Merge branch 'issue_2_pdbe_collaboration'

data/tmdet-example-annotations/1a0s.json

@@ -0,0 +1,12499 @@
+{
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+                    "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": "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": {
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+                "y": -3.0e-8,
+                "z": 9.75
+            },
+            "radius": 41,
+            "transformation_matrix": {
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+                    "t": 14.42551613
+                }
+            }
+        }
+    }
+}

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

@@ -0,0 +1,900 @@
+{
+    "data_resource": "PDBTM",
+    "resource_version": " 909",
+    "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": [
+        {
+            "chain_label": "A",
+            "additional_chain_annotations": {
+                "type": "alpha",
+                "num_tm": "1"
+            },
+            "residues": [
+                {
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+                    "aa_type": "VAL",
+                    "site_data": [
+                        {
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+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "GLN",
+                    "site_data": [
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+                    "aa_type": "LEU",
+                    "site_data": [
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+                        }
+                    ]
+                },
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+                    "site_data": [
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+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "66",
+                    "aa_type": "HIS",
+                    "site_data": [
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+                        }
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+                    "aa_type": "HIS",
+                    "site_data": [
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+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                }
+            ]
+        }
+    ],
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+            "label": "Side1"
+        },
+        {
+            "site_id": 2,
+            "label": "Side2"
+        },
+        {
+            "site_id": 3,
+            "label": "Transmembrane Alpha Helix"
+        },
+        {
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+            "label": "Transmembrane Beta strand"
+        },
+        {
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+            "label": "Transmembrane Re-entrant Loop"
+        },
+        {
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+            "label": "Interfacial Helix"
+        },
+        {
+            "site_id": 7,
+            "label": "Unknow localization"
+        },
+        {
+            "site_id": 8,
+            "label": "Membrane Inside"
+        }
+    ],
+    "evidence_code_ontology": [
+        {
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+            "eco_code": "ECO_0000246"
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+                "y": 0,
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+            "transformation_matrix": {
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+                    "t": -1.02110946
+                }
+            }
+        }
+    }
+}

data/tmdet-example-annotations/1xl4.json

@@ -0,0 +1,12198 @@
+{
+    "data_resource": "PDBTM",
+    "resource_version": " 909",
+    "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": [
+        {
+            "chain_label": "A",
+            "additional_chain_annotations": {
+                "type": "alpha",
+                "num_tm": "2"
+            },
+            "residues": [
+                {
+                    "pdb_res_label": "1",
+                    "aa_type": "MET",
+                    "site_data": [
+                        {
+                            "site_id_ref": 7,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "2",
+                    "aa_type": "THR",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "3",
+                    "aa_type": "GLY",
+                    "site_data": [
+                        {
+                            "site_id_ref": 7,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "4",
+                    "aa_type": "GLY",
+                    "site_data": [
+                        {
+                            "site_id_ref": 7,
+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
+                    "pdb_res_label": "5",
+                    "aa_type": "MET",
+                    "site_data": [
+                        {
+                            "site_id_ref": 7,
+                            "confidence_classification": "curated"
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+        },
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+            "label": "Side2"
+        },
+        {
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+            "label": "Transmembrane Alpha Helix"
+        },
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+            "label": "Transmembrane Beta strand"
+        },
+        {
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+            "label": "Transmembrane Re-entrant Loop"
+        },
+        {
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+            "label": "Interfacial Helix"
+        },
+        {
+            "site_id": 7,
+            "label": "Unknow localization"
+        },
+        {
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+            "label": "Membrane Inside"
+        }
+    ],
+    "evidence_code_ontology": [
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+                    "apply_to_chain_list": [
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+                            "new_chain_id": "C"
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+                            "new_chain_id": "D"
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+                }
+            ]
+        }
+    }
+}

data/tmdet-example-annotations/1xl6.json

@@ -0,0 +1,12195 @@
+{
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+    "software_version": "3.2.134",
+    "resource_entry_url": "http:\/\/pdbtm.enzim.hu\/?_=\/pdbtm\/1xl6",
+    "model_coordinates_url": "http:\/\/pdbtm.enzim.hu\/data\/database\/xl\/1xl6.trpdb.gz",
+    "release_date": "09\/12\/2004",
+    "pdb_id": "1xl6",
+    "includes_het_groups": false,
+    "chains": [
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+            "additional_chain_annotations": {
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+                "num_tm": "2"
+            },
+            "residues": [
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+                    "aa_type": "MET",
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data/tmdet-example-annotations/2atk.json

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+                        }
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+            "label": "Side1"
+        },
+        {
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+            "label": "Side2"
+        },
+        {
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+            "label": "Transmembrane Alpha Helix"
+        },
+        {
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+            "label": "Transmembrane Beta strand"
+        },
+        {
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+            "label": "Transmembrane Re-entrant Loop"
+        },
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+            "label": "Interfacial Helix"
+        },
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+        },
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+            "label": "Membrane Inside"
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+                }
+            ]
+        }
+    }
+}

data/tmdet-example-annotations/4x8a.json

@@ -0,0 +1,6154 @@
+{
+    "data_resource": "PDBTM",
+    "resource_version": " 917",
+    "software_version": "3.2.134",
+    "resource_entry_url": "http:\/\/pdbtm.enzim.hu\/?_=\/pdbtm\/4x8a",
+    "model_coordinates_url": "http:\/\/pdbtm.enzim.hu\/data\/database\/x8\/4x8a.trpdb.gz",
+    "release_date": "11\/11\/2021",
+    "pdb_id": "4x8a",
+    "includes_het_groups": false,
+    "chains": [
+        {
+            "chain_label": "A",
+            "additional_chain_annotations": {
+                "type": "alpha",
+                "num_tm": "2"
+            },
+            "residues": [
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+                    "aa_type": "GLY",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
+                {
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+                    "aa_type": "SER",
+                    "site_data": [
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+                {
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+                    "aa_type": "HIS",
+                    "site_data": [
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
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+                    "aa_type": "MET",
+                    "site_data": [
+                        {
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+                            "confidence_classification": "curated"
+                        }
+                    ]
+                },
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+                    "aa_type": "GLY",
+                    "site_data": [
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+                            "confidence_classification": "curated"
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+                    "aa_type": "VAL",
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+                    "site_data": [
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+                        }
+                    ]
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+            "label": "Side2"
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+            "label": "Transmembrane Alpha Helix"
+        },
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+            "label": "Transmembrane Beta strand"
+        },
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+            "label": "Transmembrane Re-entrant Loop"
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+            ]
+        }
+    }
+}

data/tmdet-example-annotations/6xvf.json

@@ -0,0 +1,31279 @@
+{
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+    "resource_version": " 909",
+    "software_version": "3.2.134",
+    "resource_entry_url": "http:\/\/pdbtm.enzim.hu\/?_=\/pdbtm\/6xvf",
+    "model_coordinates_url": "http:\/\/pdbtm.enzim.hu\/data\/database\/xv\/6xvf.trpdb.gz",
+    "release_date": "23\/07\/2020",
+    "pdb_id": "6xvf",
+    "includes_het_groups": false,
+    "chains": [
+        {
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+            "additional_chain_annotations": {
+                "type": "non_tm",
+                "num_tm": "0"
+            },
+            "residues": [
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+                    "aa_type": "ALA",
+                    "site_data": [
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+                            "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
+                        }
+                    }
+                }
+            ]
+        }
+    }
+}

package-lock.json

@@ -5,6 +5,7 @@
   "requires": true,
   "packages": {
     "": {
+      "name": "molstar",
       "version": "2.2.1",
       "license": "MIT",
       "dependencies": {
@@ -2061,7 +2062,6 @@
         "jest-resolve": "^26.6.2",
         "jest-util": "^26.6.2",
         "jest-worker": "^26.6.2",
-        "node-notifier": "^8.0.0",
         "slash": "^3.0.0",
         "source-map": "^0.6.0",
         "string-length": "^4.0.1",
@@ -4173,7 +4173,6 @@
       "dependencies": {
         "anymatch": "~3.1.1",
         "braces": "~3.0.2",
-        "fsevents": "~2.3.1",
         "glob-parent": "~5.1.0",
         "is-binary-path": "~2.1.0",
         "is-glob": "~4.0.1",
@@ -5567,6 +5566,7 @@
       "version": "3.3.2",
       "resolved": "https://registry.npmjs.org/ecstatic/-/ecstatic-3.3.2.tgz",
       "integrity": "sha512-fLf9l1hnwrHI2xn9mEDT7KIi22UDqA2jaCwyCbSUJh9a1V+LEUSL/JO/6TIz/QyuBURWUHrFL5Kg2TtO1bkkog==",
+      "deprecated": "This package is unmaintained and deprecated. See the GH Issue 259.",
       "dev": true,
       "dependencies": {
         "he": "^1.1.1",
@@ -5813,8 +5813,7 @@
         "esprima": "^4.0.1",
         "estraverse": "^5.2.0",
         "esutils": "^2.0.2",
-        "optionator": "^0.8.1",
-        "source-map": "~0.6.1"
+        "optionator": "^0.8.1"
       },
       "bin": {
         "escodegen": "bin/escodegen.js",
@@ -6866,12 +6865,6 @@
         "node": ">= 0.6"
       }
     },
-    "node_modules/fs": {
-      "version": "0.0.1-security",
-      "resolved": "https://registry.npmjs.org/fs/-/fs-0.0.1-security.tgz",
-      "integrity": "sha1-invTcYa23d84E/I4WLV+yq9eQdQ=",
-      "dev": true
-    },
     "node_modules/fs-extra": {
       "version": "9.1.0",
       "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-9.1.0.tgz",
@@ -8730,7 +8723,6 @@
         "@types/node": "*",
         "anymatch": "^3.0.3",
         "fb-watchman": "^2.0.0",
-        "fsevents": "^2.1.2",
         "graceful-fs": "^4.2.4",
         "jest-regex-util": "^26.0.0",
         "jest-serializer": "^26.6.2",
@@ -9356,7 +9348,6 @@
       "integrity": "sha512-5dgndWOriYSm5cnYaJNhalLNDKOqFwyDB/rr1E9ZsGciGvKPs8R2xYGCacuf3z6K1YKDz182fd+fY3cn3pMqXQ==",
       "dev": true,
       "dependencies": {
-        "graceful-fs": "^4.1.6",
         "universalify": "^2.0.0"
       },
       "optionalDependencies": {
@@ -12473,6 +12464,7 @@
       "version": "3.4.0",
       "resolved": "https://registry.npmjs.org/uuid/-/uuid-3.4.0.tgz",
       "integrity": "sha512-HjSDRw6gZE5JMggctHBcjVak08+KEVhSIiDzFnT9S9aegmp85S/bReBVTb4QTFaRNptJ9kuYaNhnbNEOkbKb/A==",
+      "deprecated": "Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.",
       "dev": true,
       "bin": {
         "uuid": "bin/uuid"
@@ -12695,6 +12687,7 @@
       "version": "4.1.0",
       "resolved": "https://registry.npmjs.org/sane/-/sane-4.1.0.tgz",
       "integrity": "sha512-hhbzAgTIX8O7SHfp2c8/kREfEn4qO/9q8C9beyY6+tvZ87EpoZ3i1RIEvp27YBswnNbY9mWd6paKVmKbAgLfZA==",
+      "deprecated": "some dependency vulnerabilities fixed, support for node < 10 dropped, and newer ECMAScript syntax/features added",
       "dev": true,
       "dependencies": {
         "@cnakazawa/watch": "^1.0.3",
@@ -13778,6 +13771,7 @@
       "version": "0.5.3",
       "resolved": "https://registry.npmjs.org/source-map-resolve/-/source-map-resolve-0.5.3.tgz",
       "integrity": "sha512-Htz+RnsXWk5+P2slx5Jh3Q66vhQj1Cllm0zvnaY98+NFx+Dv2CF/f5O/t8x+KaNdrdIAsruNzoh/KpialbqAnw==",
+      "deprecated": "See https://github.com/lydell/source-map-resolve#deprecated",
       "dev": true,
       "dependencies": {
         "atob": "^2.1.2",
@@ -13810,6 +13804,7 @@
       "version": "0.4.1",
       "resolved": "https://registry.npmjs.org/source-map-url/-/source-map-url-0.4.1.tgz",
       "integrity": "sha512-cPiFOTLUKvJFIg4SKVScy4ilPPW6rFgMgfuZJPNoDuMs3nC1HbMUycBoJw77xFIp6z1UJQJOfx6C9GMH80DiTw==",
+      "deprecated": "See https://github.com/lydell/source-map-url#deprecated",
       "dev": true
     },
     "node_modules/spawn-command": {
@@ -14224,6 +14219,7 @@
       "version": "0.9.18",
       "resolved": "https://registry.npmjs.org/subscriptions-transport-ws/-/subscriptions-transport-ws-0.9.18.tgz",
       "integrity": "sha512-tztzcBTNoEbuErsVQpTN2xUNN/efAZXyCyL5m3x4t6SKrEiTL2N8SaKWBFWM4u56pL79ULif3zjyeq+oV+nOaA==",
+      "deprecated": "The `subscriptions-transport-ws` package is no longer maintained. We recommend you use `graphql-ws` instead. For help migrating Apollo software to `graphql-ws`, see https://www.apollographql.com/docs/apollo-server/data/subscriptions/#switching-from-subscriptions-transport-ws    For general help using `graphql-ws`, see https://github.com/enisdenjo/graphql-ws/blob/master/README.md",
       "dev": true,
       "dependencies": {
         "backo2": "^1.0.2",
@@ -15430,6 +15426,12 @@
         "underscore": "~1.6.0"
       }
     },
+    "node_modules/webpack-version-file-plugin/node_modules/fs": {
+      "version": "0.0.1-security",
+      "resolved": "https://registry.npmjs.org/fs/-/fs-0.0.1-security.tgz",
+      "integrity": "sha1-invTcYa23d84E/I4WLV+yq9eQdQ=",
+      "dev": true
+    },
     "node_modules/webpack/node_modules/acorn": {
       "version": "8.2.4",
       "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.2.4.tgz",
@@ -21347,12 +21349,6 @@
       "resolved": "https://registry.npmjs.org/fresh/-/fresh-0.5.2.tgz",
       "integrity": "sha1-PYyt2Q2XZWn6g1qx+OSyOhBWBac="
     },
-    "fs": {
-      "version": "0.0.1-security",
-      "resolved": "https://registry.npmjs.org/fs/-/fs-0.0.1-security.tgz",
-      "integrity": "sha1-invTcYa23d84E/I4WLV+yq9eQdQ=",
-      "dev": true
-    },
     "fs-extra": {
       "version": "9.1.0",
       "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-9.1.0.tgz",
@@ -28049,6 +28045,14 @@
         "ejs": "~> 2.5.5",
         "fs": "latest",
         "underscore": "~1.6.0"
+      },
+      "dependencies": {
+        "fs": {
+          "version": "0.0.1-security",
+          "resolved": "https://registry.npmjs.org/fs/-/fs-0.0.1-security.tgz",
+          "integrity": "sha1-invTcYa23d84E/I4WLV+yq9eQdQ=",
+          "dev": true
+        }
       }
     },
     "whatwg-encoding": {

package.json

@@ -16,20 +16,24 @@
     "test": "npm run lint && jest",
     "jest": "jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
+    "build-tm": "npm run build-tsc && npm run build-extra && npm run build-webpack-tm",
     "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
     "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",
     "build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
     "build-webpack": "webpack --mode production --config ./webpack.config.production.js",
     "build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
+    "build-webpack-tm": "webpack --mode production --config ./webpack.config.tm-viewer.js",
     "watch": "concurrently -c \"green,green,gray,gray\" --names \"tsc,srv,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-servers\" \"npm:watch-extra\" \"npm:watch-webpack\"",
     "watch-viewer": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer\"",
     "watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
+    "watch-tm": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-tm\"",
     "watch-tsc": "tsc --watch --incremental",
     "watch-servers": "tsc --build tsconfig.commonjs.json --watch --incremental",
     "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
     "watch-webpack": "webpack -w --mode development --stats minimal",
     "watch-webpack-viewer": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.js",
     "watch-webpack-viewer-debug": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.debug.js",
+    "watch-webpack-tm": "webpack -w --mode development --stats minimal --config ./webpack.config.tm-viewer.js",
     "serve": "http-server -p 1338 -g",
     "model-server": "node lib/commonjs/servers/model/server.js",
     "model-server-watch": "nodemon --watch lib lib/commonjs/servers/model/server.js",
@@ -147,8 +151,9 @@
     "react": "^17.0.1",
     "react-dom": "^17.0.1",
     "rxjs": "^6.6.6",
+    "source-map-loader": "^3.0.1",
     "swagger-ui-dist": "^3.37.2",
-    "tslib": "^2.1.0",
+    "tslib": "^2.4.0",
     "util.promisify": "^1.0.1",
     "xhr2": "^0.2.0"
   }

src/apps/tm-viewer/LICENSE

@@ -0,0 +1,417 @@
+Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+
+Authors:
+
+* Gabor Tusnady (tusnady.gabor at ttk.hu)
+* Csongor Gerdan (gerdan.csongor at ttk.hu)
+
+=======================================================================
+
+Attribution-NonCommercial 4.0 International
+
+=======================================================================
+
+Creative Commons Corporation ("Creative Commons") is not a law firm and
+does not provide legal services or legal advice. Distribution of
+Creative Commons public licenses does not create a lawyer-client or
+other relationship. Creative Commons makes its licenses and related
+information available on an "as-is" basis. Creative Commons gives no
+warranties regarding its licenses, any material licensed under their
+terms and conditions, or any related information. Creative Commons
+disclaims all liability for damages resulting from their use to the
+fullest extent possible.
+
+Using Creative Commons Public Licenses
+
+Creative Commons public licenses provide a standard set of terms and
+conditions that creators and other rights holders may use to share
+original works of authorship and other material subject to copyright
+and certain other rights specified in the public license below. The
+following considerations are for informational purposes only, are not
+exhaustive, and do not form part of our licenses.
+
+     Considerations for licensors: Our public licenses are
+     intended for use by those authorized to give the public
+     permission to use material in ways otherwise restricted by
+     copyright and certain other rights. Our licenses are
+     irrevocable. Licensors should read and understand the terms
+     and conditions of the license they choose before applying it.
+     Licensors should also secure all rights necessary before
+     applying our licenses so that the public can reuse the
+     material as expected. Licensors should clearly mark any
+     material not subject to the license. This includes other CC-
+     licensed material, or material used under an exception or
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+    wiki.creativecommons.org/Considerations_for_licensors
+
+     Considerations for the public: By using one of our public
+     licenses, a licensor grants the public permission to use the
+     licensed material under specified terms and conditions. If
+     the licensor's permission is not necessary for any reason--for
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+     Although not required by our licenses, you are encouraged to
+     respect those requests where reasonable. More considerations
+     for the public:
+    wiki.creativecommons.org/Considerations_for_licensees
+
+=======================================================================
+
+Creative Commons Attribution-NonCommercial 4.0 International Public
+License
+
+By exercising the Licensed Rights (defined below), You accept and agree
+to be bound by the terms and conditions of this Creative Commons
+Attribution-NonCommercial 4.0 International Public License ("Public
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+such rights in consideration of benefits the Licensor receives from
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+conditions.
+
+
+Section 1 -- Definitions.
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+  a. Adapted Material means material subject to Copyright and Similar
+     Rights that is derived from or based upon the Licensed Material
+     and in which the Licensed Material is translated, altered,
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+  b. Adapter's License means the license You apply to Your Copyright
+     and Similar Rights in Your contributions to Adapted Material in
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+
+  c. Copyright and Similar Rights means copyright and/or similar rights
+     closely related to copyright including, without limitation,
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+     Rights, without regard to how the rights are labeled or
+     categorized. For purposes of this Public License, the rights
+     specified in Section 2(b)(1)-(2) are not Copyright and Similar
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+  d. Effective Technological Measures means those measures that, in the
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+  e. Exceptions and Limitations means fair use, fair dealing, and/or
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+
+  h. Licensor means the individual(s) or entity(ies) granting rights
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+public licenses.
+
+Creative Commons may be contacted at creativecommons.org.
+

src/apps/tm-viewer/README.md

@@ -0,0 +1,47 @@
+# TM Viewer App
+
+An application to demonstrate features of _TMDET Extension_.
+(see `src/extensions/tmdet` for more details)
+
+# 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 mode
+
+```
+$ npm run watch-tm
+```
+
+# Authors
+
+* Gabor Tusnady (tusnady.gabor at ttk.hu), Protein Bioinformatics Research Group, RCNS.
+* Csongor Gerdan (gerdan.csongor at ttk.hu), Protein Bioinformatics Research Group, RCNS.
+
+# License
+
+Creative Commons Attribution-NonCommercial 4.0 International Public
+License
+
+Please see the LICENSE file for more details or visit
+https://creativecommons.org/licenses/by-nc/4.0/.

src/apps/tm-viewer/embedded.html

@@ -0,0 +1,44 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Embedded Mol* Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            var viewer = new molstar.Viewer('app', {
+                layoutIsExpanded: true,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
+
+                viewportShowExpand: true,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+
+                pdbProvider: 'rcsb',
+                emdbProvider: 'rcsb',
+            });
+            viewer.loadPdb('7bv2');
+            viewer.loadEmdb('EMD-30210', { detail: 6 });
+
+            // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+        </script>
+    </body>
+</html>

src/apps/tm-viewer/index.html

@@ -0,0 +1,116 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>TmMol* Viewer</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+            }
+            html, body {
+                width: 100%;
+                height: 100%;
+                overflow: hidden;
+            }
+            hr {
+                margin: 10px;
+            }
+            h1, h2, h3, h4, h5 {
+                margin-top: 5px;
+                margin-bottom: 3px;
+            }
+            button {
+                padding: 2px;
+            }
+            #app {
+                max-width: 100%;
+                flex: 0 0 100%;
+                position: relative;
+                left: 2px;
+                top: 2px;
+                width: 800px;
+                height: 600px;
+            }
+
+            #controls {
+                position: absolute;
+                top: 2px;
+                left: 810px;
+                z-index: 10;
+                width: 15rem;
+                font-family: sans-serif;
+                font-size: smaller;
+            }
+
+            #controls > button {
+                /*display: block;*/
+                width: 100%;
+                text-align: left;
+                margin: 5px 0px;
+            }
+
+            #controls > input, #controls > select {
+                width: 100%;
+                display: block;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <div id="controls"></div>
+        <script type="text/javascript" src="./tm_molstar.js"></script>
+        <script type="text/javascript">
+            // init viewer
+            var viewer = new tm_molstar.Viewer('app', {
+                layoutShowControls: false,
+                layoutIsExpanded: false,
+                viewportShowExpand: true,
+                collapseLeftPanel: true
+            });
+
+            function load(pdbId) {
+                tm_molstar.loadWithUNITMPMembraneRepresentation(viewer.plugin, {
+                    structureUrl: `https://cs.litemol.org/${pdbId}/full`,
+                    regionDescriptorUrl: `http://localhost:8000/tmdet-data/${pdbId}.json`,
+                });
+            }
+
+            function $(id) { return document.getElementById(id); }
+
+            function addControl(label, action) {
+                var btn = document.createElement('button');
+                btn.onclick = action;
+                btn.innerText = label;
+                $('controls').appendChild(btn);
+            }
+
+            let idList = [
+                '1afo', // PASSED
+                '1a0s', // PASSED
+                '2atk', // PASSED
+                '1xl4', // PASSED
+                '1xl6', // PASSED
+                '4x8a', // PASSED
+                '6xvf', // TODO: slightly wrong membrane planes:
+                        // their angle with Z-axis is not 90
+            ];
+            idList.forEach((pdbId) => addControl(pdbId, () => load(pdbId)));
+            addControl('Reset', () => {
+                tm_molstar.loadInitialSnapshot(viewer.plugin)
+                setTimeout(() => viewer.plugin.clear(), 500);
+            });
+
+            // Debug section
+            var dbg = tm_molstar.DebugUtil;
+            dbg.init(viewer.plugin);
+            dbg.enableLog();
+            dbg.log("'dbg' object has been initialized. Functions can be accessed via it.");
+
+        </script>
+    </body>
+</html>

src/apps/tm-viewer/index.ts

@@ -0,0 +1,136 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+/**
+ *
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+
+import { TMDETMembraneOrientation } from '../../extensions/tmdet/behavior';
+import { createPlugin } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginSpec } from '../../mol-plugin/spec';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import './embedded.html';
+import './favicon.ico';
+import './index.html';
+
+require('mol-plugin-ui/skin/light.scss');
+
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+export { loadWithUNITMPMembraneRepresentation } from '../../extensions/tmdet/behavior';
+export { loadInitialSnapshot } from '../../extensions/tmdet/camera';
+export { DebugUtil } from '../../extensions/tmdet/debug-utils';
+
+const Extensions = {
+    'tmdet-membrane-orientation': PluginSpec.Behavior(TMDETMembraneOrientation)
+};
+
+const DefaultViewerOptions = {
+    extensions: ObjectKeys(Extensions),
+    layoutIsExpanded: true,
+    layoutShowControls: true,
+    layoutShowRemoteState: true,
+    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
+    layoutShowSequence: true,
+    layoutShowLog: true,
+    layoutShowLeftPanel: true,
+    collapseLeftPanel: false,
+    disableAntialiasing: false,
+    pixelScale: 1,
+    enableWboit: true,
+
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
+    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
+    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
+    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
+    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
+    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+};
+type ViewerOptions = typeof DefaultViewerOptions;
+
+export class Viewer {
+    plugin: PluginUIContext
+
+    constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
+        const o = { ...DefaultViewerOptions, ...options };
+        const defaultSpec = DefaultPluginUISpec();
+
+        const spec: PluginUISpec = {
+            actions: defaultSpec.actions,
+            behaviors: [
+                ...defaultSpec.behaviors,
+                ...o.extensions.map(e => Extensions[e]),
+            ],
+            animations: [...defaultSpec.animations || []],
+            customParamEditors: defaultSpec.customParamEditors,
+            layout: {
+                initial: {
+                    isExpanded: o.layoutIsExpanded,
+                    showControls: o.layoutShowControls,
+                    controlsDisplay: o.layoutControlsDisplay,
+                    regionState: {
+                        bottom: 'full',
+                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                        right: 'full',
+                        top: 'full',
+                    }
+                },
+            },
+            components: {
+                ...defaultSpec.components,
+                controls: {
+                    ...defaultSpec.components?.controls,
+                    top: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                },
+                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
+            },
+            config: [
+                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
+                [PluginConfig.General.PixelScale, o.pixelScale],
+                [PluginConfig.General.EnableWboit, o.enableWboit],
+                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
+                [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                [PluginConfig.State.DefaultServer, o.pluginStateServer],
+                [PluginConfig.State.CurrentServer, o.pluginStateServer],
+                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
+                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
+            ]
+        };
+
+        const element = typeof elementOrId === 'string'
+            ? document.getElementById(elementOrId)
+            : elementOrId;
+        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
+        this.plugin = createPlugin(element, spec);
+
+    }
+
+    handleResize() {
+        this.plugin.layout.events.updated.next();
+    }
+}

src/apps/viewer/index.html

@@ -48,24 +48,38 @@
             var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
             if (debugMode) molstar.setDebugMode(debugMode, debugMode);
 
+            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
+            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
+            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
             var viewer = new molstar.Viewer('app', {
-                layoutShowControls: true,
-                viewportShowExpand: true,
-                collapseLeftPanel: false
+                layoutShowControls: !hideControls,
+                viewportShowExpand: false,
+                collapseLeftPanel: collapseLeftPanel,
+                pdbProvider: pdbProvider || 'pdbe',
+                emdbProvider: emdbProvider || 'pdbe',
             });
 
-            // Set PDB Id here
-            var regionDescriptors = {"pdb-id":"1afo", "creation-date":"2021-09-03","is-transmembrane":1,"membrane-normal":{"x":0,"y":0,"z":17.75},"chains":[{"chain_id":"A","type":"alpha","seq":"VQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKK","regions":{"1":{"auth_ids":[62,63,64,65,66,67,68,69,70,71,72,73],"color":[255,0,0]},"H":{"auth_ids":[74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95],"color":[255,255,0]},"2":{"auth_ids":[96,97,98,99,100,101],"color":[0,0,255]}}},{"chain_id":"B","type":"alpha","seq":"VQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKK","regions":{"1":{"auth_ids":[62,63,64,65,66,67,68,69,70,71,72,73],"color":[255,0,0]},"H":{"auth_ids":[74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99],"color":[255,255,0]},"2":{"auth_ids":[100,101],"color":[0,0,255]}}}]};
-            var pdbtmId = regionDescriptors["pdb-id"];
-            regionDescriptors.format = 'mmcif'
-            viewer.loadWithUNITMPMembraneRepresentation(
-                // NOTE: Prepare CORS settings appropriately on backend
-                //       or made this index.html accessible from the same
-                //       origin (DOMAIN:PORT values).
-                //`https://DOMAIN[:PORT]/api/pdbtm/${pdbtmId}/trpdb`,
-                `https://cs.litemol.org/${pdbtmId}/full`,
-                regionDescriptors
-            );
+            var snapshotId = getParam('snapshot-id', '[^&]+').trim();
+            if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
+
+            var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
+            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
+            if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
+
+            var structureUrl = getParam('structure-url', '[^&]+').trim();
+            var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
+            var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
+            if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
+
+            var pdb = getParam('pdb', '[^&]+').trim();
+            if (pdb) viewer.loadPdb(pdb);
+
+            var pdbDev = getParam('pdb-dev', '[^&]+').trim();
+            if (pdbDev) viewer.loadPdbDev(pdbDev);
+
+            var emdb = getParam('emdb', '[^&]+').trim();
+            if (emdb) viewer.loadEmdb(emdb);
         </script>
     </body>
-</html>
+</html>

src/apps/viewer/index.ts

@@ -5,40 +5,63 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { TMDETMembraneOrientation } from '../../extensions/tmdet/behavior';
+import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
+import { CellPack } from '../../extensions/cellpack';
+import { DnatcoConfalPyramids } from '../../extensions/dnatco';
+import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+import { Mp4Export } from '../../extensions/mp4-export';
+import { GeometryExport } from '../../extensions/geo-export';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
 import { createPlugin } from '../../mol-plugin-ui';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
 import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginConfig } from '../../mol-plugin/config';
 import { PluginSpec } from '../../mol-plugin/spec';
-import { StateBuilder, StateObjectRef } from '../../mol-state';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectSelector } from '../../mol-state';
+import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
 import '../../mol-util/polyfill';
 import { ObjectKeys } from '../../mol-util/type-helpers';
 import './embedded.html';
 import './favicon.ico';
 import './index.html';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
-import { Expression } from '../../mol-script/language/expression';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { MembraneOrientation } from '../../extensions/tmdet/prop';
-import { MEMBRANE_STORAGE_KEY } from '../../extensions/tmdet/algorithm';
-import { Quat, Vec3 } from '../../mol-math/linear-algebra';
-import { PluginCommands } from '../../mol-plugin/commands';
 
 require('mol-plugin-ui/skin/light.scss');
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 
+const CustomFormats = [
+    ['g3d', G3dProvider] as const
+];
+
 const Extensions = {
-    'tmdet-membrane-orientation': PluginSpec.Behavior(TMDETMembraneOrientation)
+    'cellpack': PluginSpec.Behavior(CellPack),
+    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
+    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
+    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
+    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
+    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
+    'g3d': PluginSpec.Behavior(G3DFormat),
+    'mp4-export': PluginSpec.Behavior(Mp4Export),
+    'geo-export': PluginSpec.Behavior(GeometryExport)
 };
 
 const DefaultViewerOptions = {
+    customFormats: CustomFormats as [string, DataFormatProvider][],
     extensions: ObjectKeys(Extensions),
     layoutIsExpanded: true,
     layoutShowControls: true,
@@ -65,142 +88,9 @@ const DefaultViewerOptions = {
 };
 type ViewerOptions = typeof DefaultViewerOptions;
 
-
-export var membrane: MembraneOrientation;
-
 export class Viewer {
     plugin: PluginUIContext
 
-
-
-
-
-    ////////////////////////////// UNITMP VIEWER PROTOTYPING SECTION
-
-    async loadWithUNITMPMembraneRepresentation(url: string, regionDescriptors: any) {
-        const membraneNormal: Vec3 = Vec3.fromObj(
-            regionDescriptors['membrane-normal']
-        );
-        const membrane: MembraneOrientation = {
-            planePoint1: Vec3.fromArray(Vec3.zero(), membraneNormal, 0),
-            planePoint2: Vec3.fromArray(Vec3.zero(), membraneNormal, 0),
-            // NOTE: centroid is not 0,0,0. It is x,y,0. Right?
-            centroid: Vec3.fromArray(
-                Vec3.zero(), [ membraneNormal[0], membraneNormal[1], 0 ], 0
-            ),
-            normalVector: membraneNormal,
-
-            // TODO: radius is still just a dummy value now.
-            //       Can we send a precalculated value by our backend?
-            //
-            // (NOTE: the TMDET extension calculates and sets it during applying preset)
-            radius: regionDescriptors[ 'radius' ]
-        };
-        membrane.planePoint2[2] *= -1;
-
-        localStorage.setItem(MEMBRANE_STORAGE_KEY, JSON.stringify(membrane));
-
-        const isBinary = false;
-
-        const data = await this.plugin.builders.data.download({
-            url, label: regionDescriptors['pdb-id'], isBinary
-        }); //, { state: { isGhost: true } });
-        const trajectory = await this.plugin.builders.structure.parseTrajectory(data, regionDescriptors.format);
-        // create membrane representation
-        await this.plugin.builders.structure.hierarchy.applyPreset(
-            trajectory, 'default', { representationPreset: 'preset-membrane-orientation' as any });
-
-        const structure: StateObjectRef<PluginStateObject.Molecule.Structure> =
-            this.plugin.managers.structure.hierarchy.current.models[0].structures[0].cell;
-        const components = {
-            polymer: await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'polymer'),
-            ligand: await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'ligand'),
-            water: await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'water'),
-        };
-
-        const builder = this.plugin.builders.structure.representation;
-        const update = this.plugin.build();
-        if (components.polymer) builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { alpha: 0.5 } }, { tag: 'polymer' });
-        if (components.ligand) builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick' }, { tag: 'ligand' });
-        if (components.water) builder.buildRepresentation(update, components.water, { type: 'ball-and-stick', typeParams: { alpha: 0.6 } }, { tag: 'water' });
-        await update.commit();
-
-        regionDescriptors.chains.forEach((chain: any) => {
-
-            for(let regionKey in chain.regions) {
-              const update = this.plugin.build();
-              const region = chain.regions[regionKey];
-              this.createRegionRepresentation(chain.chain_id, region, update.to(structure));
-              update.commit();
-            }
-
-        });
-
-        //
-        // reset the camera because the membranes render 1st and the structure might not be fully visible
-        //
-        this.rotateCamera();
-
-        //requestAnimationFrame(() => this.plugin.canvas3d?.requestCameraReset());
-    }
-
-    private createRegionRepresentation(chain: string, region: any, update: StateBuilder.To<any, any>) {
-        const regionLabel: string = `${chain} | ${region.name}`;
-        const color: Color = Color.fromArray(region.color, 0);
-        const query: Expression = this.getQuery(chain, region.auth_ids as number[]);
-
-        // based on https://github.com/molstar/molstar/issues/209
-        update
-            .apply(StateTransforms.Model.StructureSelectionFromExpression, { label: regionLabel, expression: query })
-            .apply(StateTransforms.Representation.StructureRepresentation3D, createStructureRepresentationParams(this.plugin, update.selector.data, {
-                color: 'uniform',
-                colorParams: { value: color }
-            }));
-    }
-
-    private getQuery(chainId: string, auth_array: number[]): Expression {
-        const query: Expression =
-            MS.struct.generator.atomGroups({
-                'residue-test': MS.core.set.has([MS.set( ...auth_array ), MS.ammp('auth_seq_id')]),
-                'chain-test': MS.core.rel.eq([chainId, MS.ammp('label_asym_id')])
-            });
-        return query;
-    }
-
-    private rotateCamera(): void {
-        function rot90q(v: Vec3, axis: Vec3 = Vec3.create(1, 0, 0)): Vec3 {
-            const q = Quat.setAxisAngle(Quat(), axis, -Math.PI/2);
-            return Vec3.transformQuat(Vec3(), v, q);
-        }
-        function sub(v: Vec3, u: Vec3): Vec3 {
-            return Vec3.sub(Vec3(), v, u);
-        }
-        function add(v: Vec3, u: Vec3): Vec3 {
-            return Vec3.add(Vec3(), v, u);
-        }
-
-
-        const cam = this.plugin.canvas3d!.camera;
-        const snapshot = cam.getSnapshot();
-        const newSnapshot = {
-            ...snapshot,
-            // target + rotateBy90(postition - target)
-            position: add(snapshot.target, rot90q(sub(snapshot.position, snapshot.target))),
-            target: snapshot.target,
-            up: Vec3.negUnitZ
-        };
-
-        PluginCommands.Camera.Reset(this.plugin, { snapshot: newSnapshot, durationMs: 1000 });
-        //requestAnimationFrame(() => this.plugin.canvas3d?.requestCameraReset({ snapshot: newSnapshot }));
-    }
-
-    ////////////////////////////// END OF PROTOTYPING SECTION
-
-
-
-
-
-
     constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
         const o = { ...DefaultViewerOptions, ...options };
         const defaultSpec = DefaultPluginUISpec();
@@ -213,6 +103,7 @@ export class Viewer {
             ],
             animations: [...defaultSpec.animations || []],
             customParamEditors: defaultSpec.customParamEditors,
+            customFormats: o?.customFormats,
             layout: {
                 initial: {
                     isExpanded: o.layoutIsExpanded,
@@ -261,7 +152,191 @@ export class Viewer {
         this.plugin = createPlugin(element, spec);
     }
 
+    setRemoteSnapshot(id: string) {
+        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
+        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
+    }
+
+    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
+        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
+    }
+
+    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'url',
+                params: {
+                    url: Asset.Url(url),
+                    format: format as any,
+                    isBinary,
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
+                }
+            }
+        }));
+    }
+
+    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+        const plugin = this.plugin;
+
+        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
+    }
+
+    async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
+        const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
+        const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+    }
+
+    loadPdb(pdb: string, options?: LoadStructureOptions) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb' as const,
+                params: {
+                    provider: {
+                        id: pdb,
+                        server: {
+                            name: provider,
+                            params: PdbDownloadProvider[provider].defaultValue as any
+                        }
+                    },
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
+                }
+            }
+        }));
+    }
+
+    loadPdbDev(pdbDev: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb-dev' as const,
+                params: {
+                    provider: {
+                        id: pdbDev,
+                        encoding: 'bcif',
+                    },
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    loadEmdb(emdb: string, options?: { detail?: number }) {
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+            source: {
+                name: 'pdb-emd-ds' as const,
+                params: {
+                    provider: {
+                        id: emdb,
+                        server: provider,
+                    },
+                    detail: options?.detail ?? 3,
+                }
+            }
+        }));
+    }
+
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
+        const plugin = this.plugin;
+
+        if (!plugin.dataFormats.get(format)) {
+            throw new Error(`Unknown density format: ${format}`);
+        }
+
+        if (options?.isLazy) {
+            const update = this.plugin.build();
+            update.toRoot().apply(StateTransforms.Data.LazyVolume, {
+                url,
+                format,
+                entryId: options?.entryId,
+                isBinary,
+                isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
+            });
+            return update.commit();
+        }
+
+        return plugin.dataTransaction(async () => {
+            const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+
+            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
+            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
+
+            const repr = plugin.build();
+            for (const iso of isovalues) {
+                repr
+                    .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
+                    .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                        type: 'isosurface',
+                        typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                        color: 'uniform',
+                        colorParams: { value: iso.color }
+                    }));
+            }
+
+            await repr.commit();
+        });
+    }
+
     handleResize() {
         this.plugin.layout.events.updated.next();
     }
 }
+
+export interface LoadStructureOptions {
+    representationParams?: StructureRepresentationPresetProvider.CommonParams
+}
+
+export interface VolumeIsovalueInfo {
+    type: 'absolute' | 'relative',
+    value: number,
+    color: Color,
+    alpha?: number,
+    volumeIndex?: number
+}

src/extensions/tmdet/LICENSE

@@ -0,0 +1,417 @@
+Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+
+Authors:
+
+* Gabor Tusnady (tusnady.gabor at ttk.hu)
+* Csongor Gerdan (gerdan.csongor at ttk.hu)
+
+=======================================================================
+
+Attribution-NonCommercial 4.0 International
+
+=======================================================================
+
+Creative Commons Corporation ("Creative Commons") is not a law firm and
+does not provide legal services or legal advice. Distribution of
+Creative Commons public licenses does not create a lawyer-client or
+other relationship. Creative Commons makes its licenses and related
+information available on an "as-is" basis. Creative Commons gives no
+warranties regarding its licenses, any material licensed under their
+terms and conditions, or any related information. Creative Commons
+disclaims all liability for damages resulting from their use to the
+fullest extent possible.
+
+Using Creative Commons Public Licenses
+
+Creative Commons public licenses provide a standard set of terms and
+conditions that creators and other rights holders may use to share
+original works of authorship and other material subject to copyright
+and certain other rights specified in the public license below. The
+following considerations are for informational purposes only, are not
+exhaustive, and do not form part of our licenses.
+
+     Considerations for licensors: Our public licenses are
+     intended for use by those authorized to give the public
+     permission to use material in ways otherwise restricted by
+     copyright and certain other rights. Our licenses are
+     irrevocable. Licensors should read and understand the terms
+     and conditions of the license they choose before applying it.
+     Licensors should also secure all rights necessary before
+     applying our licenses so that the public can reuse the
+     material as expected. Licensors should clearly mark any
+     material not subject to the license. This includes other CC-
+     licensed material, or material used under an exception or
+     limitation to copyright. More considerations for licensors:
+    wiki.creativecommons.org/Considerations_for_licensors
+
+     Considerations for the public: By using one of our public
+     licenses, a licensor grants the public permission to use the
+     licensed material under specified terms and conditions. If
+     the licensor's permission is not necessary for any reason--for
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+     licenses grant only permissions under copyright and certain
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+     Although not required by our licenses, you are encouraged to
+     respect those requests where reasonable. More considerations
+     for the public:
+    wiki.creativecommons.org/Considerations_for_licensees
+
+=======================================================================
+
+Creative Commons Attribution-NonCommercial 4.0 International Public
+License
+
+By exercising the Licensed Rights (defined below), You accept and agree
+to be bound by the terms and conditions of this Creative Commons
+Attribution-NonCommercial 4.0 International Public License ("Public
+License"). To the extent this Public License may be interpreted as a
+contract, You are granted the Licensed Rights in consideration of Your
+acceptance of these terms and conditions, and the Licensor grants You
+such rights in consideration of benefits the Licensor receives from
+making the Licensed Material available under these terms and
+conditions.
+
+
+Section 1 -- Definitions.
+
+  a. Adapted Material means material subject to Copyright and Similar
+     Rights that is derived from or based upon the Licensed Material
+     and in which the Licensed Material is translated, altered,
+     arranged, transformed, or otherwise modified in a manner requiring
+     permission under the Copyright and Similar Rights held by the
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+     Adapted Material is always produced where the Licensed Material is
+     synched in timed relation with a moving image.
+
+  b. Adapter's License means the license You apply to Your Copyright
+     and Similar Rights in Your contributions to Adapted Material in
+     accordance with the terms and conditions of this Public License.
+
+  c. Copyright and Similar Rights means copyright and/or similar rights
+     closely related to copyright including, without limitation,
+     performance, broadcast, sound recording, and Sui Generis Database
+     Rights, without regard to how the rights are labeled or
+     categorized. For purposes of this Public License, the rights
+     specified in Section 2(b)(1)-(2) are not Copyright and Similar
+     Rights.
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+

src/extensions/tmdet/README.md

@@ -0,0 +1,55 @@
+# TMDET Extension
+
+TmMol* is a Mol* extension to visualize transmembrane regions and topology
+according to data of http://pdbtm.enzim.hu/ served by PDBe.
+
+
+# Usage
+
+`loadWithUNITMPMembraneRepresentation` call on an initialized
+`PluginUIContext` object downloads structure and annotation data
+from the given URLs.
+
+For example:
+
+```
+<script type="text/javascript" src="./tm_molstar.js"></script>
+<script type="text/javascript">
+    // init viewer
+    var viewer = new tm_molstar.Viewer('app', {
+        layoutShowControls: false,
+        layoutIsExpanded: false,
+        viewportShowExpand: true,
+        collapseLeftPanel: true
+    });
+
+    var pdbId = '1a0s';
+
+    tm_molstar.loadWithUNITMPMembraneRepresentation(viewer.plugin, {
+
+        // URL to get mmCIF/PDBx data
+        structureUrl: `https://cs.litemol.org/${pdbId}/full`,
+
+        // URL to load PDBTM information according to FunPDBe Data Exchange Format
+        regionDescriptorUrl: `http://localhost:8000/tmdet-data/${pdbId}.json`,
+    });
+...
+
+```
+
+Please see the `index.html` and `index.ts` files of the demo
+application in the `src/apps/tm-viwer` folder and example data
+files in `data/tmdet-example-annotations` folder for more details.
+
+# Authors
+
+* Gabor Tusnady (tusnady.gabor at ttk.hu), Protein Bioinformatics Research Group, RCNS.
+* Csongor Gerdan (gerdan.csongor at ttk.hu), Protein Bioinformatics Research Group, RCNS.
+
+# License
+
+Creative Commons Attribution-NonCommercial 4.0 International Public
+License
+
+Please see the LICENSE file for more details or visit
+https://creativecommons.org/licenses/by-nc/4.0/.

src/extensions/tmdet/algorithm.ts

@@ -1,259 +1,33 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
 
-import { Structure, StructureElement, StructureProperties } from '../../mol-model/structure';
-import { Task, RuntimeContext } from '../../mol-task';
-import { CentroidHelper } from '../../mol-math/geometry/centroid-helper';
-import { AccessibleSurfaceAreaParams } from '../../mol-model-props/computed/accessible-surface-area';
 import { Vec3 } from '../../mol-math/linear-algebra';
-import { getElementMoleculeType } from '../../mol-model/structure/util';
-import { MoleculeType } from '../../mol-model/structure/model/types';
-import { AccessibleSurfaceArea } from '../../mol-model-props/computed/accessible-surface-area/shrake-rupley';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { MembraneOrientation } from './prop';
 import '../../mol-util/polyfill';
 
-const LARGE_CA_THRESHOLD = 5000;
-export const MEMBRANE_STORAGE_KEY = 'MEMBRANE_STORAGE_KEY';
-
-interface TMDETContext {
-    structure: Structure,
-
-    numberOfSpherePoints: number,
-    stepSize: number,
-    minThickness: number,
-    maxThickness: number,
-    asaCutoff: number,
-    adjust: number,
-
-    offsets: ArrayLike<number>,
-    exposed: ArrayLike<number>,
-    hydrophobic: ArrayLike<boolean>,
-    centroid: Vec3,
-    extent: number,
-    large: boolean
-};
-
 export const TMDETParams = {
     numberOfSpherePoints: PD.Numeric(140, { min: 35, max: 700, step: 1 }, { description: 'Number of spheres/directions to test for membrane placement. Original value is 350.' }),
     stepSize: PD.Numeric(1, { min: 0.25, max: 4, step: 0.25 }, { description: 'Thickness of membrane slices that will be tested' }),
     minThickness: PD.Numeric(20, { min: 10, max: 30, step: 1}, { description: 'Minimum membrane thickness used during refinement' }),
     maxThickness: PD.Numeric(40, { min: 30, max: 50, step: 1}, { description: 'Maximum membrane thickness used during refinement' }),
-    asaCutoff: PD.Numeric(40, { min: 10, max: 100, step: 1 }, { description: 'Relative ASA cutoff above which residues will be considered' }),
     adjust: PD.Numeric(14, { min: 0, max: 30, step: 1 }, { description: 'Minimum length of membrane-spanning regions (original values: 14 for alpha-helices and 5 for beta sheets). Set to 0 to not optimize membrane thickness.' }),
 };
 export type TMDETParams = typeof TMDETParams
 export type TMDETProps = PD.Values<TMDETParams>
 
-/**
- * Implements:
- * Membrane positioning for high- and low-resolution protein structures through a binary classification approach
- * Guillaume Postic, Yassine Ghouzam, Vincent Guiraud, and Jean-Christophe Gelly
- * Protein Engineering, Design & Selection, 2015, 1–5
- * doi: 10.1093/protein/gzv063
- */
-export function computeTMDET(structure: Structure, props: TMDETProps) {
-    return Task.create('Compute Membrane Orientation', async runtime => {
-        return await calculate(runtime, structure, props);
-    });
-}
-
-// avoiding namespace lookup improved performance in Chrome (Aug 2020) <<<<<<<<<<<<<<<<< WTH????
-const v3add = Vec3.add;
-const v3clone = Vec3.clone;
 const v3dot = Vec3.dot;
-const v3normalize = Vec3.normalize;
-const v3scale = Vec3.scale;
-const v3set = Vec3.set;
-const v3squaredDistance = Vec3.squaredDistance;
-const v3sub = Vec3.sub;
-const v3zero = Vec3.zero;
-
-const centroidHelper = new CentroidHelper();
-async function initialize(structure: Structure, props: TMDETProps, accessibleSurfaceArea: AccessibleSurfaceArea): Promise<TMDETContext> {
-    const l = StructureElement.Location.create(structure);
-    const { label_atom_id, label_comp_id, x, y, z } = StructureProperties.atom;
-    const asaCutoff = props.asaCutoff / 100;
-    centroidHelper.reset();
-
-    const offsets = new Array<number>();
-    const exposed = new Array<number>();
-    const hydrophobic = new Array<boolean>();
-
-    const vec = v3zero();
-    for (let i = 0, il = structure.units.length; i < il; ++i) {
-        const unit = structure.units[i];
-        const { elements } = unit;
-        l.unit = unit;
-
-        for (let j = 0, jl = elements.length; j < jl; ++j) {
-            const eI = elements[j];
-            l.element = eI;
-
-            // consider only amino acids
-            if (getElementMoleculeType(unit, eI) !== MoleculeType.Protein) {
-                continue;
-            }
-
-            // only CA is considered for downstream operations
-            if (label_atom_id(l) !== 'CA' && label_atom_id(l) !== 'BB') {
-                continue;
-            }
-
-            // original ANVIL only considers canonical amino acids
-            if (!MaxAsa[label_comp_id(l)]) {
-                continue;
-            }
-
-            // while iterating use first pass to compute centroid
-            v3set(vec, x(l), y(l), z(l));
-            centroidHelper.includeStep(vec);
-
-            // keep track of offsets and exposed state to reuse
-            offsets.push(structure.serialMapping.getSerialIndex(l.unit, l.element));
-            if (AccessibleSurfaceArea.getValue(l, accessibleSurfaceArea) / MaxAsa[label_comp_id(l)] > asaCutoff) {
-                exposed.push(structure.serialMapping.getSerialIndex(l.unit, l.element));
-                hydrophobic.push(isHydrophobic(label_comp_id(l)));
-            }
-        }
-    }
-
-    // calculate centroid and extent
-    centroidHelper.finishedIncludeStep();
-    const centroid = v3clone(centroidHelper.center);
-    for (let k = 0, kl = offsets.length; k < kl; k++) {
-        setLocation(l, structure, offsets[k]);
-        v3set(vec, x(l), y(l), z(l));
-        centroidHelper.radiusStep(vec);
-    }
-    const extent = 1.2 * Math.sqrt(centroidHelper.radiusSq);
-
-    return {
-        ...props,
-        structure,
-
-        offsets,
-        exposed,
-        hydrophobic,
-        centroid,
-        extent,
-        large: offsets.length > LARGE_CA_THRESHOLD
-    };
-}
-
-export async function calculate(runtime: RuntimeContext, structure: Structure, params: TMDETProps): Promise<MembraneOrientation> {
-    // can't get away with the default 92 points here
-    const asaProps = { ...PD.getDefaultValues(AccessibleSurfaceAreaParams), probeSize: 4.0, traceOnly: true, numberOfSpherePoints: 184 };
-    const accessibleSurfaceArea = await AccessibleSurfaceArea.compute(structure, asaProps).runInContext(runtime);
-
-    const ctx = await initialize(structure, params, accessibleSurfaceArea);
-
-    const normalVector = v3zero();
-    const center =  v3zero();
-
-    // localStorage vs sessionStorage
-    const membrane: MembraneOrientation = JSON.parse(
-        window.localStorage.getItem(MEMBRANE_STORAGE_KEY)!
-    );
-    window.console.debug('membrane object from localStorage:', membrane);
-
-    window.console.debug('normal vector:', membrane.normalVector);
-    window.console.debug('plain point 1:', membrane.planePoint1);
-    window.console.debug('plain point 2:', membrane.planePoint2);
-
-    v3sub(normalVector, membrane.planePoint1, membrane.planePoint2);
-    v3normalize(normalVector, normalVector);
-    v3add(center, membrane.planePoint1, membrane.planePoint2);
-    v3scale(center, center, 0.5);
-    window.console.debug('calculated center:', center);
-
-    const candidate: MembraneCandidate = {
-        normalVector: membrane.normalVector,
-        planePoint1: membrane.planePoint1,
-        planePoint2: membrane.planePoint2,
-        stats: HphobHphil.initial(ctx) //null // TODO: WTH?
-    };
-    const extent = adjustExtent(ctx, candidate, center);
-
-    window.console.debug('result of "tmdet / calculate":', {
-        planePoint1: membrane.planePoint1,
-        planePoint2: membrane.planePoint2,
-        normalVector,
-        centroid: center,
-        radius: extent
-    });
-
-    return {
-        planePoint1: membrane.planePoint1,
-        planePoint2: membrane.planePoint2,
-        normalVector,
-        centroid: center,
-        radius: extent
-    };
-}
-
-interface MembraneCandidate {
-    planePoint1: Vec3,
-    planePoint2: Vec3,
-    stats: HphobHphil,
-    normalVector?: Vec3,
-    spherePoint?: Vec3,
-    qmax?: number
-}
-
-namespace MembraneCandidate {
-    export function initial(c1: Vec3, c2: Vec3, stats: HphobHphil): MembraneCandidate {
-        return {
-            planePoint1: c1,
-            planePoint2: c2,
-            stats
-        };
-    }
-
-    export function scored(spherePoint: Vec3, planePoint1: Vec3, planePoint2: Vec3, stats: HphobHphil, qmax: number, centroid: Vec3): MembraneCandidate {
-        const normalVector = v3zero();
-        v3sub(normalVector, centroid, spherePoint);
-        return {
-            planePoint1,
-            planePoint2,
-            stats,
-            normalVector,
-            spherePoint,
-            qmax
-        };
-    }
-}
-
-
-/** Filter for membrane residues and calculate the final extent of the membrane layer */
-function adjustExtent(ctx: TMDETContext, membrane: MembraneCandidate, centroid: Vec3): number {
-    const { offsets, structure } = ctx;
-    const { normalVector, planePoint1, planePoint2 } = membrane;
-    const l = StructureElement.Location.create(structure);
-    const testPoint = v3zero();
-    const { x, y, z } = StructureProperties.atom;
-
-    const d1 = -v3dot(normalVector!, planePoint1);
-    const d2 = -v3dot(normalVector!, planePoint2);
-    const dMin = Math.min(d1, d2);
-    const dMax = Math.max(d1, d2);
-    let extent = 0;
-
-    for (let k = 0, kl = offsets.length; k < kl; k++) {
-        setLocation(l, structure, offsets[k]);
-        v3set(testPoint, x(l), y(l), z(l));
-        if (_isInMembranePlane(testPoint, normalVector!, dMin, dMax)) {
-            const dsq = v3squaredDistance(testPoint, centroid);
-            if (dsq > extent) extent = dsq;
-        }
-    }
-
-    return Math.sqrt(extent);
-}
 
 export function isInMembranePlane(testPoint: Vec3, normalVector: Vec3, planePoint1: Vec3, planePoint2: Vec3): boolean {
     const d1 = -v3dot(normalVector, planePoint1);
@@ -265,87 +39,3 @@ function _isInMembranePlane(testPoint: Vec3, normalVector: Vec3, min: number, ma
     const d = -v3dot(normalVector, testPoint);
     return d > min && d < max;
 }
-
-
-interface HphobHphil {
-    hphob: number,
-    hphil: number
-}
-
-namespace HphobHphil {
-    export function initial(ctx: TMDETContext): HphobHphil {
-        const { exposed, hydrophobic } = ctx;
-        let hphob = 0;
-        let hphil = 0;
-        for (let k = 0, kl = exposed.length; k < kl; k++) {
-            if (hydrophobic[k]) {
-                hphob++;
-            } else {
-                hphil++;
-            }
-        }
-        return { hphob, hphil };
-    }
-
-    const testPoint = v3zero();
-    export function sliced(ctx: TMDETContext, stepSize: number, spherePoint: Vec3, diam: Vec3, diamNorm: number): HphobHphil[] {
-        const { exposed, hydrophobic, structure } = ctx;
-        const { units, serialMapping } = structure;
-        const { unitIndices, elementIndices } = serialMapping;
-        const sliceStats: HphobHphil[] = [];
-        for (let i = 0, il = diamNorm - stepSize; i < il; i += stepSize) {
-            sliceStats[sliceStats.length] = { hphob: 0, hphil: 0 };
-        }
-
-        for (let i = 0, il = exposed.length; i < il; i++) {
-            const unit = units[unitIndices[exposed[i]]];
-            const elementIndex = elementIndices[exposed[i]];
-            v3set(testPoint, unit.conformation.x(elementIndex), unit.conformation.y(elementIndex), unit.conformation.z(elementIndex));
-            v3sub(testPoint, testPoint, spherePoint);
-            if (hydrophobic[i]) {
-                sliceStats[Math.floor(v3dot(testPoint, diam) / diamNorm / stepSize)].hphob++;
-            } else {
-                sliceStats[Math.floor(v3dot(testPoint, diam) / diamNorm / stepSize)].hphil++;
-            }
-        }
-        return sliceStats;
-    }
-}
-
-/** ANVIL-specific (not general) definition of membrane-favoring amino acids */
-const HYDROPHOBIC_AMINO_ACIDS = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'TRP', 'VAL']);
-/** Returns true if ANVIL considers this as amino acid that favors being embedded in a membrane */
-export function isHydrophobic(label_comp_id: string): boolean {
-    return HYDROPHOBIC_AMINO_ACIDS.has(label_comp_id);
-}
-
-/** Accessible surface area used for normalization. ANVIL uses 'Total-Side REL' values from NACCESS, from: Hubbard, S. J., & Thornton, J. M. (1993). naccess. Computer Program, Department of Biochemistry and Molecular Biology, University College London, 2(1). */
-export const MaxAsa: { [k: string]: number } = {
-    'ALA': 69.41,
-    'ARG': 201.25,
-    'ASN': 106.24,
-    'ASP': 102.69,
-    'CYS': 96.75,
-    'GLU': 134.74,
-    'GLN': 140.99,
-    'GLY': 32.33,
-    'HIS': 147.08,
-    'ILE': 137.96,
-    'LEU': 141.12,
-    'LYS': 163.30,
-    'MET': 156.64,
-    'PHE': 164.11,
-    'PRO': 119.90,
-    'SER': 78.11,
-    'THR': 101.70,
-    'TRP': 211.26,
-    'TYR': 177.38,
-    'VAL': 114.28
-};
-
-function setLocation(l: StructureElement.Location, structure: Structure, serialIndex: number) {
-    l.structure = structure;
-    l.unit = structure.units[structure.serialMapping.unitIndices[serialIndex]];
-    l.element = structure.serialMapping.elementIndices[serialIndex];
-    return l;
-}

src/extensions/tmdet/behavior.ts

@@ -1,32 +1,53 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
+ * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { MembraneOrientationProvider, MembraneOrientation } from './prop';
-import { StateObjectRef, StateTransformer, StateTransform } from '../../mol-state';
+import { StateObject, StateObjectRef, StateObjectCell, StateTransformer, StateTransform } from '../../mol-state';
 import { Task } from '../../mol-task';
 import { PluginBehavior } from '../../mol-plugin/behavior';
-import { MembraneOrientationRepresentationProvider, MembraneOrientationParams, MembraneOrientationRepresentation } from './representation';
-import { HydrophobicityColorThemeProvider } from '../../mol-theme/color/hydrophobicity';
 import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects';
 import { PluginContext } from '../../mol-plugin/context';
 import { DefaultQueryRuntimeTable } from '../../mol-script/runtime/query/compiler';
 import { StructureSelectionQuery, StructureSelectionCategory } from '../../mol-plugin-state/helpers/structure-selection-query';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { GenericRepresentationRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+
+
+
+// TMDET imports
+import { MembraneOrientationRepresentationProvider, MembraneOrientationParams, MembraneOrientationRepresentation } from './representation';
+import { MembraneOrientationProvider, MembraneOrientation, TmDetDescriptorCache } from './prop';
+import { applyTransformations, createMembraneOrientation } from './transformation';
+import { ComponentsType, PDBTMDescriptor, PMS } from './types';
+import { registerTmDetSymmetry } from './symmetry';
+import { TmDetLabelProvider } from './labeling';
+import { TmDetColorThemeProvider } from './tmdet-color-theme';
+import { loadInitialSnapshot, rotateCamera, storeCameraSnapshot } from './camera';
+
+
 
 const Tag = MembraneOrientation.Tag;
+const TMDET_MEMBRANE_ORIENTATION = 'Membrane Orientation';
 
 export const TMDETMembraneOrientation = PluginBehavior.create<{ autoAttach: boolean }>({
     name: 'tmdet-membrane-orientation-prop',
     category: 'custom-props',
     display: {
-        name: 'Membrane Orientation',
+        name: TMDET_MEMBRANE_ORIENTATION,
         description: 'Data calculated with TMDET algorithm.'
     },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
@@ -40,6 +61,9 @@ export const TMDETMembraneOrientation = PluginBehavior.create<{ autoAttach: bool
             this.ctx.representation.structure.registry.add(MembraneOrientationRepresentationProvider);
             this.ctx.query.structure.registry.add(isTransmembrane);
 
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(TmDetColorThemeProvider);
+            this.ctx.managers.lociLabels.addProvider(TmDetLabelProvider);
+
             this.ctx.genericRepresentationControls.set(Tag.Representation, selection => {
                 const refs: GenericRepresentationRef[] = [];
                 selection.structures.forEach(structure => {
@@ -68,6 +92,9 @@ export const TMDETMembraneOrientation = PluginBehavior.create<{ autoAttach: bool
 
             this.ctx.genericRepresentationControls.delete(Tag.Representation);
             this.ctx.builders.structure.representation.unregisterPreset(MembraneOrientationPreset);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(TmDetColorThemeProvider);
+            this.ctx.managers.lociLabels.removeProvider(TmDetLabelProvider);
         }
     },
     params: () => ({
@@ -94,20 +121,123 @@ export const isTransmembrane = StructureSelectionQuery('Residues Embedded in Mem
     }
 });
 
+
+
+
+//
+// //////////////////////////// TMDET VIEWER FUNCTIONS
+//
+
+
+
+
+export let membraneOrientation: MembraneOrientation;
+
+export async function loadWithUNITMPMembraneRepresentation(plugin: PluginUIContext, params: any) {
+    storeCameraSnapshot(plugin); // store if it is not stored yet
+
+    loadInitialSnapshot(plugin); // load if there is a stored one
+    setTimeout(() => plugin.clear(), 100); // clear scene after some delay
+
+
+    setTimeout(async () => {
+        const pdbtmDescriptor: PDBTMDescriptor = await downloadRegionDescriptor(plugin, params);
+        TmDetDescriptorCache.add(pdbtmDescriptor);
+
+        membraneOrientation = createMembraneOrientation(pdbtmDescriptor);
+
+        // load structure
+        await loadStructure(plugin, params, pdbtmDescriptor);
+        // cartoon, colors etc.
+        await createStructureRepresentation(plugin, pdbtmDescriptor);
+
+        //
+        // It also resets the camera because the membranes render 1st and the structure might not be fully visible
+        //
+        rotateCamera(plugin);
+    }, 500);
+}
+
+async function downloadRegionDescriptor(plugin: PluginUIContext, params: any): Promise<any> {
+    // run a fetch task
+    const downloadResult: string = await plugin.runTask(plugin.fetch({ url: params.regionDescriptorUrl })) as string;
+    const pdbtmDescriptor: any = JSON.parse(downloadResult);
+    return pdbtmDescriptor;
+}
+
+async function createStructureRepresentation(plugin: PluginUIContext, pdbtmDescriptor: any) {
+    // get the first structure of the first model
+    const structure: StateObjectRef<PMS> = plugin.managers.structure.hierarchy.current.models[0].structures[0].cell;
+    const components = await createStructureComponents(plugin, structure);
+
+    await applyTransformations(plugin, pdbtmDescriptor);
+
+    await buildStructureRepresentation(plugin, pdbtmDescriptor, components);
+}
+
+async function createStructureComponents(plugin: PluginUIContext, structure: StateObjectCell<PMS, StateTransform<StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>>) {
+    return {
+        polymer: await plugin.builders.structure.tryCreateComponentStatic(structure, 'polymer'),
+        ligand: await plugin.builders.structure.tryCreateComponentStatic(structure, 'ligand'),
+        water: await plugin.builders.structure.tryCreateComponentStatic(structure, 'water'),
+    };
+}
+
+async function buildStructureRepresentation(plugin: PluginUIContext, pdbtmDescriptor: PDBTMDescriptor, components: ComponentsType) {
+    const builder = plugin.builders.structure.representation;
+    const update = plugin.build();
+    if (components.polymer)
+        builder.buildRepresentation(update, components.polymer, {
+                type: 'cartoon',
+                color: TmDetColorThemeProvider.name as any, colorParams: { pdbtmDescriptor }
+            },
+            { tag: 'polymer' }
+        );
+    if (components.ligand)
+        builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick' }, { tag: 'ligand' });
+    if (components.water)
+        builder.buildRepresentation(update, components.water, { type: 'ball-and-stick', typeParams: { alpha: 0.6 } }, { tag: 'water' });
+    await update.commit();
+}
+
+async function loadStructure(ctx: PluginUIContext, params: any, pdbtmDescriptor: PDBTMDescriptor): Promise<void> {
+
+    // replace original symmetry format function
+    registerTmDetSymmetry(pdbtmDescriptor);
+
+    const builders = ctx.builders;
+    const data = await builders.data.download({
+        url: params.structureUrl,
+        label: `${pdbtmDescriptor.pdb_id}`,
+        isBinary: false
+    }); // , { state: { isGhost: true } });
+    const trajectory = await builders.structure.parseTrajectory(data, 'mmcif');
+
+    // create membrane representation
+    await builders.structure.hierarchy.applyPreset(
+        trajectory, 'default', { representationPreset: 'preset-membrane-orientation' as any });
+}
+
+
+
+
 //
+// //////////////////////////// END OF TMDET VIEWER SECTION
+//
+
+
 
-export { MembraneOrientation3D };
 
-type MembraneOrientation3D = typeof MembraneOrientation3D
+type MembraneOrientation3DType = typeof MembraneOrientation3D
 const MembraneOrientation3D = PluginStateTransform.BuiltIn({
-    name: 'membrane-orientation-3d',
+    name: Tag.Representation,
     display: {
-        name: 'Membrane Orientation',
+        name: TMDET_MEMBRANE_ORIENTATION,
         description: 'Membrane Orientation planes and rims. Data calculated with TMDET algorithm.'
     },
     from: PluginStateObject.Molecule.Structure,
     to: PluginStateObject.Shape.Representation3D,
-    params: (a) => {
+    params: () => {
         return {
             ...MembraneOrientationParams,
         };
@@ -117,7 +247,7 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
         return true;
     },
     apply({ a, params }, plugin: PluginContext) {
-        return Task.create('Membrane Orientation', async ctx => {
+        return Task.create(TMDET_MEMBRANE_ORIENTATION, async ctx => {
             await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
             const repr = MembraneOrientationRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => MembraneOrientationParams);
             await repr.createOrUpdate(params, a.data).runInContext(ctx);
@@ -125,7 +255,7 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
         });
     },
     update({ a, b, newParams }, plugin: PluginContext) {
-        return Task.create('Membrane Orientation', async ctx => {
+        return Task.create(TMDET_MEMBRANE_ORIENTATION, async ctx => {
             await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
             const props = { ...b.data.repr.props, ...newParams };
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
@@ -141,7 +271,7 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
 export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
     id: 'preset-membrane-orientation',
     display: {
-        name: 'Membrane Orientation', group: 'Annotation',
+        name: TMDET_MEMBRANE_ORIENTATION, group: 'Annotation',
         description: 'Shows orientation of membrane layers. Data calculated with TMDET algorithm.' // TODO add ' or obtained via RCSB PDB'
     },
     isApplicable(a) {
@@ -154,22 +284,22 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
         if (!structureCell || !structure) return {};
 
         if (!MembraneOrientationProvider.get(structure).value) {
-            await plugin.runTask(Task.create('Membrane Orientation', async runtime => {
+            await plugin.runTask(Task.create(TMDET_MEMBRANE_ORIENTATION, async runtime => {
                 await MembraneOrientationProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure);
             }));
         }
 
         const membraneOrientation = await tryCreateMembraneOrientation(plugin, structureCell);
-        const colorTheme = HydrophobicityColorThemeProvider.name as any;
+        const colorTheme =  TmDetColorThemeProvider.name as any;
         const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
 
         return { components: preset.components, representations: { ...preset.representations, membraneOrientation } };
     }
 });
 
-export function tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<MembraneOrientation3D>, initialState?: Partial<StateTransform.State>) {
+export function tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PMS>, params?: StateTransformer.Params<MembraneOrientation3DType>, initialState?: Partial<StateTransform.State>) {
     const state = plugin.state.data;
     const membraneOrientation = state.build().to(structure)
-        .applyOrUpdateTagged('membrane-orientation-3d', MembraneOrientation3D, params, { state: initialState });
+        .applyOrUpdateTagged(Tag.Representation, MembraneOrientation3D, params, { state: initialState });
     return membraneOrientation.commit({ revertOnError: true });
 }

src/extensions/tmdet/camera.ts

@@ -0,0 +1,62 @@
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { Quat, Vec3 } from '../../mol-math/linear-algebra';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { Camera } from '../../mol-canvas3d/camera';
+import { DebugUtil } from '../../apps/tm-viewer';
+
+let initialSnapshot: Camera.Snapshot;
+
+export function storeCameraSnapshot(plugin: PluginUIContext): void {
+    if (!initialSnapshot) {
+        initialSnapshot = plugin.canvas3d!.camera.getSnapshot();
+        DebugUtil.log('initialSnapshot stored:', initialSnapshot);
+    }
+}
+
+export function loadInitialSnapshot(plugin: PluginUIContext): void {
+    if (!initialSnapshot) {
+        DebugUtil.log('initialSnapshot is undefined');
+    } else {
+        DebugUtil.log('Loading initial snapshot:', initialSnapshot);
+        PluginCommands.Camera.Reset(plugin, { snapshot: initialSnapshot });
+    }
+}
+
+export async function rotateCamera(plugin: PluginUIContext) {
+    function rot90q(v: Vec3, axis: Vec3 = Vec3.create(1, 0, 0)): Vec3 {
+        const q = Quat.setAxisAngle(Quat(), axis, -Math.PI/2);
+        return Vec3.transformQuat(Vec3(), v, q);
+    }
+    function sub(v: Vec3, u: Vec3): Vec3 {
+        return Vec3.sub(Vec3(), v, u);
+    }
+    function add(v: Vec3, u: Vec3): Vec3 {
+        return Vec3.add(Vec3(), v, u);
+    }
+
+    const cam = plugin.canvas3d!.camera;
+    const snapshot = cam.getSnapshot();
+    const newSnapshot = {
+        ...snapshot,
+        // target + rotateBy90(postition - target)
+        position: add(snapshot.target, rot90q(sub(snapshot.position, snapshot.target))),
+        target: snapshot.target,
+        up: Vec3.negUnitZ
+    };
+    const duration = 100;
+    PluginCommands.Camera.Reset(plugin, { snapshot: newSnapshot, durationMs: duration }).then(() => {
+        setTimeout(()=> {
+            requestAnimationFrame(() => plugin.canvas3d?.requestCameraReset());
+        }, duration + 50); // The 2nd reset needs some delay
+    });
+
+}

src/extensions/tmdet/debug-utils.ts

@@ -0,0 +1,177 @@
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+
+import { mmCIF_Database } from "../../mol-io/reader/cif/schema/mmcif";
+import { Mat4, Vec3 } from "../../mol-math/linear-algebra";
+import { MmcifFormat } from "../../mol-model-formats/structure/mmcif";
+import { Model } from "../../mol-model/structure";
+import { AtomicConformation } from "../../mol-model/structure/model/properties/atomic";
+import { createStructureRepresentationParams } from "../../mol-plugin-state/helpers/structure-representation-params";
+import { StateTransforms } from "../../mol-plugin-state/transforms";
+import { PluginUIContext } from "../../mol-plugin-ui/context";
+import { Expression } from "../../mol-script/language/expression";
+import { Color } from "../../mol-util/color";
+import { rotateCamera as RC } from "./camera";
+import { TmDetDescriptorCache } from "./prop";
+import { getChainExpression as GCE, getCurrentHierarchy as GCH, transformationForStateTransform, transformWholeModel } from "./transformation";
+import { PDBTMTransformationMatrix } from "./types";
+
+export namespace DebugUtil {
+    let plugin: PluginUIContext;
+    let logEnabled = false;
+
+    export function init(ctx: PluginUIContext) {
+        plugin = ctx;
+    }
+
+    //
+    // logging
+    //
+    export function enableLog() {
+        logEnabled = true;
+    }
+
+    export function disableLog() {
+        logEnabled = false;
+    }
+
+    export function log(...args: any[]) {
+        if (logEnabled) {
+            console.log(...args);
+        }
+    }
+
+    //
+    //
+    // lin.alg.
+    //
+
+    export function transformVector(v: Vec3, matrix: Mat4): Vec3 {
+        const result = Vec3.transformMat4(Vec3(), v, matrix);
+        log("transformVector: Input v & matrix:", v, Mat4.makeTable(matrix));
+        log("transformVector: Result vector:", result);
+        return result;
+    }
+
+    export function descriptorMxToMat4(matrix: PDBTMTransformationMatrix): Mat4 {
+        log("descriptorMxToMat4: Input:", matrix);
+        const result = transformationForStateTransform(matrix);
+        log("descriptorMxToMat4: Result:", result);
+        return result;
+    }
+
+
+    //
+    // structure utils
+    //
+
+    export const getChainExpression = GCE;
+
+    export function getCellOfFirstStructure() {
+        return getCell();
+    }
+
+    export function getCell(structureIndex: number = 0, modelIndex: number = 0) {
+        return getCurrentHierarchy().models[structureIndex].structures[modelIndex].cell;
+    }
+
+    export function getCurrentHierarchy() {
+        return GCH(plugin);
+    }
+
+    export function getModelOfFirstStructure() {
+        return getCellOfFirstStructure().obj?.data.model;
+    }
+
+    // in case of mmCIF format
+    export function dumpAtomProperties(authAtomId: number) {
+        const model: Model|undefined = getModelOfFirstStructure();
+        log("First model:", model);
+        if(!model) {
+            return;
+        }
+
+        const rowCount = model.atomicHierarchy.atoms._rowCount;
+        const conformation: AtomicConformation = model.atomicConformation;
+        const db: mmCIF_Database = (model.sourceData as MmcifFormat).data.db;
+        const atom_site = db.atom_site;
+        for (let index = 0; index < rowCount; index++) {
+            if (conformation.atomId.value(index) == authAtomId) {
+                log("Model Atom Conformation:", {
+                    atomIdParameter: authAtomId,
+                    atomId: conformation.atomId.value(index),
+                    coords: [
+                        conformation.x[index],
+                        conformation.y[index],
+                        conformation.z[index]
+                    ],
+                    xyzDefined: conformation.xyzDefined
+                });
+
+                log("Atom Source Data (mmCIF database):", {
+                    authId: atom_site.auth_atom_id.value(index),
+                    compId: atom_site.auth_comp_id.value(index),
+                    authAsymId: atom_site.auth_asym_id.value(index),
+                    authSeqId: atom_site.auth_seq_id.value(index),
+                    coords: [
+                        atom_site.Cartn_x.value(index),
+                        atom_site.Cartn_y.value(index),
+                        atom_site.Cartn_z.value(index)
+                    ]
+                });
+            }
+        }
+    }
+
+
+    export function getCachesOfEachStructure() {
+        let sIndex = 0;
+        getCurrentHierarchy().structures.forEach(struct => {
+            let cIndex = 0;
+            struct.components.forEach(component => {
+                log(`struct: ${sIndex}; component: ${cIndex}`, component.cell.cache);
+                cIndex++;
+            });
+            sIndex++;
+        });
+    }
+
+    export function color(expression: Expression, color: number[], structureIndex: number = 0, modelIndex: number = 0) {
+        const structure = getCell(structureIndex, modelIndex);
+        const stateBuilder = plugin.build().to(structure);
+        stateBuilder.apply(
+            StateTransforms.Model.StructureSelectionFromExpression,
+            { expression: expression }
+        )
+        .apply(
+            StateTransforms.Representation.StructureRepresentation3D,
+            createStructureRepresentationParams(plugin, structure.obj?.data, {
+                type: 'ball-and-stick',
+                color: 'uniform', colorParams: { value: Color.fromArray(color, 0) }
+            })
+        );
+        stateBuilder.commit();
+    }
+
+    export function transform(entityId: string) {
+        const tmx = TmDetDescriptorCache.get(entityId)?.additional_entry_annotations.membrane.transformation_matrix;
+        transformWholeModel(plugin, tmx!);
+    }
+
+    //
+    // Camera
+    //
+    export function rotateCamera() {
+        RC(plugin);
+    }
+
+    export function requestCameraReset() {
+        requestAnimationFrame(() => plugin.canvas3d?.requestCameraReset({ durationMs: 1000 }));
+    }
+}

src/extensions/tmdet/labeling.ts

@@ -0,0 +1,97 @@
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+
+import { Loci } from '../../mol-model/loci';
+import { StructureElement } from '../../mol-model/structure';
+import { LociLabel, LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
+import { TmDetChainListCache, TmDetDescriptorCache } from './prop';
+import { createResidueListsPerChain, getChainAndResidueIds } from './tmdet-color-theme';
+import { ChainList, getResidue, ResidueItem } from './types';
+
+const siteLabels = [
+    "Side1",
+    "Side2",
+    "TM alpha",
+    "TM beta",
+    "TM re-entrant loop",
+    "Interfacial Helix",
+    "Unknown localization",
+    "Membrane Inside"
+];
+const DefaultResidueLabel = 6; // Unknown localization
+
+
+export const TmDetLabelProvider: LociLabelProvider = {
+    label: (loci: Loci): LociLabel => {
+        let labelText = siteLabels[DefaultResidueLabel];
+
+        if (loci.kind == 'element-loci') {
+            const unit = loci.elements[0].unit;
+            const pdbId = unit.model.entryId;
+
+            const descriptor = TmDetDescriptorCache.get(pdbId);
+            if (!descriptor) {
+                return labelText;
+            }
+
+            let chainList =  TmDetChainListCache.get(pdbId);
+            if (!chainList) {
+                chainList = createResidueListsPerChain(descriptor.chains);
+                TmDetChainListCache.set(pdbId, chainList);
+            }
+
+            const location = StructureElement.Loci.getFirstLocation(loci);
+            const { chainId, residueId } = getChainAndResidueIds(location!);
+            const residue = getResidue(chainList, chainId!, residueId!);
+            if (residue) {
+                labelText = siteLabels[residue?.siteId];
+                let regionText = getRegionText(chainList, chainId!, residue);
+                labelText = `${labelText}: ${regionText}`
+            }
+
+        }
+        return labelText;
+    }
+}
+
+function getRegionText(chainList: ChainList, chainId: string, residue: ResidueItem): string {
+    let value = "Unknown region range";
+
+    const chain = chainList.filter((chain) => chain.chainId === chainId)[0];
+    if (chain) {
+        // find start of region
+        const residues = chain.residues;
+        const  authId = parseInt(residue.authId!)
+        let previous = residues[residues.length-1];
+        for (let i = residues.length-1; i > 0; i--) {
+            const current = residues[i];
+            const currentId = parseInt(current.authId!);
+            // cancel loop when siteId changes
+            if (currentId < authId && current.siteId != residue.siteId) {
+                break;
+            }
+            previous = current;
+        }
+        value = `[ ${previous.authId}`;
+
+        // find end of region
+        previous = residues[0];
+        for (let current of residues) {
+            const currentId = parseInt(current.authId!);
+            // cancel loop when siteId changes
+            if (authId < currentId && current.siteId !== residue.siteId) {
+                break;
+            }
+            previous = current;
+        }
+        value = `${value}-${previous.authId} ]`;
+    }
+
+    return value;
+}

src/extensions/tmdet/prop.ts

@@ -1,20 +1,30 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
 
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Structure, StructureProperties, Unit } from '../../mol-model/structure';
 import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
-import { TMDETParams, TMDETProps, computeTMDET, isInMembranePlane } from './algorithm';
+import { isInMembranePlane, TMDETParams } from './algorithm';
 import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
 import { CustomProperty } from '../../mol-model-props/common/custom-property';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
 import { CustomPropSymbol } from '../../mol-script/language/symbol';
 import { Type } from '../../mol-script/language/type';
+import { membraneOrientation } from './behavior';
+import { ChainList, PDBTMDescriptor } from './types';
 
 export const MembraneOrientationParams = {
     ...TMDETParams
@@ -24,6 +34,54 @@ export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
 
 export { MembraneOrientation };
 
+/**
+ * Simple storage to made PDBTM descriptor available globally.
+ *
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+class DescriptorCache {
+    private map: Map<string, PDBTMDescriptor>;
+
+    constructor() {
+        this.map = new Map<string, PDBTMDescriptor>();
+    }
+
+    add(descriptor: PDBTMDescriptor) {
+        const key = descriptor.pdb_id.toLowerCase();
+        if (!this.map.has(key)) {
+            this.map.set(key, descriptor);
+        }
+    }
+
+    get(key: string) {
+        key = key.toLowerCase();
+        return this.map.get(key);
+    }
+
+}
+export const TmDetDescriptorCache = new DescriptorCache();
+
+class ChainListCache {
+    private map: Map<string, ChainList>;
+
+    constructor() {
+        this.map = new Map<string, ChainList>();
+    }
+
+    set(key: string, chains: ChainList) {
+        key = key.toLowerCase();
+        if (!this.map.has(key)) {
+            this.map.set(key, chains);
+        }
+    }
+
+    get(key: string) {
+        key = key.toLowerCase();
+        return this.map.get(key);
+    }
+}
+export const TmDetChainListCache = new ChainListCache();
+
 interface MembraneOrientation {
     // point in membrane boundary
     readonly planePoint1: Vec3,
@@ -51,14 +109,14 @@ namespace MembraneOrientation {
                 const membraneOrientation = MembraneOrientationProvider.get(structure).value;
                 if (!membraneOrientation) return 0;
                 Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
-                const { normalVector, planePoint1, planePoint2 } = membraneOrientation!;
+                const { normalVector, planePoint1, planePoint2 } = membraneOrientation;
                 return isInMembranePlane(pos, normalVector, planePoint1, planePoint2);
             })
     };
 }
 
 export const MembraneOrientationProvider: CustomStructureProperty.Provider<MembraneOrientationParams, MembraneOrientation> = CustomStructureProperty.createProvider({
-    label: 'Membrane Orientation',
+    label: 'TMDET Membrane Orientation Provider',
     descriptor: CustomPropertyDescriptor({
         name: 'tmdet_computed_membrane_orientation',
         symbols: MembraneOrientation.symbols,
@@ -66,15 +124,16 @@ export const MembraneOrientationProvider: CustomStructureProperty.Provider<Membr
     }),
     type: 'root',
     defaultParams: MembraneOrientationParams,
-    getParams: (data: Structure) => MembraneOrientationParams,
+//    getParams: (data: Structure) => MembraneOrientationParams,
+    getParams: function(data: Structure) {
+        //DebugUtil.log('getParams:: DEBUG', MembraneOrientationParams);
+        return MembraneOrientationParams;
+    },
     isApplicable: (data: Structure) => true,
     obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<MembraneOrientationProps>) => {
-        const p = { ...PD.getDefaultValues(MembraneOrientationParams), ...props };
-        return { value: await computeAnvil(ctx, data, p) };
+        //DebugUtil.log('obtain:: DEBUG', data.customPropertyDescriptors);
+        let result = membraneOrientation;
+        //DebugUtil.log("RESULT of 'obtain:'", result);
+        return { value: result };
     }
 });
-
-async function computeAnvil(ctx: CustomProperty.Context, data: Structure, props: Partial<TMDETProps>): Promise<MembraneOrientation> {
-    const p = { ...PD.getDefaultValues(TMDETParams), ...props };
-    return await computeTMDET(data, p).runInContext(ctx.runtime);
-}

src/extensions/tmdet/representation.ts

@@ -1,8 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
+ * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 
 import { ParamDefinition as PD } from '../../mol-util/param-definition';

src/extensions/tmdet/symmetry.ts

@@ -0,0 +1,100 @@
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { Column, Table } from '../../mol-data/db';
+import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { Model } from '../../mol-model/structure';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+import { PDBTMDescriptor } from './types';
+
+
+export function registerTmDetSymmetry(pdbtmDescriptor: PDBTMDescriptor) {
+    ModelSymmetry.Provider.formatRegistry.remove('mmCIF');
+    const excludedChains = constructChainListFromOperations(pdbtmDescriptor);
+    ModelSymmetry.Provider.formatRegistry.add('mmCIF',  function(model: Model) {
+        return tmDetSymmetryFromMmCif(model, excludedChains);
+    });
+}
+
+function constructChainListFromOperations(pdbtmDescriptor: PDBTMDescriptor): string[] {
+    const excludedChains: string[] = [];
+    // add chain deletes
+    const biomatrix = pdbtmDescriptor.additional_entry_annotations.biomatrix;
+    if (biomatrix != undefined && biomatrix.chain_deletes != undefined) {
+        biomatrix.chain_deletes.forEach(
+            chainId => excludedChains.push(chainId)
+        );
+    }
+    // exclude result of transformations
+    if (biomatrix != undefined && biomatrix.matrix_list != undefined) {
+        biomatrix.matrix_list.forEach(
+            matrix => matrix.apply_to_chain_list.forEach(
+                applyItem => excludedChains.push(applyItem.new_chain_id)
+            )
+        );
+    }
+
+    return excludedChains;
+}
+
+function tmDetSymmetryFromMmCif(model: Model, chainsForOperExpression: string[]) {
+    if (!MmcifFormat.is(model.sourceData)) return;
+
+    let data = model.sourceData.data.db;
+    let asymIdColumnData: string[][] = [];
+    // update chains (asym) for each author_defined_assemly
+    // NOTE: We assume that the first assembly is an author defined assembly.
+    const currentAssemblyId: string = data.pdbx_struct_assembly_gen.assembly_id.value(0);
+    const result: string[][] = createAsymIdColumnData(
+        data.pdbx_struct_assembly_gen, currentAssemblyId, chainsForOperExpression
+    );
+    asymIdColumnData = asymIdColumnData.concat(result);
+
+    const asym_id_list_column = Column.ofStringListArray(asymIdColumnData);
+    // create table with new column
+    let updated_pdbx_struct_assembly_gen = Table.ofColumns(
+        data.pdbx_struct_assembly_gen._schema,
+        {
+            assembly_id: data.pdbx_struct_assembly_gen.assembly_id,
+            asym_id_list: asym_id_list_column,
+            oper_expression: data.pdbx_struct_assembly_gen.oper_expression
+        }
+    );
+
+    return ModelSymmetry.fromData({
+        symmetry: data.symmetry,
+        cell: data.cell,
+        struct_ncs_oper: data.struct_ncs_oper,
+        atom_sites: data.atom_sites,
+        pdbx_struct_assembly: data.pdbx_struct_assembly,
+        pdbx_struct_assembly_gen: updated_pdbx_struct_assembly_gen,
+        pdbx_struct_oper_list: data.pdbx_struct_oper_list
+    });
+}
+
+function createAsymIdColumnData(pdbx_struct_assembly_gen: Table<mmCIF_Schema['pdbx_struct_assembly_gen']>, assemblyId: string, chains: string[]) {
+
+    const asym_id_list: string[][] = [];
+    for (let i = 0; i < pdbx_struct_assembly_gen._rowCount; i++) {
+        const currentAsymIdList = pdbx_struct_assembly_gen.asym_id_list.value(i);
+        asym_id_list.push(
+            (assemblyId == pdbx_struct_assembly_gen.assembly_id.value(i))
+                ? minus(currentAsymIdList, chains)
+                : currentAsymIdList
+        );
+    }
+    return asym_id_list;
+}
+
+// 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));
+}

src/extensions/tmdet/tmdet-color-theme.ts

@@ -0,0 +1,140 @@
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+
+import { StructureElement, Unit } from '../../mol-model/structure';
+import { ColorTheme } from '../../mol-theme/color';
+import { ThemeDataContext } from '../../mol-theme/theme';
+import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Location } from '../../mol-model/location';
+import { ChainList, getResidue, PDBTMChain } from './types';
+import { TmDetChainListCache, TmDetDescriptorCache } from './prop';
+
+
+export type TmDetColorThemeParams = {
+    pdbtmDescriptor: any
+};
+
+export function TmDetColorTheme(
+    ctx: ThemeDataContext,
+    props: PD.Values<TmDetColorThemeParams>
+): ColorTheme<TmDetColorThemeParams> {
+    let descriptorChains: PDBTMChain[] = [];
+    let pdbtmDescriptor = props.pdbtmDescriptor;
+    const pdbId = ctx.structure?.model.entryId;
+
+    // If it is not given as parameter,
+    // but there is one in the cache for this structure.
+    if (!pdbtmDescriptor) {
+        if (pdbId) {
+            pdbtmDescriptor = TmDetDescriptorCache.get(pdbId);
+        }
+    }
+    if (pdbtmDescriptor) {
+        descriptorChains = pdbtmDescriptor.chains;
+    }
+
+    const chainList = createResidueListsPerChain(descriptorChains);
+    if (pdbId) {
+        TmDetChainListCache.set(pdbId, chainList);
+    }
+
+    return {
+        factory: TmDetColorTheme,
+        granularity: 'group', //'residue' as any,
+        color: (location: Location) => getColor(location, chainList),
+        props: props,
+        description: 'TMDet...',
+    };
+}
+
+const DefaultResidueColor = ColorNames.lightgrey;
+
+//TODO: colors of not curated sites
+const siteColors = [
+    Color.fromArray([255,100,100], 0), // Side1
+    Color.fromArray([100,100,255], 0), // Side2
+    Color.fromArray([255,255,  0], 0), // TM alpha
+    Color.fromArray([255,255,  0], 0), // TM beta
+    Color.fromArray([255,127,  0], 0), // TM re-entrant loop
+    Color.fromArray([0,255,    0], 0), // Interfacial Helix
+    Color.fromArray([196,196,196], 0), // Unknow localization
+    Color.fromArray([0,255,    0], 0)  // Membrane Inside
+];
+
+
+function getColor(location: Location, chains: ChainList): Color {
+    let color = DefaultResidueColor;
+
+    // TODO: How to solve cases when chain operation occurs?
+    if (StructureElement.Location.is(location) && Unit.isAtomic(location.unit)) {
+
+        const { chainId, residueId } = getChainAndResidueIds(location);
+        color = residueColor(chains, chainId!, residueId!);
+    }
+    return color;
+}
+
+export function getChainAndResidueIds(location: Location) {
+    let chainId = undefined;
+    let residueId = undefined;
+
+    if (StructureElement.Location.is(location) && Unit.isAtomic(location.unit)) {
+        const atomicHierarchy = location.unit.model.atomicHierarchy;
+        const residueIdx = StructureElement.residueIndex(location);
+        const chainIdx = StructureElement.Location.chainIndex(location);
+
+        residueId = atomicHierarchy.residues.auth_seq_id.value(residueIdx).toString();
+        chainId = atomicHierarchy.chains.auth_asym_id.value(chainIdx).toString();
+    }
+    return {
+        chainId: chainId,
+        residueId: residueId
+    };
+}
+
+export function createResidueListsPerChain(chains: PDBTMChain[]) {
+    const chainList: ChainList = [];
+
+    chains.forEach((chain: PDBTMChain) => {
+        chainList.push({ chainId: chain.chain_label, residues: [] });
+        chain.residues.forEach((residue) => {
+            chainList[chainList.length - 1].residues.push({
+                authId: residue.pdb_res_label,
+                siteId: residue.site_data![0].site_id_ref - 1
+            });
+        });
+    });
+
+    return chainList;
+}
+
+function residueColor(chains: ChainList, chainId: string, residueId: string): Color {
+    let color = DefaultResidueColor;
+
+    const residue = getResidue(chains, chainId, residueId);
+    if (residue) {
+        color = siteColors[residue.siteId];
+    }
+
+    return color;
+}
+
+// Provider
+
+export const TmDetColorThemeProvider: ColorTheme.Provider<TmDetColorThemeParams, 'tmdet-custom-color-theme'> = {
+    name: 'tmdet-custom-color-theme',
+    label: 'TMDet Topology Theme',
+    category: 'TMDet',
+    factory: TmDetColorTheme,
+    getParams: () => ({ pdbtmDescriptor: { isOptional: true } }),
+    defaultValues: { pdbtmDescriptor: undefined },
+    isApplicable: () => true,
+};

src/extensions/tmdet/transformation.ts

@@ -0,0 +1,177 @@
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { PDBTMDescriptor, PDBTMTransformationMatrix, PMS } from './types';
+import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { StateObjectRef, StateBuilder } from '../../mol-state';
+import { Expression } from '../../mol-script/language/expression';
+import { MembraneOrientation } from './prop';
+import { TmDetColorThemeProvider } from './tmdet-color-theme';
+import { DebugUtil } from '../../apps/tm-viewer';
+
+export async function applyTransformations(plugin: PluginUIContext, pdbtmDescriptor: PDBTMDescriptor) {
+    const annotations = pdbtmDescriptor.additional_entry_annotations;
+
+    const membraneTransformation = transformationForStateTransform(pdbtmDescriptor.additional_entry_annotations.membrane.transformation_matrix);
+
+    if (annotations.biomatrix) {
+        annotations.biomatrix.matrix_list.forEach(function(mx) {
+            mx.apply_to_chain_list.forEach(async function(chainPair) {
+                let id  = chainPair.chain_id;
+                let newId = chainPair.new_chain_id;
+                const mtx = transformationForStateTransform(mx.transformation_matrix);
+                const composedTransformation = Mat4.mul(Mat4(), membraneTransformation, mtx);
+                chainTransformation(plugin, composedTransformation, id, newId);
+                // await plugin.runTask(Task.create(`TMDET: Transform '${id}' into '${newId}'`, async () => {
+                //     chainTransformation(plugin, mx.transformation_matrix, id, newId);
+                // }));
+            });
+        });
+    }
+
+    // WARNING: the components cannot be accessed here (created by chainTransformations in the above loop)
+    //          Maybe due to some kind of synchronization behavior.
+    //          plugin.runTask with "await" also cannot synchronize here.
+    //
+    // So this function call transforms only already existing components due to a side effect of another issue.
+    transformWholeModel(plugin, pdbtmDescriptor.additional_entry_annotations.membrane.transformation_matrix);
+    // await plugin.runTask(Task.create(`TMDET: Apply membrane transformation`, async () => {
+    //     transformWholeModel(plugin, pdbtmDescriptor.additional_entry_annotations.membrane.transformation_matrix);
+    // }));
+
+}
+
+export function transformWholeModel(plugin: PluginUIContext, membraneMatrix: PDBTMTransformationMatrix) {
+    //
+    // membrane transformation
+    //
+    const membraneTransformation = transformationForStateTransform(membraneMatrix);
+
+    // transform each component
+    DebugUtil.log("STRUCTURES", getCurrentHierarchy(plugin).structures);
+    getCurrentHierarchy(plugin).structures[0].components.forEach(component => {
+        const structure: StateObjectRef<PMS> = component.cell;
+        const update: StateBuilder.To<any, any> = plugin.build().to(structure);
+
+        const label = component.cell.obj!.label.toUpperCase();
+        DebugUtil.log("memb.transform of", label, component.cell.obj?.id);
+        DebugUtil.log(`${label} component.cell.obj:`, component.cell.obj);
+        // DebugUtil.log(`${label} component:`, component);
+
+        update
+            .apply(StateTransforms.Model.TransformStructureConformation, {
+                "transform": { name: "matrix", params: { data: membraneTransformation, transpose: false } }
+            });
+        update.commit();
+    });
+}
+
+/**
+ * Perform transformation on a chain.
+ *
+ * @param plugin UI context
+ * @param transformationMatrix 4x4 matrix describes transformation and translation
+ * @param chainId Id of chain to be selected for transformation
+ */
+export function chainTransformation(plugin: PluginUIContext, transformationMatrix: Mat4, chainId: string, newId: string): void {
+    const query: Expression = getChainExpression(chainId);
+
+//    const transformation = transformationForStateTransform(transformationMatrix);
+    const transformation = transformationMatrix;
+    const structure: StateObjectRef<PMS> = plugin.managers.structure.hierarchy.current.models[0].structures[0].cell;
+    const update: StateBuilder.To<any, any> = plugin.build().to(structure);
+
+    update
+        .apply(
+            StateTransforms.Model.StructureSelectionFromExpression,
+            { label: newId, expression: query }
+        )
+        .apply(StateTransforms.Model.TransformStructureConformation, {
+            "transform": { name: "matrix", params: { data: transformation, transpose: false } }
+        })
+        .apply(
+            StateTransforms.Representation.StructureRepresentation3D,
+            createStructureRepresentationParams(plugin, structure.obj?.data, {
+                type: 'cartoon',
+                color: TmDetColorThemeProvider.name as any //, colorParams: { pdbtmDescriptor }
+            })
+        );
+    update.commit();
+    DebugUtil.log(`${chainId}->${newId} DONE`);
+}
+
+// function vadd(a: Vec3, b: Vec3): Vec3 {
+//     return Vec3.add(Vec3.zero(), a, b);
+// }
+
+function vneg(u: Vec3): Vec3 {
+    return Vec3.negate(Vec3.zero(), u);
+}
+
+export function createMembraneOrientation(pdbtmDescriptor: PDBTMDescriptor): MembraneOrientation {
+    const membrane = pdbtmDescriptor.additional_entry_annotations.membrane;
+
+    const membraneNormal: Vec3 = Vec3.fromObj(membrane.normal);
+    const result: MembraneOrientation = {
+        planePoint1: membraneNormal,
+        planePoint2: vneg(membraneNormal),
+        centroid: Vec3.zero(),
+        normalVector: membraneNormal,
+
+        // (NOTE: the TMDET extension calculates and sets it during applying preset)
+        radius: membrane.radius
+    };
+
+    return result;
+}
+
+export function transformationForStateTransform(tmatrix: PDBTMTransformationMatrix): Mat4 {
+    // matrix expected in column-major order
+    const mx: Mat4 = Mat4.fromArray(Mat4.zero(),
+        [
+            tmatrix.rowx.x, tmatrix.rowy.x, tmatrix.rowz.x, 0,
+            tmatrix.rowx.y, tmatrix.rowy.y, tmatrix.rowz.y, 0,
+            tmatrix.rowx.z, tmatrix.rowy.z, tmatrix.rowz.z, 0,
+                         0,              0,              0, 1
+        ], 0
+    );
+    Mat4.setTranslation(mx, Vec3.create(
+        tmatrix.rowx.t,
+        tmatrix.rowy.t,
+        tmatrix.rowz.t
+    ));
+    // TODO: DebugUtil.log('MAT4\n', Mat4.makeTable(mx));
+    return mx;
+}
+
+export function getAtomGroupExpression(chainId: string, auth_array: number[]): Expression {
+    // TODO DebugUtil.log('auth_array:', auth_array);
+    const query: Expression =
+        MS.struct.generator.atomGroups({
+            'residue-test': MS.core.set.has([MS.set( ...auth_array ), MS.ammp('auth_seq_id')]),
+            'chain-test': MS.core.rel.eq([chainId, MS.ammp('label_asym_id')])
+        });
+    return query;
+}
+
+export function getChainExpression(chainId: string): Expression {
+    const query: Expression =
+        MS.struct.generator.atomGroups({
+            'chain-test': MS.core.rel.eq([chainId, MS.ammp('label_asym_id')])
+        });
+    return query;
+}
+
+export function getCurrentHierarchy(plugin: PluginUIContext) {
+    return plugin.managers.structure.hierarchy.current;
+}

src/extensions/tmdet/types.ts

@@ -0,0 +1,86 @@
+/**
+ * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
+ *
+ * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
+ *
+ * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
+ * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
+ */
+
+import { PluginStateObject } from "../../mol-plugin-state/objects";
+import { StateObject, StateTransformer } from '../../mol-state';
+import { StateObjectSelector } from "../../mol-state/object";
+
+export type PMS = PluginStateObject.Molecule.Structure;
+
+type PDBTMChainLabel = string;
+export type PDBTMChain = {
+    chain_label: PDBTMChainLabel,
+    additional_chain_annotations: {
+        type: string,
+        num_tm: number
+    },
+    residues: {
+        pdb_res_label?: string,
+        aa_type?: string,
+        site_data?: { site_id_ref: number, confidence_classification: string }[]
+    }[]
+};
+export type PDBTMRegion = { site: string, auth_ids: number[], color: number[] };
+export type PDBTMVec3 = { x: number, y: number, z: number };
+type PDBTMTransformationMatrixRow = { x: number, y: number, z: number, t: number };
+export type PDBTMTransformationMatrix = {
+    rowx: PDBTMTransformationMatrixRow,
+    rowy: PDBTMTransformationMatrixRow,
+    rowz: PDBTMTransformationMatrixRow
+};
+export type PDBTMDescriptor = {
+    pdb_id: string,
+    chains: PDBTMChain[],
+    site: { site_id: number, label: string }[],
+    additional_entry_annotations: {
+        membrane: {
+            normal: PDBTMVec3,
+            transformation_matrix: PDBTMTransformationMatrix,
+            radius: number
+        },
+        biomatrix: {
+            chain_deletes: string[],
+            matrix_list: {
+                matrix_id: string,
+                apply_to_chain_list: {
+                    chain_id: PDBTMChainLabel,
+                    new_chain_id: PDBTMChainLabel
+                }[],
+                transformation_matrix: PDBTMTransformationMatrix
+            }[]
+        }
+    }
+};
+
+type StructureComponentType = StateObjectSelector<
+        PMS,
+        StateTransformer<StateObject<any, StateObject.Type<any>>,
+        StateObject<any, StateObject.Type<any>>, any>
+    > | undefined;
+
+export type ComponentsType = { polymer: StructureComponentType; ligand: StructureComponentType; water: StructureComponentType };
+
+// for coloring and labeling
+export type ResidueItem = {
+    authId: string|undefined,
+    siteId: number
+};
+export type ChainList = {
+    chainId: string,
+    residues: ResidueItem[]
+}[];
+export function getResidue(chains: ChainList, chainId: string, residueId: string): ResidueItem|undefined {
+    let result = undefined;
+    const chain = chains.filter((chain) => chain.chainId === chainId)[0];
+    if (chain) {
+        result = chain.residues.filter((res) => res.authId === residueId)[0];
+    }
+
+    return result;
+}

webpack.config.common.js

@@ -21,7 +21,12 @@ const sharedConfig = {
                     { loader: 'css-loader', options: { sourceMap: false } },
                     { loader: 'sass-loader', options: { sourceMap: false } },
                 ]
-            }
+            },
+            {
+                test: /\.js$/,
+                enforce: 'pre',
+                use: ['source-map-loader'],
+            },
         ]
     },
     plugins: [

webpack.config.production.js

@@ -4,6 +4,7 @@ const examples = ['proteopedia-wrapper', 'basic-wrapper', 'lighting', 'alpha-orb
 
 module.exports = [
     createApp('viewer', 'molstar'),
+    createApp('tm-viewer', 'tm_molstar'),
     createApp('docking-viewer', 'molstar'),
     ...examples.map(createExample)
-];
+];

webpack.config.tm-viewer.js

@@ -0,0 +1,5 @@
+const common = require('./webpack.config.common.js');
+const createApp = common.createApp;
+module.exports = [
+    createApp('tm-viewer', 'tm_molstar')
+];