moorhen 0.8.0 → 0.8.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "moorhen",
-  "version": "0.8.0",
+  "version": "0.8.2",
   "private": false,
   "main": "moorhen.js",
   "types": "./types/main.d.ts",
@@ -79,8 +79,8 @@
     "make-linux": "npm run build && electron-forge make --platform linux",
     "make-win32": "npm run build && electron-forge make --platform win32",
     "create-docs": "npm run create-version && npx jsdoc -c jsdoc.json",
-    "test": "npm run create-version && npx tsc && npm run transpile-ts-worker-jest && ln -s ./public/baby-gru/wasm/moorhen.data ./moorhen.data && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit",
-    "test-react": "npm run create-version && npx tsc && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit --selectProjects react-components"
+    "test": "npm run create-version && npx tsc && npm run transpile-ts-worker-jest && ln -s ./public/baby-gru/wasm/moorhen.data ./moorhen.data && ln -s ./public/baby-gru ./baby-gru && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit",
+    "test-react": "npm run create-version && npx tsc && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit --testPathIgnorePatterns=moorhenContainer.test.jsx --selectProjects react-components"
   },
   "eslintConfig": {
     "extends": [

package/types/moorhen.d.ts

@@ -880,8 +880,6 @@ export namespace moorhen {
         miscAppSettings: {
             defaultExpandDisplayCards: boolean; 
             transparentModalsOnMouseOut: boolean; 
-            enableRefineAfterMod: boolean; 
-            animateRefine: boolean;
         };
         generalStates: {
             devMode: boolean; 
@@ -899,8 +897,6 @@ export namespace moorhen {
             newCootCommandExit: boolean;
             newCootCommandStart: boolean;        
             showResidueSelection: boolean;
-            useRamaRefinementRestraints: boolean;
-            useTorsionRefinementRestraints: boolean;        
         };
         sharedSession: {
             isInSharedSession: boolean;
@@ -913,6 +909,9 @@ export namespace moorhen {
             cursorStyle: string;
         };
         activePopUps: {
+            goToResiduePopUp: {
+                show: boolean;
+            };
             matchingLigandPopUp: {
                 show: boolean;
                 refMolNo: number;
@@ -969,6 +968,13 @@ export namespace moorhen {
             showScoresToast: boolean;
             moleculeUpdate: { switch: boolean, molNo: number };
         };
+        refinementSettings: {
+            useRamaRefinementRestraints: boolean;
+            useTorsionRefinementRestraints: boolean;        
+            enableRefineAfterMod: boolean; 
+            animateRefine: boolean;
+            refinementSelection: 'SINGLE' | 'TRIPLE' | 'SPHERE';
+        };
     }
     
     type actionButtonSettings = {

package/baby-gru/wasm/RDKit_minimal.js

@@ -1 +0,0 @@
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pr.ErrnoError(28);if("."!==(l=Q.relative(t,o)).charAt(0))throw new pr.ErrnoError(55);try{u=pr.lookupNode(n,s)}catch(r){}if(c!==u){var h=pr.isDir(c.mode),d=pr.mayDelete(e,i,h);if(d)throw new pr.ErrnoError(d);if(d=u?pr.mayDelete(n,s,h):pr.mayCreate(n,s))throw new pr.ErrnoError(d);if(!e.node_ops.rename)throw new pr.ErrnoError(63);if(pr.isMountpoint(c)||u&&pr.isMountpoint(u))throw new pr.ErrnoError(10);if(n!==e&&(d=pr.nodePermissions(e,"w")))throw new pr.ErrnoError(d);pr.hashRemoveNode(c);try{e.node_ops.rename(c,n,s)}catch(r){throw r}finally{pr.hashAddNode(c)}}},rmdir(r){var t=pr.lookupPath(r,{parent:!0}).node,e=J.basename(r),n=pr.lookupNode(t,e),o=pr.mayDelete(t,e,!0);if(o)throw new pr.ErrnoError(o);if(!t.node_ops.rmdir)throw new pr.ErrnoError(63);if(pr.isMountpoint(n))throw new pr.ErrnoError(10);t.node_ops.rmdir(t,e),pr.destroyNode(n)},readdir(r){var t=pr.lookupPath(r,{follow:!0}).node;if(!t.node_ops.readdir)throw new pr.ErrnoError(54);return t.node_ops.readdir(t)},unlink(r){var t=pr.lookupPath(r,{parent:!0}).node;if(!t)throw new pr.ErrnoError(44);var e=J.basename(r),n=pr.lookupNode(t,e),o=pr.mayDelete(t,e,!1);if(o)throw new pr.ErrnoError(o);if(!t.node_ops.unlink)throw new pr.ErrnoError(63);if(pr.isMountpoint(n))throw new pr.ErrnoError(10);t.node_ops.unlink(t,e),pr.destroyNode(n)},readlink(r){var t=pr.lookupPath(r).node;if(!t)throw new pr.ErrnoError(44);if(!t.node_ops.readlink)throw new pr.ErrnoError(28);return Q.resolve(pr.getPath(t.parent),t.node_ops.readlink(t))},stat(r,t){var e=pr.lookupPath(r,{follow:!t}).node;if(!e)throw new pr.ErrnoError(44);if(!e.node_ops.getattr)throw new pr.ErrnoError(63);return e.node_ops.getattr(e)},lstat:r=>pr.stat(r,!0),chmod(r,t,e){var n;if(!(n="string"==typeof r?pr.lookupPath(r,{follow:!e}).node:r).node_ops.setattr)throw new pr.ErrnoError(63);n.node_ops.setattr(n,{mode:4095&t|-4096&n.mode,timestamp:Date.now()})},lchmod(r,t){pr.chmod(r,t,!0)},fchmod(r,t){var e=pr.getStreamChecked(r);pr.chmod(e.node,t)},chown(r,t,e,n){var o;if(!(o="string"==typeof r?pr.lookupPath(r,{follow:!n}).node:r).node_ops.setattr)throw new pr.ErrnoError(63);o.node_ops.setattr(o,{timestamp:Date.now()})},lchown(r,t,e){pr.chown(r,t,e,!0)},fchown(r,t,e){var n=pr.getStreamChecked(r);pr.chown(n.node,t,e)},truncate(r,t){if(t<0)throw new pr.ErrnoError(28);var e;if(!(e="string"==typeof r?pr.lookupPath(r,{follow:!0}).node:r).node_ops.setattr)throw new pr.ErrnoError(63);if(pr.isDir(e.mode))throw new pr.ErrnoError(31);if(!pr.isFile(e.mode))throw new pr.ErrnoError(28);var n=pr.nodePermissions(e,"w");if(n)throw new pr.ErrnoError(n);e.node_ops.setattr(e,{size:t,timestamp:Date.now()})},ftruncate(r,t){var e=pr.getStreamChecked(r);if(0==(2097155&e.flags))throw new pr.ErrnoError(28);pr.truncate(e.node,t)},utime(r,t,e){var n=pr.lookupPath(r,{follow:!0}).node;n.node_ops.setattr(n,{timestamp:Math.max(t,e)})},open(r,t,e){if(""===r)throw new pr.ErrnoError(44);var n;if(e=void 0===e?438:e,e=64&(t="string"==typeof t?(r=>{var t={r:0,"r+":2,w:577,"w+":578,a:1089,"a+":1090}[r];if(void 0===t)throw new Error(`Unknown file open mode: ${r}`);return t})(t):t)?4095&e|32768:0,"object"==typeof r)n=r;else{r=J.normalize(r);try{n=pr.lookupPath(r,{follow:!(131072&t)}).node}catch(r){}}var a=!1;if(64&t)if(n){if(128&t)throw new pr.ErrnoError(20)}else n=pr.mknod(r,e,0),a=!0;if(!n)throw new pr.ErrnoError(44);if(pr.isChrdev(n.mode)&&(t&=-513),65536&t&&!pr.isDir(n.mode))throw new pr.ErrnoError(54);if(!a){var i=pr.mayOpen(n,t);if(i)throw new pr.ErrnoError(i)}512&t&&!a&&pr.truncate(n,0),t&=-131713;var s=pr.createStream({node:n,path:pr.getPath(n),flags:t,seekable:!0,position:0,stream_ops:n.stream_ops,ungotten:[],error:!1});return s.stream_ops.open&&s.stream_ops.open(s),!o.logReadFiles||1&t||(pr.readFiles||(pr.readFiles={}),r in pr.readFiles||(pr.readFiles[r]=1)),s},close(r){if(pr.isClosed(r))throw new pr.ErrnoError(8);r.getdents&&(r.getdents=null);try{r.stream_ops.close&&r.stream_ops.close(r)}catch(r){throw 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pr.ErrnoError(28);r.seekable&&1024&r.flags&&pr.llseek(r,0,2);var i=void 0!==o;if(i){if(!r.seekable)throw new pr.ErrnoError(70)}else o=r.position;var s=r.stream_ops.write(r,t,e,n,o,a);return i||(r.position+=s),s},allocate(r,t,e){if(pr.isClosed(r))throw new pr.ErrnoError(8);if(t<0||e<=0)throw new pr.ErrnoError(28);if(0==(2097155&r.flags))throw new pr.ErrnoError(8);if(!pr.isFile(r.node.mode)&&!pr.isDir(r.node.mode))throw new pr.ErrnoError(43);if(!r.stream_ops.allocate)throw new pr.ErrnoError(138);r.stream_ops.allocate(r,t,e)},mmap(r,t,e,n,o){if(0!=(2&n)&&0==(2&o)&&2!=(2097155&r.flags))throw new pr.ErrnoError(2);if(1==(2097155&r.flags))throw new pr.ErrnoError(2);if(!r.stream_ops.mmap)throw new pr.ErrnoError(43);return r.stream_ops.mmap(r,t,e,n,o)},msync:(r,t,e,n,o)=>r.stream_ops.msync?r.stream_ops.msync(r,t,e,n,o):0,munmap:r=>0,ioctl(r,t,e){if(!r.stream_ops.ioctl)throw new pr.ErrnoError(59);return 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pr.ErrnoError(e);pr.currentPath=t.path},createDefaultDirectories(){pr.mkdir("/tmp"),pr.mkdir("/home"),pr.mkdir("/home/web_user")},createDefaultDevices(){pr.mkdir("/dev"),pr.registerDevice(pr.makedev(1,3),{read:()=>0,write:(r,t,e,n,o)=>n}),pr.mkdev("/dev/null",pr.makedev(1,3)),cr.register(pr.makedev(5,0),cr.default_tty_ops),cr.register(pr.makedev(6,0),cr.default_tty1_ops),pr.mkdev("/dev/tty",pr.makedev(5,0)),pr.mkdev("/dev/tty1",pr.makedev(6,0));var r=new Uint8Array(1024),t=0,e=()=>(0===t&&(t=Z(r).byteLength),r[--t]);pr.createDevice("/dev","random",e),pr.createDevice("/dev","urandom",e),pr.mkdir("/dev/shm"),pr.mkdir("/dev/shm/tmp")},createSpecialDirectories(){pr.mkdir("/proc");var r=pr.mkdir("/proc/self");pr.mkdir("/proc/self/fd"),pr.mount({mount(){var t=pr.createNode(r,"fd",16895,73);return t.node_ops={lookup(r,t){var e=+t,n=pr.getStreamChecked(e),o={parent:null,mount:{mountpoint:"fake"},node_ops:{readlink:()=>n.path}};return 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