@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.2

package/lib/RcsbFvExamples/ExternalDataProvider.js

@@ -0,0 +1,951 @@
+import { __awaiter } from "tslib";
+import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { buildDataProviderFv } from "../RcsbFvWeb/RcsbFvBuilder";
+import { rcsbRequestCtxManager } from "../RcsbRequest/RcsbRequestContextManager";
+import { Assertions } from "../RcsbUtils/Helpers/Assertions";
+var assertElementListDefined = Assertions.assertElementListDefined;
+import { AlignmentReference } from "../RcsbUtils/PairwiseAlignmentTools/AlignmentReference";
+const alignment = {
+    "info": {
+        "uuid": "e6e216de-c650-4ad5-bd81-45e75dfbe180",
+        "status": "COMPLETE"
+    },
+    "meta": {
+        "alignment_mode": "pairwise",
+        "alignment_method": "fatcat-rigid"
+    },
+    "results": [
+        {
+            "structures": [
+                {
+                    "entry_id": "101M",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                },
+                {
+                    "entry_id": "1ASH",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                }
+            ],
+            "structure_alignment": [
+                {
+                    "regions": [
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 4,
+                                "beg_index": 0,
+                                "length": 47
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 52,
+                                "beg_index": 52,
+                                "length": 70
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 124,
+                                "beg_index": 128,
+                                "length": 22
+                            }
+                        ],
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 1,
+                                "beg_index": 0,
+                                "length": 17
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 22,
+                                "beg_index": 21,
+                                "length": 61
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 86,
+                                "beg_index": 86,
+                                "length": 14
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 101,
+                                "beg_index": 101,
+                                "length": 47
+                            }
+                        ]
+                    ],
+                    "transformations": [
+                        [
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1
+                        ],
+                        [
+                            -0.7671995717115603,
+                            -0.5623954843039239,
+                            0.30840904072376607,
+                            0,
+                            -0.6011420900233072,
+                            0.4627787494512096,
+                            -0.6515090303739346,
+                            0,
+                            0.2236805864799372,
+                            -0.6852351043918645,
+                            -0.6931232552303105,
+                            0,
+                            37.48154540719762,
+                            28.2044983569036,
+                            -7.345065372687518,
+                            1
+                        ]
+                    ],
+                    "summary": {
+                        "scores": [
+                            {
+                                "value": 1.95,
+                                "type": "RMSD"
+                            },
+                            {
+                                "value": 330.13,
+                                "type": "similarity-score"
+                            }
+                        ],
+                        "n_aln_residue_pairs": 139
+                    }
+                }
+            ],
+            "sequence_alignment": [
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 4,
+                            "beg_index": 0,
+                            "length": 17
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 21,
+                            "beg_index": 21,
+                            "length": 62
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 83,
+                            "beg_index": 86,
+                            "length": 14
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 97,
+                            "beg_index": 101,
+                            "length": 49
+                        }
+                    ],
+                    "gaps": [
+                        {
+                            "beg_index": 17,
+                            "length": 4
+                        },
+                        {
+                            "beg_index": 83,
+                            "length": 3
+                        },
+                        {
+                            "beg_index": 100,
+                            "length": 1
+                        }
+                    ]
+                },
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 1,
+                            "beg_index": 0,
+                            "length": 51
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 52,
+                            "beg_index": 52,
+                            "length": 74
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 126,
+                            "beg_index": 128,
+                            "length": 22
+                        }
+                    ],
+                    "gaps": [
+                        {
+                            "beg_index": 51,
+                            "length": 1
+                        },
+                        {
+                            "beg_index": 126,
+                            "length": 2
+                        }
+                    ]
+                }
+            ],
+            "summary": {
+                "scores": [
+                    {
+                        "value": 0.15,
+                        "type": "sequence-identity"
+                    },
+                    {
+                        "value": 1.94,
+                        "type": "RMSD"
+                    },
+                    {
+                        "value": 0.79,
+                        "type": "TM-score"
+                    },
+                    {
+                        "value": 330.13,
+                        "type": "similarity-score"
+                    },
+                    {
+                        "value": 0.34,
+                        "type": "sequence-similarity"
+                    }
+                ],
+                "n_aln_residue_pairs": 139,
+                "n_modeled_residues": [
+                    154,
+                    147
+                ],
+                "seq_aln_len": 150,
+                "aln_coverage": [
+                    90,
+                    95
+                ]
+            }
+        },
+        {
+            "structures": [
+                {
+                    "entry_id": "101M",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                },
+                {
+                    "entry_id": "4HHB",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                }
+            ],
+            "structure_alignment": [
+                {
+                    "regions": [
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 2,
+                                "beg_index": 0,
+                                "length": 48
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 56,
+                                "beg_index": 54,
+                                "length": 93
+                            }
+                        ],
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 1,
+                                "beg_index": 0,
+                                "length": 141
+                            }
+                        ]
+                    ],
+                    "transformations": [
+                        [
+                            1,
+                            0,
+                            0,
+                            0,
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+                            0,
+                            0,
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+                        ],
+                        [
+                            0.5659010881349978,
+                            0.8158255303919226,
+                            0.11909938038614465,
+                            0,
+                            0.49060456462775587,
+                            -0.21711201635870375,
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+                            7.329736404913569,
+                            7.069768946221407,
+                            1
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+                    ],
+                    "summary": {
+                        "scores": [
+                            {
+                                "value": 1.41,
+                                "type": "RMSD"
+                            },
+                            {
+                                "value": 360.42,
+                                "type": "similarity-score"
+                            }
+                        ],
+                        "n_aln_residue_pairs": 141
+                    }
+                }
+            ],
+            "sequence_alignment": [
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 2,
+                            "beg_index": 0,
+                            "length": 147
+                        }
+                    ]
+                },
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 1,
+                            "beg_index": 0,
+                            "length": 48
+                        },
+                        {
+                            "asym_id": "A",
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+                            "beg_index": 54,
+                            "length": 93
+                        }
+                    ],
+                    "gaps": [
+                        {
+                            "beg_index": 48,
+                            "length": 6
+                        }
+                    ]
+                }
+            ],
+            "summary": {
+                "scores": [
+                    {
+                        "value": 1.63,
+                        "type": "RMSD"
+                    },
+                    {
+                        "value": 360.42,
+                        "type": "similarity-score"
+                    },
+                    {
+                        "value": 0.26,
+                        "type": "sequence-identity"
+                    },
+                    {
+                        "value": 0.83,
+                        "type": "TM-score"
+                    },
+                    {
+                        "value": 0.4,
+                        "type": "sequence-similarity"
+                    }
+                ],
+                "n_aln_residue_pairs": 141,
+                "n_modeled_residues": [
+                    154,
+                    141
+                ],
+                "seq_aln_len": 147,
+                "aln_coverage": [
+                    92,
+                    100
+                ]
+            }
+        },
+        {
+            "structures": [
+                {
+                    "entry_id": "101M",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                },
+                {
+                    "entry_id": "3IA3",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                }
+            ],
+            "structure_alignment": [
+                {
+                    "regions": [
+                        [
+                            {
+                                "asym_id": "A",
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+                                "beg_index": 0,
+                                "length": 2
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+                            {
+                                "asym_id": "A",
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+                            {
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+                            {
+                                "asym_id": "A",
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+                                "length": 64
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+                        ],
+                        [
+                            {
+                                "asym_id": "A",
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+                                "beg_index": 0,
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+                                "asym_id": "A",
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+                            {
+                                "asym_id": "A",
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+                                "beg_index": 99,
+                                "length": 23
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+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 62,
+                                "beg_index": 124,
+                                "length": 30
+                            }
+                        ]
+                    ],
+                    "transformations": [
+                        [
+                            1,
+                            0,
+                            0,
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+                        [
+                            0.5053504853280419,
+                            -0.8551690322642134,
+                            -0.11535516128462073,
+                            0,
+                            0.8381805444620154,
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+                    "summary": {
+                        "scores": [
+                            {
+                                "value": 10.35,
+                                "type": "RMSD"
+                            },
+                            {
+                                "value": 163.43,
+                                "type": "similarity-score"
+                            }
+                        ],
+                        "n_aln_residue_pairs": 83
+                    }
+                }
+            ],
+            "sequence_alignment": [
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
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+                            "beg_index": 0,
+                            "length": 95
+                        },
+                        {
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+                        {
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+                    ],
+                    "gaps": [
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+                        {
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+                    ]
+                },
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
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+                        {
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+                        {
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+                    ],
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+            ],
+            "summary": {
+                "scores": [
+                    {
+                        "value": 0.38,
+                        "type": "TM-score"
+                    },
+                    {
+                        "value": 4.06,
+                        "type": "RMSD"
+                    },
+                    {
+                        "value": 163.43,
+                        "type": "similarity-score"
+                    },
+                    {
+                        "value": 0.13,
+                        "type": "sequence-identity"
+                    },
+                    {
+                        "value": 0.29,
+                        "type": "sequence-similarity"
+                    }
+                ],
+                "n_aln_residue_pairs": 83,
+                "n_modeled_residues": [
+                    154,
+                    90
+                ],
+                "seq_aln_len": 154,
+                "aln_coverage": [
+                    54,
+                    92
+                ]
+            }
+        },
+        {
+            "structures": [
+                {
+                    "entry_id": "101M",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                },
+                {
+                    "entry_id": "3IA3",
+                    "selection": {
+                        "asym_id": "B"
+                    }
+                }
+            ],
+            "structure_alignment": [
+                {
+                    "regions": [
+                        [
+                            {
+                                "asym_id": "A",
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+                                "beg_index": 0,
+                                "length": 18
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+                            {
+                                "asym_id": "A",
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+                                "beg_index": 22,
+                                "length": 30
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+                            {
+                                "asym_id": "A",
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+                                "beg_index": 58,
+                                "length": 85
+                            }
+                        ],
+                        [
+                            {
+                                "asym_id": "B",
+                                "beg_seq_id": 6,
+                                "beg_index": 0,
+                                "length": 4
+                            },
+                            {
+                                "asym_id": "B",
+                                "beg_seq_id": 11,
+                                "beg_index": 5,
+                                "length": 129
+                            }
+                        ]
+                    ],
+                    "transformations": [
+                        [
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
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+                            0,
+                            0,
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+                        [
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+                            6.001546353485595,
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+                    "summary": {
+                        "scores": [
+                            {
+                                "value": 278.41,
+                                "type": "similarity-score"
+                            },
+                            {
+                                "value": 2.79,
+                                "type": "RMSD"
+                            }
+                        ],
+                        "n_aln_residue_pairs": 133
+                    }
+                }
+            ],
+            "sequence_alignment": [
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 1,
+                            "beg_index": 0,
+                            "length": 4
+                        },
+                        {
+                            "asym_id": "A",
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+                            "beg_index": 5,
+                            "length": 138
+                        }
+                    ],
+                    "gaps": [
+                        {
+                            "beg_index": 4,
+                            "length": 1
+                        }
+                    ]
+                },
+                {
+                    "regions": [
+                        {
+                            "asym_id": "B",
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+                            "beg_index": 0,
+                            "length": 19
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+                        {
+                            "asym_id": "B",
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+                        {
+                            "asym_id": "B",
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+                            "beg_index": 58,
+                            "length": 85
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+                    ],
+                    "gaps": [
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+                            "length": 3
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+                        {
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+                    ]
+                }
+            ],
+            "summary": {
+                "scores": [
+                    {
+                        "value": 278.41,
+                        "type": "similarity-score"
+                    },
+                    {
+                        "value": 0.35,
+                        "type": "sequence-similarity"
+                    },
+                    {
+                        "value": 3.03,
+                        "type": "RMSD"
+                    },
+                    {
+                        "value": 0.66,
+                        "type": "TM-score"
+                    },
+                    {
+                        "value": 0.2,
+                        "type": "sequence-identity"
+                    }
+                ],
+                "n_aln_residue_pairs": 133,
+                "n_modeled_residues": [
+                    154,
+                    135
+                ],
+                "seq_aln_len": 143,
+                "aln_coverage": [
+                    86,
+                    99
+                ]
+            }
+        }
+    ]
+};
+class RcsbStructuralAlignmentProvider {
+    constructor(alignment) {
+        this.alignmentResponse = undefined;
+        this.alignment = alignment;
+    }
+    data() {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (this.alignmentResponse)
+                return this.alignmentResponse;
+            return new Promise((resolve) => {
+                alignmentTransform(this.alignment).then(ar => {
+                    this.alignmentResponse = ar;
+                    resolve(ar);
+                });
+            });
+        });
+    }
+    collect(requestConfig, filter) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
+                resolve(yield this.data());
+            }));
+        });
+    }
+    getTargets() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
+                var _a, _b;
+                resolve((_b = (_a = (yield this.data()).target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a; return (_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "NA"; })) !== null && _b !== void 0 ? _b : []);
+            }));
+        });
+    }
+    getAlignmentLength() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
+                var _a;
+                const ends = (_a = (yield this.data()).target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a, _b, _c; return (_c = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a[((_b = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _b === void 0 ? void 0 : _b.length) - 1]) === null || _c === void 0 ? void 0 : _c.query_end; });
+                assertElementListDefined(ends);
+                resolve(Math.max(...ends));
+            }));
+        });
+    }
+    getAlignment() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
+                resolve(this.data());
+            }));
+        });
+    }
+}
+function alignmentTransform(alignment) {
+    var _a, _b;
+    return __awaiter(this, void 0, void 0, function* () {
+        const alignmentRef = mergeAlignments(alignment.results);
+        const out = alignmentRef.buildAlignments();
+        const instance_ids = (_a = out.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
+        assertElementListDefined(instance_ids);
+        const seqs = yield rcsbRequestCtxManager.getInstanceSequences(instance_ids);
+        (_b = out.target_alignment) === null || _b === void 0 ? void 0 : _b.forEach(ta => {
+            var _a;
+            const seq = (_a = seqs.find(s => s.rcsbId === (ta === null || ta === void 0 ? void 0 : ta.target_id))) === null || _a === void 0 ? void 0 : _a.sequence;
+            if (seq && ta)
+                ta.target_sequence = seq;
+        });
+        return out;
+    });
+}
+function app() {
+    return __awaiter(this, void 0, void 0, function* () {
+        yield buildDataProviderFv("pfv", {
+            alignments: {
+                collector: new RcsbStructuralAlignmentProvider(alignment),
+                context: {
+                    queryId: "structural-alignment",
+                    to: SequenceReference.PdbInstance
+                }
+            }
+        }, {
+            boardConfig: {
+                rowTitleWidth: 100
+            }
+        });
+    });
+}
+app().then(() => {
+});
+function mergeAlignments(results) {
+    const result = results[0];
+    if (!result)
+        throw "Results not available";
+    const alignmentRef = new AlignmentReference(getInstanceId(result, 0), getInstanceId(result), transformToGapedDomain(result.sequence_alignment[0].regions), transformToGapedDomain(result.sequence_alignment[1].regions));
+    results.slice(1).forEach(result => {
+        alignmentRef.addAlignment(getInstanceId(result), transformToGapedDomain(result.sequence_alignment[0].regions), transformToGapedDomain(result.sequence_alignment[1].regions));
+    });
+    return alignmentRef;
+}
+function getInstanceId(result, index = 1) {
+    return `${result.structures[index].entry_id}.${result.structures[index].selection.asym_id}`;
+}
+function transformToGapedDomain(regions) {
+    const out = [];
+    let prevRegionEnd = 0;
+    regions.forEach(region => {
+        const beg = region.beg_index + 1;
+        const end = region.beg_index + region.length;
+        if (beg > (prevRegionEnd + 1)) {
+            const nGaps = beg - (prevRegionEnd + 1);
+            out.push(...Array(nGaps).fill(undefined));
+        }
+        prevRegionEnd = end;
+        const seqBeg = region.beg_seq_id;
+        const seqEnd = region.beg_seq_id + region.length - 1;
+        for (let i = seqBeg; i <= seqEnd; i++) {
+            out.push(i);
+        }
+    });
+    return out;
+}