NMR

.github/workflows/node.js.yml

@@ -11,11 +11,73 @@ jobs:
       uses: actions/setup-node@v3
       with:
         node-version: '16.14.0'
+    - name: Check versions
+      run: |
+          main_version=$(grep -E '^# 3DBIONOTES-WS v[0-9.]+' README.md | sed -E 's/^# 3DBIONOTES-WS v([0-9.]+)$/\1/')
+          viewer_protvista_version=$(cat app/views/webserver/viewer.html.haml | grep -Eo 'protvista-pdb-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}')
+          viewer_pdbe_molstar_version=$(cat app/views/webserver/viewer.html.haml | grep -Eo 'pdbe-molstar-plugin-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}')
+          cd app/assets/javascripts/covid19
+          bio_covid19_version=$(cat package.json | jq -r '.version')
+          cd ../3dbio_viewer
+          bio_viewer_version=$(cat package.json | jq -r '.version')
+          protvista_version=$(cat package.json | jq -r '.dependencies["@3dbionotes/protvista-pdb"]')
+          pdbe_molstar_version=$(cat package.json | jq -r '.dependencies["@3dbionotes/pdbe-molstar"]')
+          index_protvista_version=$(cat public/index.html | grep -Eo 'protvista-pdb-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}')
+          index_pdbe_molstar_version=$(cat public/index.html | grep -Eo 'pdbe-molstar-plugin-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}')
+          if [ "$bio_viewer_version" != "$bio_covid19_version" ] ||
+            [ "$main_version" != "$bio_covid19_version" ]; then
+            echo "3dbio_viewer version doesn't match with covid19 version"
+            echo "3dbio_viewer: $bio_viewer_version"
+            echo "covid19: $bio_covid19_version"
+            echo "README.md version: $main_version"
+            exit 1
+          fi
+
+          if [ "$viewer_protvista_version" != "$index_protvista_version" ] ||
+            [ "$viewer_pdbe_molstar_version" != "$index_pdbe_molstar_version" ] ||
+            [ "$(echo "$index_protvista_version" | sed 's/protvista-pdb-//')" != "$protvista_version" ] ||
+            [ "$(echo "$index_pdbe_molstar_version" | sed 's/pdbe-molstar-plugin-//')" != "$pdbe_molstar_version" ]; then
+            echo "Versions don't match:"
+            echo "Viewer and index protvista: $viewer_protvista_version, $index_protvista_version"
+            echo "Viewer and index pdbe-molstar: $viewer_pdbe_molstar_version, $index_pdbe_molstar_version"
+            echo "3dbio_viewer dependency and index protvista: $protvista_version, $(echo "$index_protvista_version" | sed 's/protvista-pdb-//')"
+            echo "3dbio_viewer dependency and index pdbe-molstar: $pdbe_molstar_version, $(echo "$index_pdbe_molstar_version" | sed 's/pdbe-molstar-plugin-//'), "
+            exit 1
+          fi
+
+          echo "3dbio_viewer versions match"
+          echo "README.md version: $main_version"
+          echo "3DBIONOTES version: $bio_viewer_version"
+          echo "protvista-pdb version: $protvista_version"
+          echo "pdbe-molstar version: $pdbe_molstar_version"
     - name: Install and build (3dbio_viewer)
       run: |
           cd app/assets/javascripts/3dbio_viewer
           yarn install
           yarn build
+    - name: Check build dependency versions (3dbioviewer)
+      run: |
+          cd app/assets/javascripts/3dbio_viewer
+          index_protvista_version=$(cat public/index.html | grep -Eo 'protvista-pdb-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}')
+          index_pdbe_molstar_version=$(cat public/index.html | grep -Eo 'pdbe-molstar-plugin-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}')
+          build_pdbe_molstar_file="build/pdbe-molstar/$index_pdbe_molstar_version.js"
+          if [ -f "$build_pdbe_molstar_file" ]; then
+            echo "Build file $build_pdbe_molstar_file exists."
+          else
+            echo "Build file $build_pdbe_molstar_file does not exist."
+            exit 1
+          fi
+
+          build_protvista_file="build/protvista-pdb/$index_protvista_version.js"
+          if [ -f "$build_protvista_file" ]; then
+            echo "Build file $build_protvista_file exists."
+          else
+            echo "Build file $build_protvista_file does not exist."
+            exit 1
+          fi
+    - name: Run tests (3dbio_viewer)
+      run: |
+          cd app/assets/javascripts/3dbio_viewer
           yarn test:nowatch
     - name: Install and build (covid19)
       run: |

app/assets/javascripts/3dbio_viewer/package.json

@@ -4,7 +4,7 @@
     "private": true,
     "dependencies": {
         "@3dbionotes/pdbe-molstar": "3.1.0-est-2",
-        "@3dbionotes/protvista-pdb": "2.0.1-est-2",
+        "@3dbionotes/protvista-pdb": "2.0.1-est-2-beta.1",
         "@material-ui/core": "^4.11.2",
         "@material-ui/data-grid": "4.0.0-alpha.35",
         "@material-ui/icons": "^4.11.2",
@@ -14,6 +14,7 @@
         "classnames": "^2.2.6",
         "d2-ui-components": "^2.4.0",
         "data-loader": "^3.0.0",
+        "file-saver": "^2.0.5",
         "fluture": "^13.0.1",
         "jszip": "^3.10.1",
         "purify-ts": "^1.1.0",
@@ -42,8 +43,10 @@
         "@types/axios": "^0.14.0",
         "@types/classnames": "^2.2.11",
         "@types/express": "^4.17.11",
+        "@types/file-saver": "^2.0.7",
         "@types/hookrouter": "^2.2.5",
         "@types/jest": "^26.0.15",
+        "@types/mime-types": "^2.1.4",
         "@types/node": "^12.0.0",
         "@types/react": "17.0.2",
         "@types/react-dom": "17.0.2",
@@ -114,4 +117,4 @@
             "\\.(jpg|jpeg|png|svg)$": "<rootDir>/config/fileMock.js"
         }
     }
-}
+}

app/assets/javascripts/3dbio_viewer/public/index.html

@@ -17,7 +17,7 @@
             type="text/css"
         />
 
-        <script src="/protvista-pdb/protvista-pdb-2.0.1-est-2.js"></script>
+        <script src="/protvista-pdb/protvista-pdb-2.0.1-est-2-beta.1.js"></script>
         <script src="/pdbe-molstar/pdbe-molstar-plugin-3.1.0-est-2.js"></script>
 
         <title>3dbio Viewer</title>

app/assets/javascripts/3dbio_viewer/src/compositionRoot.ts

@@ -21,6 +21,11 @@ import { BionotesOrganismRepository } from "./data/repositories/BionotesOrganism
 import { ExportAllAnnotationsUseCase } from "./domain/usecases/ExportAllAnnotationsUseCase";
 import { AnnotationsExportApiRepository } from "./data/repositories/AnnotationsExportApiRepository";
 import { ExportAnnotationsUseCase } from "./domain/usecases/ExportAnnotationsUseCase";
+import { GetPartialNMRTargetUseCase } from "./domain/usecases/GetPartialNMRTargetUseCase";
+import { SaveNMRTargetUseCase } from "./domain/usecases/SaveNMRTargetUseCase";
+import { NMRApiRepository } from "./data/repositories/NMRApiRepository";
+import { GetSourcesUseCase } from "./domain/usecases/GetSourcesUseCase";
+import { SourcesApiRepository } from "./data/repositories/SourcesApiRepository";
 
 export function getCompositionRoot() {
     const pdbRepository = new ApiPdbRepository();
@@ -33,8 +38,11 @@ export function getCompositionRoot() {
     const ontologyRepository = new BionotesOntologyRepository();
     const organismRepository = new BionotesOrganismRepository();
     const annotationsExportRepository = new AnnotationsExportApiRepository();
+    const nmrRepository = new NMRApiRepository();
+    const sourcesRepository = new SourcesApiRepository();
 
     return {
+        getSources: new GetSourcesUseCase(sourcesRepository),
         getPdb: new GetPdbUseCase(pdbRepository, ontologyRepository, organismRepository),
         getPdbInfo: new GetPdbInfoUseCase(pdbInfoRepository),
         searchDbModels: new SearchDbModelsUseCase(dbModelRepository),
@@ -50,6 +58,8 @@ export function getCompositionRoot() {
         exportAnnotations: new ExportAnnotationsUseCase(annotationsExportRepository),
         buildNetwork: new BuildNetworkUseCase(networkRepository),
         getNetwork: new GetNetworkUseCase(networkRepository),
+        getPartialNMR: new GetPartialNMRTargetUseCase(nmrRepository),
+        saveNMR: new SaveNMRTargetUseCase(nmrRepository),
     };
 }
 

app/assets/javascripts/3dbio_viewer/src/data/NMRScreening.ts

@@ -0,0 +1,79 @@
+import _ from "lodash";
+import { Codec, GetType, nullType, number, oneOf, string } from "purify-ts";
+import { NMRFragmentTarget } from "../domain/entities/Protein";
+import { commonLigand, pdbLigandC } from "./PdbLigands";
+
+const featureTypeCodec = Codec.interface({
+    dataSource: string,
+    name: string, // binding | not binding
+    description: string,
+    externalLink: string,
+});
+
+export const nmrFragmentCodec = Codec.interface({
+    name: string,
+    description: string,
+    externalLink: string,
+    pdbentry: nullType,
+    uniprotentry: string,
+    ligandentity: oneOf([Codec.interface(commonLigand), pdbLigandC]),
+    details: Codec.interface({
+        type: string, // binding | notbinding
+        entity: string, // NMR target
+    }),
+    start: number,
+    end: number,
+    featureType: featureTypeCodec,
+});
+
+export type NMRScreeningFragment = GetType<typeof nmrFragmentCodec>;
+
+export function getNMR(nmrScreenings: NMRScreeningFragment[]): NMRFragmentTarget[] {
+    const fragments = nmrScreenings.map(nmr => ({
+        ...nmr,
+        binding: !nmr.details.type.toLowerCase().includes("not"),
+    }));
+
+    const targets = _(fragments)
+        .groupBy(i => i.details.entity)
+        .toPairs()
+        .value();
+
+    return targets.flatMap(([name, targetFragments]) => {
+        const fragments = targetFragments.map(
+            ({ name, description, externalLink, binding, ligandentity, start, end }) => ({
+                name,
+                description,
+                externalLink,
+                binding,
+                ligand: {
+                    ...ligandentity,
+                    inChI: ligandentity.IUPACInChIkey,
+                    smiles: ligandentity.canonicalSMILES,
+                    pubchemId: ligandentity.pubChemCompoundId,
+                    formula: ligandentity.formula,
+                    imageDataResource: undefined,
+                },
+                start,
+                end,
+            })
+        );
+
+        const start = _.first(fragments.map(({ start }) => start));
+        const end = _.first(fragments.map(({ end }) => end));
+        const uniprotId = _.first(targetFragments.map(({ uniprotentry }) => uniprotentry));
+        if (!start || !end || !uniprotId) return [];
+
+        return [
+            {
+                name,
+                uniprotId,
+                fragments,
+                bindingCount: fragments.filter(({ binding }) => binding).length,
+                notBindingCount: fragments.filter(({ binding }) => !binding).length,
+                start,
+                end,
+            },
+        ];
+    });
+}

app/assets/javascripts/3dbio_viewer/src/data/NMRTarget.ts

@@ -0,0 +1,11 @@
+import _ from "lodash";
+import { Codec, GetType, number, string } from "purify-ts";
+
+export const nmrTargetCodec = Codec.interface({
+    entity: string,
+    start: number,
+    end: number,
+    uniprot_acc: string,
+});
+
+export type NMRTarget = GetType<typeof nmrTargetCodec>;

app/assets/javascripts/3dbio_viewer/src/data/Ontologies.ts

@@ -1,14 +1,10 @@
-import { array, Codec, GetType, nullType, number, oneOf, string } from "purify-ts";
-
-function maybeNull<Data>(type: Codec<Data>) {
-    return oneOf([type, nullType]);
-}
+import { array, Codec, GetType, nullable, number, string } from "purify-ts";
 
 function getOntologiesResponse<T>(codec: Codec<T>) {
     return Codec.interface({
         count: number,
-        next: maybeNull(string),
-        previous: maybeNull(string),
+        next: nullable(string),
+        previous: nullable(string),
         results: codec,
     });
 }

app/assets/javascripts/3dbio_viewer/src/data/Organisms.ts

@@ -1,16 +1,12 @@
 import _ from "lodash";
-import { array, Codec, GetType, nullType, number, oneOf, string } from "purify-ts";
+import { array, Codec, GetType, nullable, number, string } from "purify-ts";
 import { Organism } from "../domain/entities/LigandImageData";
 
-function maybeNull<Data>(type: Codec<Data>) {
-    return oneOf([type, nullType]);
-}
-
 function getOrganismsResponse<T>(codec: Codec<T>) {
     return Codec.interface({
         count: number,
-        next: maybeNull(string),
-        previous: maybeNull(string),
+        next: nullable(string),
+        previous: nullable(string),
         results: codec,
     });
 }

app/assets/javascripts/3dbio_viewer/src/data/PdbLigands.ts

@@ -121,18 +121,22 @@ const imageDataC = Codec.interface({
     assays: array(assayC),
 });
 
-export const pdbLigandC = Codec.interface({
+export const commonLigand = {
     IUPACInChIkey: string,
-    dbId: string,
-    pubChemCompoundId: string,
     name: string,
     formula: string,
     formula_weight: number,
     imageLink: string,
     externalLink: string,
+    pubChemCompoundId: string,
     IUPACInChI: string,
     isomericSMILES: string,
     canonicalSMILES: string,
+};
+
+export const pdbLigandC = Codec.interface({
+    ...commonLigand,
+    dbId: string,
     imageData: optional(array(imageDataC)), //it shouldn't be an array...
 });
 
@@ -256,6 +260,9 @@ export function getPdbLigand(pdbLigandOptions: PdbLigandsOptions): PdbLigand {
         name: ligand.name,
         inChI: ligand.IUPACInChIkey,
         imageDataResource: idr,
+        smiles: ligand.canonicalSMILES,
+        formula: ligand.formula,
+        pubchemId: ligand.pubChemCompoundId,
     };
 }
 

app/assets/javascripts/3dbio_viewer/src/data/codec-utils.ts

@@ -0,0 +1,21 @@
+import { Codec, array, nullable, number, optional, string } from "purify-ts";
+
+export function paginationCodec<Data>(type: Codec<Data>): Codec<Pagination<Data>> {
+    return Codec.interface({
+        count: number,
+        next: optional(nullable(string)),
+        previous: optional(nullable(string)),
+        results: array(type),
+    });
+}
+
+export function getResults<Data>(pagination?: Pagination<Data>) {
+    return pagination?.results ?? [];
+}
+
+export type Pagination<K> = {
+    count: number;
+    next: string | null | undefined;
+    previous: string | null | undefined;
+    results: K[];
+};