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Update fixtures
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@lauraluebbert
lauraluebbert authored Sep 1, 2023
1 parent b08dae2 commit 364e071
Showing 1 changed file with 113 additions and 24 deletions.
137 changes: 113 additions & 24 deletions tests/fixtures/test_pdb.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -188,7 +188,7 @@
],
"rcsb_latest_revision": {
"major_revision": 1,
"minor_revision": 4
"minor_revision": 3
}
}
},
Expand Down Expand Up @@ -701,6 +701,7 @@
"name": "Mogul bond angle outlier",
"ordinal": 3,
"provenance_source": "PDB",
"reference_scheme": "PDB entity",
"type": "MOGUL_ANGLE_OUTLIER",
"feature_value": [
{
Expand Down Expand Up @@ -728,6 +729,7 @@
"name": "Mogul bond distance outlier",
"ordinal": 4,
"provenance_source": "PDB",
"reference_scheme": "PDB entity",
"type": "MOGUL_BOND_OUTLIER",
"feature_value": [
{
Expand Down Expand Up @@ -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"
}
]
Expand All @@ -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"
},
{
Expand Down Expand Up @@ -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"
}
Expand Down Expand Up @@ -1167,7 +1237,7 @@
"rcsb_id": "2FBW.J",
"rcsb_latest_revision": {
"major_revision": 2,
"minor_revision": 0
"minor_revision": 1
}
}
},
Expand Down Expand Up @@ -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": [
Expand All @@ -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": [
Expand All @@ -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": [
Expand All @@ -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": [
{
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -5852,7 +5941,7 @@
"rcsb_id": "2FBW.E",
"rcsb_latest_revision": {
"major_revision": 2,
"minor_revision": 0
"minor_revision": 1
}
}
},
Expand Down

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