uncertainty_estimate_type": "Z-Score" + }, + { + "comp_id": "Y3P", + "details": "C3,C2 angle=1.32 Z=-2.21", + "reference": 1.36, + "reported": 1.32, + "uncertainty_estimate": -2.21, + "uncertainty_estimate_type": "Z-Score" + }, + { + "comp_id": "Y3P", + "details": "O3,C2 angle=1.39 Z=2.06", + "reference": 1.34, "reported": 1.39, - "uncertainty_estimate": 3.43, + "uncertainty_estimate": 2.06, "uncertainty_estimate_type": "Z-Score" } ] @@ -1038,12 +1108,12 @@ }, { "comp_id": "Y3P", - "count": 0, + "count": 3, "type": "MOGUL_ANGLE_OUTLIER" }, { "comp_id": "Y3P", - "count": 1, + "count": 5, "type": "MOGUL_BOND_OUTLIER" }, { @@ -1072,14 +1142,14 @@ "is_best_instance": "N", "is_subject_of_investigation": "Y", "is_subject_of_investigation_provenance": "Author", - "mogul_angle_outliers": 0, - "mogul_angles_rmsz": 0.56, - "mogul_bond_outliers": 1, - "mogul_bonds_rmsz": 2.75, + "mogul_angle_outliers": 3, + "mogul_angles_rmsz": 1.62, + "mogul_bond_outliers": 5, + "mogul_bonds_rmsz": 2.76, "ranking_model_fit": 0.7558, - "ranking_model_geometry": 0.2397, + "ranking_model_geometry": 0.1111, "score_model_fit": -0.954, - "score_model_geometry": 0.7063, + "score_model_geometry": 1.5147, "stereo_outliers": 0, "type": "RCSB_LIGAND_QUALITY_SCORE_2021" } @@ -1167,7 +1237,7 @@ "rcsb_id": "2FBW.J", "rcsb_latest_revision": { "major_revision": 2, - "minor_revision": 0 + "minor_revision": 1 } } }, @@ -4594,12 +4664,31 @@ } ] }, + { + "assignment_version": "V1.0", + "description": "Some atom coordinates in this residue are reported with zero-occupancy in model 1", + "feature_id": "1", + "name": "atom coordinates with zero occupancy", + "ordinal": 161, + "provenance_source": "PDB", + "type": "ZERO_OCCUPANCY_ATOM_XYZ", + "feature_positions": [ + { + "beg_seq_id": 355, + "end_seq_id": 355 + }, + { + "beg_seq_id": 447, + "end_seq_id": 447 + } + ] + }, { "assignment_version": "V1.0", "description": "Molprobity rotamer outlier in instance E model 1", "feature_id": "ROTAMER_OUTLIER_1", "name": "Molprobity rotamer outlier", - "ordinal": 168, + "ordinal": 171, "provenance_source": "PDB", "type": "ROTAMER_OUTLIER", "feature_positions": [ @@ -4622,7 +4711,7 @@ "description": "Real space density correlation value < 0.65 in instance E model 1", "feature_id": "RSCC_OUTLIER_2", "name": "Real space density correlation value < 0.65", - "ordinal": 169, + "ordinal": 172, "provenance_source": "PDB", "type": "RSCC_OUTLIER", "feature_positions": [ @@ -4636,7 +4725,7 @@ "description": "Real space R-value Z score > 2 in instance E model 1", "feature_id": "RSRZ_OUTLIER_3", "name": "Real space R-value Z score > 2", - "ordinal": 170, + "ordinal": 173, "provenance_source": "PDB", "type": "RSRZ_OUTLIER", "feature_positions": [ @@ -4648,8 +4737,8 @@ { "description": "The Accessible Surface Area considering this polymer entity instance by itself (unbound).", "name": "Unbound ASA", - "ordinal": 171, - "provenance_source": "biojava-structure-6.0.5", + "ordinal": 174, + "provenance_source": "biojava-7.0.1", "type": "ASA", "feature_positions": [ { @@ -5644,8 +5733,8 @@ "type": "UNOBSERVED_RESIDUE_XYZ" }, { - "count": 0, - "coverage": 0.0, + "count": 1, + "coverage": 0.00322, "maximum_length": 0, "maximum_value": 0.0, "minimum_length": 0, @@ -5852,7 +5941,7 @@ "rcsb_id": "2FBW.E", "rcsb_latest_revision": { "major_revision": 2, - "minor_revision": 0 + "minor_revision": 1 } } },