Issue #660: working 5un1.json (1q90 also added)

data/tmdet-example-annotations/1q90.json

@@ -0,0 +1,19561 @@
+{
+    "data_resource": "PDBTM",
+    "resource_version": " 909",
+    "software_version": "3.2.134",
+    "resource_entry_url": "http://pdbtm.unitmp.org/entry/1q90",
+    "model_coordinates_url": "http://pdbtm.unitmp.org/api/v1/entry/1q90.trpdb",
+    "release_date": "08/03/2004",
+    "pdb_id": "1q90",
+    "includes_het_groups": false,
+    "chains": [
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+            "additional_chain_annotations": {
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+                "num_tm": "1"
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+                    "aa_type": "TRP",
+                    "site_data": [
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+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "GLY",
+                    "site_data": [
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+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "ARG",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "SER",
+                    "site_data": [
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+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "LEU",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                }
+            ]
+        }
+    ],
+    "sites": [
+        {
+            "site_id": 1,
+            "label": "Side1"
+        },
+        {
+            "site_id": 2,
+            "label": "Side2"
+        },
+        {
+            "site_id": 3,
+            "label": "Transmembrane Alpha Helix"
+        },
+        {
+            "site_id": 4,
+            "label": "Transmembrane Beta strand"
+        },
+        {
+            "site_id": 5,
+            "label": "Transmembrane Re-entrant Loop"
+        },
+        {
+            "site_id": 6,
+            "label": "Interfacial Helix"
+        },
+        {
+            "site_id": 7,
+            "label": "Unknown localization"
+        },
+        {
+            "site_id": 8,
+            "label": "Membrane Inside"
+        }
+    ],
+    "evidence_code_ontology": [
+        {
+            "eco_term": "computational combinatorial evidence used in automatic assertion",
+            "eco_code": "ECO_0000246"
+        }
+    ],
+    "additional_entry_annotations": {
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+                "y": 1.0e-8,
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+                "A-3",
+                "B-3",
+                "C-3",
+                "D-3",
+                "R-3",
+                "G-3",
+                "L-3",
+                "M-3",
+                "N-3",
+                "A-4",
+                "B-4",
+                "C-4",
+                "D-4",
+                "R-4",
+                "G-4",
+                "L-4",
+                "M-4",
+                "N-4",
+                "A-5",
+                "B-5",
+                "C-5",
+                "D-5",
+                "R-5",
+                "G-5",
+                "L-5",
+                "M-5",
+                "N-5"
+            ],
+            "matrix_list": [
+                {
+                    "matrix_id": "1",
+                    "apply_to_chain_list": [
+                        {
+                            "chain_id": "A",
+                            "new_chain_id": "A-2"
+                        },
+                        {
+                            "chain_id": "B",
+                            "new_chain_id": "B-2"
+                        },
+                        {
+                            "chain_id": "C",
+                            "new_chain_id": "C-2"
+                        },
+                        {
+                            "chain_id": "D",
+                            "new_chain_id": "D-2"
+                        },
+                        {
+                            "chain_id": "R",
+                            "new_chain_id": "R-2"
+                        },
+                        {
+                            "chain_id": "G",
+                            "new_chain_id": "G-2"
+                        },
+                        {
+                            "chain_id": "L",
+                            "new_chain_id": "L-2"
+                        },
+                        {
+                            "chain_id": "M",
+                            "new_chain_id": "M-2"
+                        },
+                        {
+                            "chain_id": "N",
+                            "new_chain_id": "N-2"
+                        }
+                    ],
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+                        "rowx": {
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+                    "apply_to_chain_list": [
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+                            "new_chain_id": "A-3"
+                        },
+                        {
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+                            "new_chain_id": "B-3"
+                        },
+                        {
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+                            "new_chain_id": "C-3"
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+                            "new_chain_id": "R-3"
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+                        {
+                            "chain_id": "G",
+                            "new_chain_id": "G-3"
+                        },
+                        {
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+                            "new_chain_id": "L-3"
+                        },
+                        {
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+                            "new_chain_id": "M-3"
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+                        {
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+                            "new_chain_id": "N-3"
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+                            "new_chain_id": "A-4"
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+                        {
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+                            "new_chain_id": "C-4"
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+                        {
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+                            "new_chain_id": "R-4"
+                        },
+                        {
+                            "chain_id": "G",
+                            "new_chain_id": "G-4"
+                        },
+                        {
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+                            "new_chain_id": "L-4"
+                        },
+                        {
+                            "chain_id": "M",
+                            "new_chain_id": "M-4"
+                        },
+                        {
+                            "chain_id": "N",
+                            "new_chain_id": "N-4"
+                        }
+                    ],
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+                },
+                {
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+                    "apply_to_chain_list": [
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+                            "new_chain_id": "A-5"
+                        },
+                        {
+                            "chain_id": "B",
+                            "new_chain_id": "B-5"
+                        },
+                        {
+                            "chain_id": "C",
+                            "new_chain_id": "C-5"
+                        },
+                        {
+                            "chain_id": "D",
+                            "new_chain_id": "D-5"
+                        },
+                        {
+                            "chain_id": "R",
+                            "new_chain_id": "R-5"
+                        },
+                        {
+                            "chain_id": "G",
+                            "new_chain_id": "G-5"
+                        },
+                        {
+                            "chain_id": "L",
+                            "new_chain_id": "L-5"
+                        },
+                        {
+                            "chain_id": "M",
+                            "new_chain_id": "M-5"
+                        },
+                        {
+                            "chain_id": "N",
+                            "new_chain_id": "N-5"
+                        }
+                    ],
+                    "transformation_matrix": {
+                        "rowx": {
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+                        }
+                    }
+                }
+            ]
+        }
+    }
+}

data/tmdet-example-annotations/5un1.json

@@ -0,0 +1,16733 @@
+{
+    "data_resource": "PDBTM",
+    "resource_version": " 909",
+    "software_version": "3.2.134",
+    "resource_entry_url": "http://pdbtm.unitmp.org/entry/5un1",
+    "model_coordinates_url": "http://pdbtm.unitmp.org/api/v1/entry/5un1.trpdb",
+    "release_date": "14/07/2023",
+    "pdb_id": "5un1",
+    "includes_het_groups": false,
+    "chains": [
+        {
+            "chain_label": "G",
+            "additional_chain_annotations": {
+                "type": "alpha",
+                "num_tm": "3"
+            },
+            "residues": [
+                {
+                    "pdb_res_label": "394",
+                    "aa_type": "MET",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "395",
+                    "aa_type": "SER",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "396",
+                    "aa_type": "THR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "397",
+                    "aa_type": "ARG",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "398",
+                    "aa_type": "LEU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "399",
+                    "aa_type": "LYS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "400",
+                    "aa_type": "ILE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "401",
+                    "aa_type": "VAL",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "402",
+                    "aa_type": "THR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "403",
+                    "aa_type": "ILE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "404",
+                    "aa_type": "HIS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "GLN",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "406",
+                    "aa_type": "GLU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "407",
+                    "aa_type": "PRO",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "PHE",
+                    "site_data": [
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+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "VAL",
+                    "site_data": [
+                        {
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "410",
+                    "aa_type": "TYR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "VAL",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "412",
+                    "aa_type": "ARG",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "413",
+                    "aa_type": "PRO",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
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+                },
+                {
+                    "pdb_res_label": "805",
+                    "aa_type": "PHE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "806",
+                    "aa_type": "TYR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "807",
+                    "aa_type": "MET",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "808",
+                    "aa_type": "LEU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "809",
+                    "aa_type": "ALA",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "810",
+                    "aa_type": "ALA",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "811",
+                    "aa_type": "ALA",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "812",
+                    "aa_type": "MET",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "813",
+                    "aa_type": "ALA",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "814",
+                    "aa_type": "LEU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "815",
+                    "aa_type": "SER",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "816",
+                    "aa_type": "LEU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "817",
+                    "aa_type": "ILE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "818",
+                    "aa_type": "THR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "819",
+                    "aa_type": "PHE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "820",
+                    "aa_type": "ILE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "821",
+                    "aa_type": "MET",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "822",
+                    "aa_type": "GLU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "823",
+                    "aa_type": "HIS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "824",
+                    "aa_type": "LEU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "825",
+                    "aa_type": "PHE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "826",
+                    "aa_type": "TYR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "827",
+                    "aa_type": "LYS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "828",
+                    "aa_type": "SER",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                }
+            ]
+        }
+    ],
+    "sites": [
+        {
+            "site_id": 1,
+            "label": "Side1"
+        },
+        {
+            "site_id": 2,
+            "label": "Side2"
+        },
+        {
+            "site_id": 3,
+            "label": "Transmembrane Alpha Helix"
+        },
+        {
+            "site_id": 4,
+            "label": "Transmembrane Beta strand"
+        },
+        {
+            "site_id": 5,
+            "label": "Transmembrane Re-entrant Loop"
+        },
+        {
+            "site_id": 6,
+            "label": "Interfacial Helix"
+        },
+        {
+            "site_id": 7,
+            "label": "Unknown localization"
+        },
+        {
+            "site_id": 8,
+            "label": "Membrane Inside"
+        }
+    ],
+    "evidence_code_ontology": [
+        {
+            "eco_term": "computational combinatorial evidence used in automatic assertion",
+            "eco_code": "ECO_0000246"
+        }
+    ],
+    "additional_entry_annotations": {
+        "membrane": {
+            "normal": {
+                "x": 0.09473176,
+                "y": 0.31647986,
+                "z": 11.74535561
+            },
+            "radius": 32,
+            "transformation_matrix": {
+                "rowx": {
+                    "x": 0.81848097,
+                    "y": 0.09706692,
+                    "z": -0.56627476,
+                    "t": 35.74074173
+                },
+                "rowy": {
+                    "x": -0.01529707,
+                    "y": 0.98895711,
+                    "z": 0.14741017,
+                    "t": 16.7484417
+                },
+                "rowz": {
+                    "x": 0.57433009,
+                    "y": -0.11199008,
+                    "z": 0.81092745,
+                    "t": 40.79182816
+                }
+            }
+        },
+        "biomatrix": {
+            "chain_deletes": [
+            "G", "B", "C", "H"
+            ]
+        }
+    }
+}

src/extensions/tmdet/symmetry.ts

@@ -88,7 +88,7 @@ function tmDetSymmetryFromMmCif(model: Model, excludedChains: string[]) {
     const only_identity_operation = Table.ofRows(
         data.pdbx_struct_oper_list._schema, [ Table.getRow(data.pdbx_struct_oper_list, 0) ]
     );
-    DebugUtil.log('oper_list table: first row', Table.formatToString(only_identity_operation));
+    DebugUtil.log('oper_list table: updated first row', Table.formatToString(only_identity_operation));
 
     return ModelSymmetry.fromData({
         symmetry: data.symmetry,
@@ -118,7 +118,8 @@ function createAsymIdColumnData(pdbx_struct_assembly_gen: Table<mmCIF_Schema['pd
 // difference of two string arrays (interpreted as sets)
 function minus(a: string[], b: string[]): string[] {
     const b_set = new Set(b);
-    return a.filter(x => !b_set.has(x));
+    const difference = a.filter(x => !b_set.has(x));
+    return Array.from(new Set(difference).values());
 }
 
 // union of two string arrays (interpreted as sets)