Feature #232: in progress plane transformation

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": {

src/apps/viewer/index.html

@@ -36,7 +36,7 @@
         </style>
         <link rel="stylesheet" type="text/css" href="molstar.css" />
     </head>
-    <body>
+    <body onload="loadPdb()">
         <div id="app"></div>
         <script type="text/javascript" src="./molstar.js"></script>
         <script type="text/javascript">
@@ -55,17 +55,19 @@
             });
 
             // 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 regionDescriptors = {"pdb-id":"1afo","creation-date":"2021-09-03","is-transmembrane":1,"membrane-normal":{"x":Math.sin(Math.PI/2)*17.5,"y":0,"z":Math.cos(Math.PI/2)*17.5},"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.chains
-            );
+            function loadPdb() {
+                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
+                );
+            }
         </script>
     </body>
 </html>

src/apps/viewer/index.ts

@@ -65,7 +65,7 @@ const DefaultViewerOptions = {
 type ViewerOptions = typeof DefaultViewerOptions;
 
 
-export var membrane: MembraneOrientation;
+export let membrane: MembraneOrientation;
 
 export class Viewer {
     plugin: PluginUIContext
@@ -74,12 +74,13 @@ export class Viewer {
 
 
 
-    ////////////////////////////// UNITMP VIEWER PROTOTYPING SECTION
+    // //////////////////////////// UNITMP VIEWER PROTOTYPING SECTION
 
     async loadWithUNITMPMembraneRepresentation(url: string, regionDescriptors: any) {
         const membraneNormal: Vec3 = Vec3.fromObj(
             regionDescriptors['membrane-normal']
         );
+        console.log('DEBUG-01');
         const membrane: MembraneOrientation = {
             planePoint1: Vec3.fromArray(Vec3.zero(), membraneNormal, 0),
             planePoint2: Vec3.fromArray(Vec3.zero(), membraneNormal, 0),
@@ -89,22 +90,22 @@ export class Viewer {
             ),
             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;
 
-        window.console.debug('before store:', membrane);
+
+
+        console.log('DEBUG-02');
+
         localStorage.setItem(MEMBRANE_STORAGE_KEY, JSON.stringify(membrane));
 
         const isBinary = false;
 
         const data = await this.plugin.builders.data.download({
             url, label: `UniTMP: ${regionDescriptors['pdb-id']}`, isBinary
-        }); //, { state: { isGhost: true } });
+        }); // , { state: { isGhost: true } });
         const trajectory = await this.plugin.builders.structure.parseTrajectory(data, regionDescriptors.format);
         // create membrane representation
         await this.plugin.builders.structure.hierarchy.applyPreset(
@@ -128,10 +129,10 @@ export class Viewer {
         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();
+                const update = this.plugin.build();
+                const region = chain.regions[regionKey];
+                this.createRegionRepresentation(chain.chain_id, region, update.to(structure));
+                update.commit();
             }
 
         });
@@ -165,7 +166,7 @@ export class Viewer {
         return query;
     }
 
-    ////////////////////////////// END OF PROTOTYPING SECTION
+    // //////////////////////////// END OF PROTOTYPING SECTION
 
 
 

src/extensions/tmdet/algorithm.ts

@@ -36,7 +36,7 @@ interface TMDETContext {
     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.' }),
@@ -159,34 +159,22 @@ export async function calculate(runtime: RuntimeContext, structure: Structure, p
     const membrane: MembraneOrientation = JSON.parse(
         window.localStorage.getItem(MEMBRANE_STORAGE_KEY)!
     );
+    // TODO:
     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?
+        stats: HphobHphil.initial(ctx)
     };
     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,