merge master, update lint & CHANGELOG, remove alignMotif

.eslintrc.json

@@ -31,14 +31,38 @@
         "no-unsafe-finally": "warn",
         "no-var": "error",
         "spaced-comment": "error",
-        "semi": "warn"
+        "semi": "warn",
+        "no-restricted-syntax": [
+            "error",
+            {
+                "selector": "ExportDefaultDeclaration",
+                "message": "Default exports are not allowed"
+            }
+        ],
+        "no-throw-literal": "error",
+        "key-spacing": "error",
+        "object-curly-spacing": ["error", "always"],
+        "array-bracket-spacing": "error",
+        "space-in-parens": "error",
+        "computed-property-spacing": "error",
+        "prefer-const": ["error", {
+            "destructuring": "all",
+            "ignoreReadBeforeAssign": false
+        }],
+        "space-before-function-paren": "off",
+        "func-call-spacing": "off",
+        "no-multi-spaces": "error",
+        "block-spacing": "error",
+        "keyword-spacing": "off",
+        "space-before-blocks": "error",
+        "semi-spacing": "error"
     },
     "overrides": [
         {
             "files": ["**/*.ts", "**/*.tsx"],
             "parser": "@typescript-eslint/parser",
             "parserOptions": {
-                "project": ["tsconfig.json"],
+                "project": ["tsconfig.json", "tsconfig.commonjs.json"],
                 "sourceType": "module"
             },
             "plugins": [
@@ -82,7 +106,14 @@
                     "error",
                     "1tbs", { "allowSingleLine": true }
                 ],
-                "@typescript-eslint/comma-spacing": "error"
+                "@typescript-eslint/comma-spacing": "error",
+                "@typescript-eslint/space-before-function-paren": ["error", {
+                    "anonymous": "always",
+                    "named": "never",
+                    "asyncArrow": "always"
+                }],
+                "@typescript-eslint/func-call-spacing": ["error"],
+                "@typescript-eslint/keyword-spacing": ["error"]
             }
         }
     ]

CHANGELOG.md

@@ -15,7 +15,8 @@
   - `positions` and `selection` props renamed to `targets` of type `Target[]`
 - Changed loading methods signature 
   - Added optional configuration parameter `config?: {props?: PresetProps; matrix?: Mat4; reprProvider?: TrajectoryHierarchyPresetProvider, params?: P}`
-  - The loading configuration includes an optional trajectory preset provider `TrajectoryHierarchyPresetProvider` 
+  - The loading configuration includes an optional trajectory preset provider `TrajectoryHierarchyPresetProvider`
+- Remove `alignMotif` methods (& pecos-integration) as the strucmotif service now reports RMSD and transformations for all hits
 
 ## [1.9.0] - 2021-09-29
 ### Added

src/viewer/helpers/superpose/pecos-integration.ts

@@ -1,110 +0,0 @@
-import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
-
-const ALIGNMENT_URL = 'https://alignment.rcsb.org/api/v1-beta/';
-
-// TODO probably move to selection.ts
-export type Residue = { label_asym_id: string, struct_oper_id?: string, label_seq_id: number };
-export type MotifSelection = { entry_id: string, residue_ids: Residue[] }
-export type MotifAlignmentRequest = {
-    query: {
-        entry_id: string,
-        residue_ids: Residue[]
-    },
-    hits: ({
-        id: string,
-        assembly_id: string,
-    } & MotifSelection)[]
-}
-
-export async function alignMotifs(query: MotifSelection, hit: MotifSelection): Promise<{ rmsd: number, matrix: Mat4 }> {
-    const q = {
-        options: {
-            return_sequence_data: false
-        },
-        context: {
-            mode: 'pairwise',
-            method: {
-                name: 'qcp',
-                parameters: {
-                    atom_pairing_strategy: 'all'
-                }
-            },
-            structures: [
-                {
-                    entry_id: query.entry_id,
-                    residue_ids: convertToPecosIdentifiers(query.residue_ids)
-                },
-                {
-                    entry_id: hit.entry_id,
-                    residue_ids: convertToPecosIdentifiers(hit.residue_ids)
-                }
-            ]
-        }
-    };
-
-    const formData = new FormData();
-    formData.append('query', JSON.stringify(q));
-
-    const r = await fetch(ALIGNMENT_URL + 'structures/submit', { method: 'POST', body: formData });
-
-    if (r.status !== 200) {
-        throw new Error('Failed to submit the job');
-    }
-
-    const uuid = await r.text();
-    const url = ALIGNMENT_URL + 'structures/results?uuid=' + uuid;
-    // polls every 25ms for up to 10 seconds
-    const result = await pollUntilDone(url, 25, 10 * 1000);
-
-    const { alignment_summary, blocks } = result.results[0];
-    return { rmsd: alignment_summary.scores[0].value, matrix: blocks[0].transformations[0] };
-}
-
-// convert strucmotif/arches residue identifiers to the pecos/sierra flavor
-function convertToPecosIdentifiers(identifiers: Residue[]) {
-    return identifiers.map(i => {
-        const o = Object.create(null);
-        Object.assign(o, {
-            asym_id: i.label_asym_id,
-            seq_id: i.label_seq_id
-        });
-        if (i.struct_oper_id) Object.assign(o, { struct_oper_id: i.struct_oper_id });
-        return o;
-    });
-}
-
-// create a promise that resolves after a short delay
-function delay(t: number) {
-    return new Promise(function(resolve) {
-        setTimeout(resolve, t);
-    });
-}
-
-/**
- * Poll until results are available.
- * @param url is the URL to request
- * @param interval is how often to poll
- * @param timeout is how long to poll waiting for a result (0 means try forever)
- */
-async function pollUntilDone(url: string, interval: number, timeout: number) {
-    const start = Date.now();
-    async function run(): Promise<any> {
-        const r = await fetch(url);
-        const data = await r.json();
-        if (data.info.status === 'COMPLETE') {
-            // we know we're done here, return from here whatever you
-            // want the final resolved value of the promise to be
-            return data;
-        } else if (data.info.status === 'ERROR') {
-            throw new Error('Failed to complete the job. Error: ' + data.info.message);
-        } else {
-            if (timeout !== 0 && Date.now() - start > timeout) {
-                throw new Error('timeout error on pollUntilDone');
-            } else {
-                // run again with a short delay
-                return delay(interval).then(run);
-            }
-        }
-    }
-    return run();
-}

src/viewer/index.html

@@ -492,17 +492,24 @@
                                 }
                             }, {
                                 pdbId: '3RU4',
-                                props: {
-                                    kind: 'motif',
-                                    assemblyId: '1',
-                                    label: '3RU4 #2: 0.26 Å',
-                                    targets: [
-                                        { labelAsymId: 'D', structOperId: '2', labelSeqId: 42 },
-                                        { labelAsymId: 'D', structOperId: '2', labelSeqId: 87 },
-                                        { labelAsymId: 'E', structOperId: '2', labelSeqId: 46 }
+                                config: {
+                                    props: {
+                                        kind: 'motif',
+                                        assemblyId: '1',
+                                        label: '3RU4 #2: 0.26 Å',
+                                        targets: [
+                                            { labelAsymId: 'D', structOperId: '2', labelSeqId: 42 },
+                                            { labelAsymId: 'D', structOperId: '2', labelSeqId: 87 },
+                                            { labelAsymId: 'E', structOperId: '2', labelSeqId: 46 }
+                                        ]
+                                    },
+                                    matrix: [
+                                        -0.049396686, -0.99700946, -0.059431925, 0.0,
+                                        -0.7568329, 0.076193266, -0.6491522, 0.0,
+                                        0.6517392, 0.012914069, -0.7583332, 0.0,
+                                        20.371853, 11.498471, 45.705563, 1.0
                                     ]
-                                },
-                                matrix: [-0.049396686, -0.99700946, -0.059431925, 0.0, -0.7568329, 0.076193266, -0.6491522, 0.0, 0.6517392, 0.012914069, -0.7583332, 0.0, 20.371853, 11.498471, 45.705563, 1.0]
+                                }
                             }
                         ]);
                     });
@@ -562,11 +569,11 @@
                                 label: '1LAP',
                                 kind: 'motif',
                                 targets: [
-                                    {label_asym_id: 'A', label_seq_id: 332, struct_oper_id: '1'},
-                                    {label_asym_id: 'A', label_seq_id: 334, struct_oper_id: '1'},
-                                    {label_asym_id: 'A', label_seq_id: 255, struct_oper_id: '1'},
-                                    {label_asym_id: 'A', label_seq_id: 273, struct_oper_id: '1'},
-                                    {label_asym_id: 'A', label_seq_id: 250, struct_oper_id: '1'}
+                                    { labelAsymId: 'A', labelSeqId: 332, structOperId: '1' },
+                                    { labelAsymId: 'A', labelSeqId: 334, structOperId: '1' },
+                                    { labelAsymId: 'A', labelSeqId: 255, structOperId: '1' },
+                                    { labelAsymId: 'A', labelSeqId: 273, structOperId: '1' },
+                                    { labelAsymId: 'A', labelSeqId: 250, structOperId: '1' }
                                 ],
                             }
                         });
@@ -576,14 +583,14 @@
                         const label = 'AF-F1Q6S1-F1 @ 0.23 RMSD';
                         const targets = [
                             // AF target must be devoid of struct_oper_id
-                            { label_asym_id: 'A', label_seq_id: 260 },
-                            { label_asym_id: 'A', label_seq_id: 265 },
-                            { label_asym_id: 'A', label_seq_id: 283 },
-                            { label_asym_id: 'A', label_seq_id: 342 },
-                            { label_asym_id: 'A', label_seq_id: 344 }
+                            { labelAsymId: 'A', labelSeqId: 260 },
+                            { labelAsymId: 'A', labelSeqId: 265 },
+                            { labelAsymId: 'A', labelSeqId: 283 },
+                            { labelAsymId: 'A', labelSeqId: 342 },
+                            { labelAsymId: 'A', labelSeqId: 344 }
                         ];
-                        const mat = [-0.471, 0.856, 0.215, 0, 0.405, -0.007, 0.914, 0, 0.784, 0.518, -0.343, 0, 54.981, 65.575, 12.287, 1];
-                        return viewer.loadStructureFromUrl(url, 'mmcif', false, { props: { kind: 'motif', label, targets } }, mat);
+                        const matrix = [-0.471, 0.856, 0.215, 0, 0.405, -0.007, 0.914, 0, 0.784, 0.518, -0.343, 0, 54.981, 65.575, 12.287, 1];
+                        return viewer.loadStructureFromUrl(url, 'mmcif', false, { props: { kind: 'motif', label, targets }, matrix });
                     })
                     .then(function() {
                         viewer.resetCamera(0)

src/viewer/index.ts

@@ -31,14 +31,13 @@ import { PluginLayoutControlsDisplay } from 'molstar/lib/mol-plugin/layout';
 import { SuperposeColorThemeProvider } from './helpers/superpose/color';
 import { encodeStructureData, downloadAsZipFile } from './helpers/export';
 import { setFocusFromRange, removeComponent, clearSelection, createComponent, select } from './helpers/viewer';
-import {SelectBase, SelectRange, SelectTarget, Target} from './helpers/selection';
+import { SelectBase, SelectRange, SelectTarget, Target } from './helpers/selection';
 import { StructureRepresentationRegistry } from 'molstar/lib/mol-repr/structure/registry';
 import { Mp4Export } from 'molstar/lib/extensions/mp4-export';
 import { DefaultPluginUISpec, PluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
 import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
 import { ANVILMembraneOrientation, MembraneOrientationPreset } from 'molstar/lib/extensions/anvil/behavior';
 import { MembraneOrientationRepresentationProvider } from 'molstar/lib/extensions/anvil/representation';
-import { MotifAlignmentRequest, alignMotifs } from './helpers/superpose/pecos-integration';
 import { AlphaFoldConfidenceScore } from './helpers/af-confidence/behavior';
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
 import { TrajectoryHierarchyPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset';
@@ -205,7 +204,7 @@ export class Viewer {
         return this._plugin;
     }
 
-    pluginCall(f: (plugin: PluginContext) => void){
+    pluginCall(f: (plugin: PluginContext) => void) {
         f(this.plugin);
     }
 
@@ -219,9 +218,9 @@ export class Viewer {
         if (!expandedChanged) return;
 
         if (currExpanded && !this._plugin.layout.state.showControls) {
-            this._plugin.layout.setProps({showControls: true});
+            this._plugin.layout.setProps({ showControls: true });
         } else if (!currExpanded && this._plugin.layout.state.showControls) {
-            this._plugin.layout.setProps({showControls: false});
+            this._plugin.layout.setProps({ showControls: false });
         }
         this.prevExpanded = this._plugin.layout.state.isExpanded;
     }
@@ -235,7 +234,7 @@ export class Viewer {
         return PluginCommands.State.RemoveObject(this._plugin, { state, ref: state.tree.root.ref });
     }
 
-    async loadPdbId<P>(pdbId: string, config?: {props?: PresetProps; matrix?: Mat4; reprProvider?: TrajectoryHierarchyPresetProvider, params?: P}) {
+    async loadPdbId<P>(pdbId: string, config?: { props?: PresetProps; matrix?: Mat4; reprProvider?: TrajectoryHierarchyPresetProvider, params?: P }) {
         for (const provider of this.modelUrlProviders) {
             try {
                 const p = provider(pdbId);
@@ -254,33 +253,6 @@ export class Viewer {
         this.resetCamera(0);
     }
 
-    async alignMotifs(request: MotifAlignmentRequest) {
-        const { query, hits } = request;
-
-        await this.loadPdbId(query.entry_id,
-            {
-                props: {
-                    kind: 'motif',
-                    label: query.entry_id,
-                    targets: query.residue_ids
-                }
-            });
-
-        for (const hit of hits) {
-            const { rmsd, matrix } = await alignMotifs(query, hit);
-            await this.loadPdbId(hit.entry_id, {
-                props: {
-                    kind: 'motif',
-                    assemblyId: hit.assembly_id,
-                    label: `${hit.entry_id} #${hit.id}: ${rmsd.toFixed(2)} RMSD`,
-                    targets: hit.residue_ids
-                },
-                matrix
-            });
-            this.resetCamera(0);
-        }
-    }
-
     loadStructureFromUrl<P>(url: string, format: BuiltInTrajectoryFormat, isBinary: boolean, config?: {props?: PresetProps; matrix?: Mat4; reprProvider?: TrajectoryHierarchyPresetProvider, params?: P}) {
         return this.customState.modelLoader.load({ fileOrUrl: url, format, isBinary }, config?.props, config?.matrix, config?.reprProvider, config?.params);
     }
@@ -322,7 +294,7 @@ export class Viewer {
         await createComponent(this._plugin, label, targets, representationType);
     }
 
-    removeComponent(componentLabel: string): void{
+    removeComponent(componentLabel: string): void {
         removeComponent(this._plugin, componentLabel);
     }
 }