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Issue #2: added test data and TM Viewer readme

cycle20 2 роки тому
батько
коміт
4c87e677d6

+ 12499 - 0
data/tmdet-example-annotations/1a0s.json

@@ -0,0 +1,12499 @@
+{
+    "data_resource": "PDBTM",
+    "resource_version": " 909",
+    "software_version": "3.2.134",
+    "resource_entry_url": "http:\/\/pdbtm.enzim.hu\/?_=\/pdbtm\/1a0s",
+    "model_coordinates_url": "http:\/\/pdbtm.enzim.hu\/data\/database\/a0\/1a0s.trpdb.gz",
+    "release_date": "10\/08\/2003",
+    "pdb_id": "1a0s",
+    "includes_het_groups": false,
+    "chains": [
+        {
+            "chain_label": "P",
+            "additional_chain_annotations": {
+                "type": "beta",
+                "num_tm": "18"
+            },
+            "residues": [
+                {
+                    "pdb_res_label": "71",
+                    "aa_type": "SER",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "72",
+                    "aa_type": "GLY",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "73",
+                    "aa_type": "PHE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "74",
+                    "aa_type": "GLU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "75",
+                    "aa_type": "PHE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "HIS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "GLY",
+                    "site_data": [
+                        {
+                            "site_id_ref": 4,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "TYR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 4,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "ALA",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
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+                    "aa_type": "ARG",
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+                            "confidence_classification": "curated"
+                        }
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+                            "confidence_classification": "curated"
+                        }
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+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
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+                    "aa_type": "VAL",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
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+                    "aa_type": "ILE",
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+                            "confidence_classification": "curated"
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+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
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+                    "aa_type": "ASN",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
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+                        }
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+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
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+                {
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+                    "aa_type": "ALA",
+                    "site_data": [
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+                        }
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+                    "aa_type": "SER",
+                    "site_data": [
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+                        }
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+                    "aa_type": "THR",
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+                        }
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+                        }
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+        },
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+            }
+        }
+    }
+}

+ 900 - 0
data/tmdet-example-annotations/1afo.json

@@ -0,0 +1,900 @@
+{
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+    "software_version": "3.2.134",
+    "resource_entry_url": "http:\/\/pdbtm.enzim.hu\/?_=\/pdbtm\/1afo",
+    "model_coordinates_url": "http:\/\/pdbtm.enzim.hu\/data\/database\/af\/1afo.trpdb.gz",
+    "release_date": "10\/08\/2003",
+    "pdb_id": "1afo",
+    "includes_het_groups": false,
+    "chains": [
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+                "num_tm": "1"
+            },
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+    }
+}

+ 12198 - 0
data/tmdet-example-annotations/1xl4.json

@@ -0,0 +1,12198 @@
+{
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+    "software_version": "3.2.134",
+    "resource_entry_url": "http:\/\/pdbtm.enzim.hu\/?_=\/pdbtm\/1xl4",
+    "model_coordinates_url": "http:\/\/pdbtm.enzim.hu\/data\/database\/xl\/1xl4.trpdb.gz",
+    "release_date": "09\/12\/2004",
+    "pdb_id": "1xl4",
+    "includes_het_groups": false,
+    "chains": [
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+}

+ 12195 - 0
data/tmdet-example-annotations/1xl6.json

@@ -0,0 +1,12195 @@
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+}

+ 5173 - 0
data/tmdet-example-annotations/2atk.json

@@ -0,0 +1,5173 @@
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+    }
+}

+ 6154 - 0
data/tmdet-example-annotations/4x8a.json

@@ -0,0 +1,6154 @@
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+    }
+}

+ 31279 - 0
data/tmdet-example-annotations/6xvf.json

@@ -0,0 +1,31279 @@
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+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "42",
+                    "aa_type": "ILE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "43",
+                    "aa_type": "TYR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "44",
+                    "aa_type": "GLU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "45",
+                    "aa_type": "HIS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "46",
+                    "aa_type": "ILE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "47",
+                    "aa_type": "ASN",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "48",
+                    "aa_type": "GLU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "49",
+                    "aa_type": "GLY",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "50",
+                    "aa_type": "LYS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "51",
+                    "aa_type": "LEU",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "52",
+                    "aa_type": "TRP",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "53",
+                    "aa_type": "LYS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "54",
+                    "aa_type": "HIS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "55",
+                    "aa_type": "ILE",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "56",
+                    "aa_type": "LYS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "57",
+                    "aa_type": "HIS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "58",
+                    "aa_type": "LYS",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "59",
+                    "aa_type": "TYR",
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "60",
+                    "aa_type": "GLU",
+                    "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": "Unknow 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": 1.00165713,
+                "y": 1.07907689,
+                "z": 12.91635799
+            },
+            "radius": 52,
+            "transformation_matrix": {
+                "rowx": {
+                    "x": 0.49429464,
+                    "y": 0.85614365,
+                    "z": 0.15063491,
+                    "t": 93.97259521
+                },
+                "rowy": {
+                    "x": 0.07531746,
+                    "y": 0.13045363,
+                    "z": -0.98858941,
+                    "t": 44.3111763
+                },
+                "rowz": {
+                    "x": -0.86602557,
+                    "y": 0.49999991,
+                    "z": -3.0e-8,
+                    "t": -13.08006477
+                }
+            }
+        },
+        "biomatrix": {
+            "chain_deletes": [
+                "K",
+                "M",
+                "P"
+            ],
+            "matrix_list": [
+                {
+                    "matrix_id": "1",
+                    "apply_to_chain_list": [
+                        {
+                            "chain_id": "A",
+                            "new_chain_id": "K"
+                        },
+                        {
+                            "chain_id": "B",
+                            "new_chain_id": "L"
+                        },
+                        {
+                            "chain_id": "C",
+                            "new_chain_id": "M"
+                        },
+                        {
+                            "chain_id": "D",
+                            "new_chain_id": "N"
+                        },
+                        {
+                            "chain_id": "E",
+                            "new_chain_id": "O"
+                        },
+                        {
+                            "chain_id": "F",
+                            "new_chain_id": "P"
+                        },
+                        {
+                            "chain_id": "G",
+                            "new_chain_id": "Q"
+                        },
+                        {
+                            "chain_id": "H",
+                            "new_chain_id": "R"
+                        },
+                        {
+                            "chain_id": "I",
+                            "new_chain_id": "S"
+                        },
+                        {
+                            "chain_id": "J",
+                            "new_chain_id": "T"
+                        }
+                    ],
+                    "transformation_matrix": {
+                        "rowx": {
+                            "x": 0.5,
+                            "y": -0.86602497,
+                            "z": 0,
+                            "t": -104.93450165
+                        },
+                        "rowy": {
+                            "x": -0.86602497,
+                            "y": -0.5,
+                            "z": 0,
+                            "t": -181.75189209
+                        },
+                        "rowz": {
+                            "x": 0,
+                            "y": 0,
+                            "z": -1,
+                            "t": 57.06967163
+                        }
+                    }
+                }
+            ]
+        }
+    }
+}

+ 33 - 0
src/apps/tm-viewer/README.md

@@ -0,0 +1,33 @@
+# TM Viewer App
+
+An application to demonstrate features of _TMDET Extension_.
+
+# Build
+
+```
+$ npm run build-tm
+$ cp -vuR data/tmdet-example-annotations build/tm-viewer/tmdet-data
+'data/tmdet-example-annotations' -> 'build/tm-viewer/tmdet-data'
+'data/tmdet-example-annotations/1afo.json' -> 'build/tm-viewer/tmdet-data/1afo.json'
+'data/tmdet-example-annotations/1a0s.json' -> 'build/tm-viewer/tmdet-data/1a0s.json'
+'data/tmdet-example-annotations/2atk.json' -> 'build/tm-viewer/tmdet-data/2atk.json'
+'data/tmdet-example-annotations/1xl4.json' -> 'build/tm-viewer/tmdet-data/1xl4.json'
+'data/tmdet-example-annotations/1xl6.json' -> 'build/tm-viewer/tmdet-data/1xl6.json'
+'data/tmdet-example-annotations/4x8a.json' -> 'build/tm-viewer/tmdet-data/4x8a.json'
+'data/tmdet-example-annotations/6xvf.json' -> 'build/tm-viewer/tmdet-data/6xvf.json'
+```
+
+# Run
+
+```
+$ cd build/tm-viewer
+$ npx http-server -a 127.0.0.1 -p 8000
+```
+
+Open `http://localhost:8000/` in web browser.
+
+# Development
+
+```
+$ npm run watch-tm
+```

+ 1 - 1
src/apps/tm-viewer/index.html

@@ -76,7 +76,7 @@
             function load(pdbId) {
                 tm_molstar.loadWithUNITMPMembraneRepresentation(viewer.plugin, {
                     structureUrl: `https://cs.litemol.org/${pdbId}/full`,
-                    regionDescriptorUrl: `http://localhost:8000/build/data/${pdbId}.json`,
+                    regionDescriptorUrl: `http://localhost:8000/tmdet-data/${pdbId}.json`,
                 });
             }
 

+ 3 - 0
src/extensions/tmdet/README.md

@@ -0,0 +1,3 @@
+# TMDET Extension
+
+TODO