moorhen 0.9.0 → 0.9.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "moorhen",
-  "version": "0.9.0",
+  "version": "0.9.2",
   "private": false,
   "main": "moorhen.js",
   "types": "./types/main.d.ts",
@@ -26,7 +26,7 @@
     "forge": {
       "packagerConfig": {
         "ignore": [
-          "^/public/baby-gru$",
+          "^/public$",
           "^/public/favicon.ico$",
           "^/public/index.html",
           "^/public/logo192.png",
@@ -64,15 +64,17 @@
   },
   "dependencies": {},
   "scripts": {
+    "transpile-graphql-codegen": "npx graphql-codegen",
     "transpile-protobuf": "npx pbjs -t static-module -w es6 -o ./src/protobuf/MoorhenSession.js ./src/protobuf/MoorhenSession.proto",
     "create-version": "npx genversion -e -p ./package.json -d -s ./src/version.js",
-    "transpile-ts-worker": "npx tsc --module es2015 --lib webworker --skipLibCheck public/baby-gru/CootWorker.ts && sed -i.bak '/export {}/d' public/baby-gru/CootWorker.js && rm public/baby-gru/CootWorker.js.bak",
-    "transpile-ts-worker-jest": "npx tsc --module es2015 --lib webworker --skipLibCheck public/baby-gru/CootWorker.ts && sed -i.bak 's/export {}/export { doCootCommand, setModules }/g' public/baby-gru/CootWorker.js && sed -i.bak '/importScripts.*;/d' public/baby-gru/CootWorker.js && sed -i.bak 's/onmessage/function setModules(arg0, arg1) { molecules_container = arg0; cootModule = arg1 }; let postMessage = () => {}; let onmessage/g' public/baby-gru/CootWorker.js && rm public/baby-gru/CootWorker.js.bak",
-    "prestart": "npm run create-version && npm run transpile-ts-worker && npm run transpile-protobuf",
+    "transpile-ts-worker": "npx tsc --module es2015 --lib webworker --skipLibCheck public/CootWorker.ts && sed -i.bak '/export {}/d' public/CootWorker.js && rm public/CootWorker.js.bak",
+    "transpile-ts-worker-jest": "npx tsc --module es2015 --lib webworker --skipLibCheck public/CootWorker.ts && sed -i.bak 's/export {}/export { doCootCommand, setModules }/g' public/CootWorker.js && sed -i.bak '/importScripts.*;/d' public/CootWorker.js && sed -i.bak 's/onmessage/function setModules(arg0, arg1) { molecules_container = arg0; cootModule = arg1 }; let postMessage = () => {}; let onmessage/g' public/CootWorker.js && rm public/CootWorker.js.bak",
+    "prestart": "npm run create-version && npm run transpile-ts-worker && npm run transpile-protobuf && npm run transpile-graphql-codegen",
     "start": "vite",
-    "prebuild": "npm run create-version && npm run transpile-ts-worker && npm run transpile-protobuf",
+    "prebuild": "npm run create-version && npm run transpile-ts-worker && npm run transpile-protobuf && npm run transpile-graphql-codegen",
     "build": "vite build",
     "build-release": "npm run prebuild && webpack --mode production --devtool inline-source-map",
+    "build-release-dev": "npm run prebuild && webpack --mode development --devtool inline-source-map",
     "dev": "concurrently -k \"BROWSER=none npm start\" \"npm:electron\"",
     "electron": "wait-on tcp:3000 && electron-forge start",
     "package": "npm run build && electron-forge package",
@@ -80,8 +82,8 @@
     "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 && npm run transpile-protobuf && 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 && npm run transpile-protobuf && npx tsc && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit --testPathIgnorePatterns=MoorhenContainer.test.jsx --testPathIgnorePatterns=MoorhenLigandMenu.test.jsx --testPathIgnorePatterns=MoorhenEditMenu.test.jsx --selectProjects react-components"
+    "test": "npm run create-version && npm run transpile-protobuf && npm run transpile-graphql-codegen && npx tsc && npm run transpile-ts-worker-jest && ln -s ./public/moorhen.data ./moorhen.data && ln -s ./public/ ./baby-gru && node --trace-warnings --experimental-vm-modules node_modules/jest/bin/jest.js --forceExit",
+    "test-react": "npm run create-version && npm run transpile-protobuf && npm run transpile-graphql-codegen && npx tsc && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit --testPathIgnorePatterns=MoorhenContainer.test.jsx --testPathIgnorePatterns=MoorhenLigandMenu.test.jsx --testPathIgnorePatterns=MoorhenEditMenu.test.jsx --selectProjects react-components"
   },
   "eslintConfig": {
     "extends": [
@@ -102,6 +104,7 @@
     ]
   },
   "devDependencies": {
+    "@apollo/client": "^3.10.7",
     "@babel/preset-env": "^7.20.2",
     "@babel/preset-react": "^7.18.6",
     "@electron-forge/cli": "^6.0.5",
@@ -109,11 +112,14 @@
     "@electron-forge/maker-rpm": "^6.0.5",
     "@electron-forge/maker-squirrel": "^6.0.5",
     "@electron-forge/maker-zip": "^6.0.5",
-    "@emotion/react": "^11.10.4",
-    "@emotion/styled": "^11.10.4",
+    "@emotion/react": "^11.11.4",
+    "@emotion/styled": "^11.11.5",
+    "@graphql-codegen/cli": "^5.0.2",
+    "@graphql-codegen/client-preset": "^4.3.1",
+    "@graphql-typed-document-node/core": "^3.2.0",
     "@mui/icons-material": "^5.10.9",
     "@mui/lab": "^5.0.0-alpha.140",
-    "@mui/material": "^5.10.10",
+    "@mui/material": "^5.15.19",
     "@mui/x-tree-view": "^6.17.0",
     "@reduxjs/toolkit": "^1.9.7",
     "@testing-library/dom": "^9.3.4",
@@ -144,6 +150,7 @@
     "express": "^4.18.2",
     "genversion": "^3.1.1",
     "gl-matrix": "^3.4.3",
+    "graphql": "^16.9.0",
     "html-react-parser": "^1.4.14",
     "html-webpack-plugin": "^5.5.0",
     "iris-validation": "^0.1.10",
@@ -173,17 +180,20 @@
     "rc-tree": "4.2.2",
     "re-resizable": "^6.9.11",
     "react": "^18.1.0",
-    "react-bootstrap": "^2.3.1",
+    "react-bootstrap": "^2.10.4",
     "react-bootstrap-typeahead": "^6.0.0-alpha.11",
     "react-chartjs-2": "^4.1.0",
     "react-color": "^2.19.3",
     "react-colorful": "^5.6.1",
     "react-dom": "^18.1.0",
     "react-draggable": "^4.4.5",
+    "react-hotkeys": "^2.0.0",
     "react-plotly.js": "^2.5.1",
     "react-redux": "^8.1.3",
     "react-simple-code-editor": "^0.13.1",
     "reactcss": "^1.2.3",
+    "sass": "^1.77.4",
+    "sass-loader": "^14.2.1",
     "style-loader": "^3.3.1",
     "styled-components": "^5.3.9",
     "taffydb": "^2.7.3",

package/public/CootWorker.js

@@ -0,0 +1 @@
+var cootModule,molecules_container,ccp4Module,__assign=this&&this.__assign||function(){return __assign=Object.assign||function(e){for(var r,a=1,t=arguments.length;a<t;a++)for(var o in r=arguments[a])Object.prototype.hasOwnProperty.call(r,o)&&(e[o]=r[o]);return e},__assign.apply(this,arguments)};importScripts("./moorhen.js"),importScripts("./web_example.js");var guid=function(){var e=Date.now();return"xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx".replace(/[xy]/g,(function(r){var a=(e+16*Math.random())%16|0;return e=Math.floor(e/16),("x"===r?a:3&a|8).toString(16)}))},print=function(e){},parseMonLibListCif=function(e){for(var r=cootModule.parse_mon_lib_list_cif(e),a=r.size(),t=[],o=0;o<a;o++){var s=r.get(o);t.push({three_letter_code:s.three_letter_code,name:s.name.replaceAll("'","").toLowerCase()})}return r.delete(),t},instancedMeshToMeshData=function(e,r,a,t){void 0===a&&(a=!1),void 0===t&&(t=1e4);for(var o=[],s=[],n=[],i=[],c=[],_=[],l=[],u=[],d=[],m=e.geom,p=e.markup,h=m.size(),g=0;g<h;g++){var f=a,v=[],y=[],b=[],S=[],M=[],z=[],A=[],T=m.get(g);"spherical-atoms"===T.name&&(f=!0);for(var x=T.vertices,F=T.triangles,k=F.size(),w=0;w<k;w++){var I=F.get(w).point_id;r?(v.push(I[0]),v.push(I[2]),v.push(I[1])):(v.push(I[0]),v.push(I[1]),v.push(I[2]))}F.delete();for(var J=x.size(),D=0;D<J;D++){var C=x.get(D),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var R=C.normal;b.push(R[0]),b.push(R[1]),b.push(R[2])}x.delete();var P=T.instancing_data_A,L=P.size();if(L>0)for(var E=0;E<L;E++){var U=(q=P.get(E)).position;z.push(U[0]),z.push(U[1]),z.push(U[2]);var O=q.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var j=q.size;S.push(j[0]),S.push(j[1]),S.push(j[2]),A.push.apply(A,[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1])}P.delete();var B=T.instancing_data_B,V=B.size();if(V>0)for(E=0;E<V;E++){var q;if(!((j=(q=B.get(E)).size)[2]>t)){S.push(j[0]),S.push(j[1]),S.push(j[2]);U=q.position;z.push(U[0]),z.push(U[1]),z.push(U[2]);O=q.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var H=q.orientation;A.push(H[0][0]),A.push(H[0][1]),A.push(H[0][2]),A.push(H[0][3]),A.push(H[1][0]),A.push(H[1][1]),A.push(H[1][2]),A.push(H[1][3]),A.push(H[2][0]),A.push(H[2][1]),A.push(H[2][2]),A.push(H[2][3]),A.push(H[3][0]),A.push(H[3][1]),A.push(H[3][2]),A.push(H[3][3])}}B.delete(),n.push(b),s.push(y),o.push(v),i.push(S),_.push(z),l.push(A),c.push(M),u.push(!0),f?d.push("PERFECT_SPHERES"):d.push("TRIANGLES")}m.delete();var K=simpleMeshToMeshData(p);return K.idx_tri.length>0&&K.idx_tri[0].length>0&&K.idx_tri[0][0].length>0?a?{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[_,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[s,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d],idx_tri:[o],vert_tri:[s],norm_tri:[n],col_tri:[c],instance_use_colors:[u],instance_sizes:[i],instance_origins:[_],instance_orientations:[l]}},simpleMeshToMeshData=function(e,r,a){void 0===r&&(r=!1),void 0===a&&(a=!1);var t=!1,o=(performance.now(),e.vertices),s=e.triangles,n=o.size(),i=s.size(),c=new Uint32Array(3*i),_=new Float32Array(3*n),l=new Float32Array(3*n),u=new Float32Array(4*n);cootModule.getPositionsFromSimpleMesh2(e,_),cootModule.getColoursFromSimpleMesh2(e,u),r?(a?cootModule.getReversedNormalsFromSimpleMesh3(e,l):cootModule.getReversedNormalsFromSimpleMesh2(e,l),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,c)):(cootModule.getNormalsFromSimpleMesh2(e,l),cootModule.getTriangleIndicesFromSimpleMesh2(e,c));performance.now();var d=_,m=u,p=l,h=c;return o.delete(),s.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[h]],vert_tri:[[d]],norm_tri:[[p]],col_tri:[[m]]}},SuperposeResultsToJSArray=function(e){for(var r=e.aligned_pairs,a=r.size(),t=[],o=0;o<a;o++){var s=r.get(o),n=s.first,i=n.residue_spec,c=s.second,_=c.residue_spec,l={reference:{chainId:i.chain_id,insCode:i.ins_code,seqNum:i.res_no,restype:"UNK",value:n.function_value,label:n.label},moving:{chainId:_.chain_id,insCode:_.ins_code,seqNum:_.res_no,restype:"UNK",value:c.function_value,label:c.label}};t.push(l)}return r.delete(),{referenceSequence:e.alignment.first,movingSequence:e.alignment.second,supperposeInfo:e.superpose_info,alignedPairsData:t}},colourRulesToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(o)}return e.delete(),r},stringArrayArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){for(var o=e.get(t),s=o.size(),n=[],i=0;i<s;i++){var c=o.get(i);n.push(c)}r.push(n),o.delete()}return e.delete(),r},floatArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(o)}return e.delete(),r},mapMoleculeCentreInfoToJSObject=function(e){var r=e.updated_centre,a={updated_centre:[r.x(),r.y(),r.z()],success:e.success,suggested_radius:e.suggested_radius,suggested_contour_level:e.suggested_contour_level};return r.delete(),a},textureAsFloatsToJSTextureAsFloats=function(e){var r=e.width*e.height,a=new Float32Array(r);performance.now();cootModule.getTextureArray(e,a);performance.now();return{width:e.width,height:e.height,x_size:e.x_size,y_size:e.y_size,z_position:e.z_position,image_data:a}},fitLigandInfoArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(__assign({},o))}return e.delete(),r},intArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(o)}return e.delete(),r},stringArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(o)}return e.delete(),r},export_map_as_gltf=function(e,r,a,t,o,s){var n="".concat(guid(),".glb");molecules_container.export_map_molecule_as_gltf(e,r,a,t,o,s,n);var i=cootModule.FS.readFile(n,{encoding:"binary"});return cootModule.FS_unlink(n),i.buffer},export_molecular_represenation_as_gltf=function(e,r,a,t){var o="".concat(guid(),".glb");molecules_container.export_molecular_represenation_as_gltf(e,r,a,t,o);var s=cootModule.FS.readFile(o,{encoding:"binary"});return cootModule.FS_unlink(o),s.buffer},export_molecule_as_gltf=function(e,r,a,t,o,s,n,i,c){var _="".concat(guid(),".glb");molecules_container.export_model_molecule_as_gltf(e,r,a,t,o,s,n,i,c,_);var l=cootModule.FS.readFile(_,{encoding:"binary"});return cootModule.FS_unlink(_),l.buffer},symmetryToJSData=function(e){for(var r=[],a=e.first,t=e.second,o=a.symm_trans,s=o.size(),n=0;n<s;n++){var i=o.get(n),c=i.first,_=i.second,l=t.get(n);r.push({x:c.x(),y:c.y(),z:c.z(),asString:c.symm_as_string,isym:c.isym(),us:_.us,ws:_.ws,vs:_.vs,matrix:l}),c.delete()}return o.delete(),t.delete(),r},mmrrccStatsToJSArray=function(e){var r=function(e){for(var r=[],a=e.keys(),t=a.size(),o=0;o<t;o++){var s=a.get(o),n=e.get(s);r.push({resNum:s.res_no,insCode:s.ins_code,modelNumber:s.model_number,chainId:s.chain_id,n:n.n,correlation:n.correlation()}),n.delete()}return a.delete(),r},a=e.first,t=e.second,o={"All atoms":r(a),"Side-chains":r(t)};return 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e.delete(),r},interestingPlaceDataToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t),s=o.residue_spec;r.push({intUserData:s.int_user_data,modelNumber:s.model_number,chainId:s.chain_id,insCode:s.ins_code,resNum:s.res_no,featureType:o.feature_type,featureValue:o.feature_value,buttonLabel:o.button_label,badness:o.badness,coordX:o.x,coordY:o.y,coordZ:o.z})}return e.delete(),r},histogramInfoToJSData=function(e){var r=e.counts;return{counts:intArrayToJSArray(r),bin_width:e.bin_width,base:e.base}},autoReadMtzInfoVectToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push({idx:o.idx,F:o.F,phi:o.phi,w:o.w,weights_used:o.weights_used,Rfree:o.Rfree?o.Rfree.split("/")[3]:"",F_obs:o.F_obs?o.F_obs.split("/")[3]:"",sigF_obs:o.sigF_obs?o.sigF_obs.split("/")[3]:""})}if(e.delete(),r.some((function(e){return-1===e.idx}))){var s=r.find((function(e){return-1===e.idx}));s&&s.F_obs&&s.Rfree&&s.sigF_obs&&r.forEach((function(e){e.F_obs=s.F_obs,e.sigF_obs=s.sigF_obs,e.Rfree=s.Rfree})),r=r.filter((function(e){return-1!==e.idx}))}return r},ramachandranDataToJSArray=function(e,r){for(var a=[],t=e.size(),o=0;o<t;o++){var s=e.get(o),n=s.phi_psi;n.chain_id===r&&a.push({chainId:n.chain_id,insCode:n.ins_code,seqNum:n.residue_number,restype:s.residue_name(),isOutlier:!s.is_allowed_flag,phi:n.phi(),psi:n.psi(),is_pre_pro:"PRO"===s.residue_name()}),s.delete(),n.delete()}return e.delete(),a},vectorPairStringIntToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t),s={residue:o.first,slice:o.second};r.push(s)}return e.delete(),r},vectorPairClipperCoordFloatToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t),s=o.second,n=o.first,i={x:n.x(),y:n.y(),z:n.z()};n.delete(),r.push({value:s,coord:i})}return e.delete(),r},simpleMeshToLineMeshData=function(e,r){var a=!1,t=(performance.now(),e.vertices),o=e.triangles,s=o.size(),n=t.size(),i=new Uint32Array(6*s),c=new Float32Array(3*n),_=new Float32Array(3*n),l=new Float32Array(4*n);cootModule.getLineIndicesFromSimpleMesh2(e,i),cootModule.getPositionsFromSimpleMesh2(e,c),cootModule.getNormalsFromSimpleMesh2(e,_),cootModule.getColoursFromSimpleMesh2(e,l);performance.now();var u=i,d=c,m=_,p=l;return t.delete(),o.delete(),r?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[u]],vert_tri:[[d]],additional_norm_tri:[[m]],norm_tri:[[m]],col_tri:[[p]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[u]],vert_tri:[[d]],norm_tri:[[m]],col_tri:[[p]]}},auto_read_mtz=function(e){var r=guid(),a=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(r,".mtz"),a,!0,!0);var t="./".concat(r,".mtz"),o=molecules_container.auto_read_mtz(t);return cootModule.FS_unlink(t),o},replace_map_by_mtz_from_file=function(e,r,a){var t=guid(),o="./".concat(t,".mtz"),s=new Uint8Array(r);cootModule.FS_createDataFile(".",o,s,!0,!0);var n=[e,o,a.F,a.PHI,"",!1],i=molecules_container.replace_map_by_mtz_from_file.apply(molecules_container,n);return cootModule.FS_unlink(o),i},new_positions_for_residue_atoms=function(e,r){var a=0,t=new cootModule.Vectormoved_residue_t;return r.forEach((function(e){if(e.length>0){var r=e[0],a=new cootModule.moved_residue_t(r.chain_id,parseInt(r.res_no),"");e.forEach((function(e){var r=new cootModule.moved_atom_t(e.name,e.alt_loc,e.x,e.y,e.z,-1);a.add_atom(r),r.delete()})),t.push_back(a),a.delete()}})),a+=molecules_container.new_positions_for_atoms_in_residues(e,t),t.delete(),a},read_mtz=function(e,r,a){var t=guid(),o=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(t,".mtz"),o,!0,!0);var s="./".concat(t,".mtz"),n=[s,a.F,a.PHI,"",!1,a.isDifference],i=molecules_container.read_mtz.apply(molecules_container,n);return cootModule.FS_unlink(s),i},associate_data_mtz_file_with_map=function(e,r,a,t,o){var s=new Uint8Array(r.data);cootModule.FS_createDataFile(".","".concat(r.fileName,".mtz"),s,!0,!0);var n="./".concat(r.fileName,".mtz"),i=[e,n,a,t,o];return molecules_container.associate_data_mtz_file_with_map.apply(molecules_container,i),n},read_ccp4_map=function(e,r,a){var t=guid(),o=new Uint8Array(e),s="";r.endsWith(".map.gz")?s="map.gz":r.endsWith(".mrc.gz")&&(s="mrc.gz"),cootModule.FS_createDataFile(".","".concat(t).concat(s),o,!0,!0);var n="./".concat(t).concat(s),i=[n,a],c=-1;try{c=molecules_container.read_ccp4_map.apply(molecules_container,i)}catch(e){console.warn(e)}finally{cootModule.FS_unlink(n)}return c},setUserDefinedBondColours=function(e,r,a){void 0===a&&(a=!1);var t=new cootModule.MapIntFloat4,o=new cootModule.VectorStringUInt_pair;r.forEach((function(e,r){t.set(r+51,e.rgba);var a={first:e.cid,second:r+51};o.push_back(a)})),molecules_container.set_user_defined_bond_colours(e,t),molecules_container.set_user_defined_atom_colour_by_selection(e,o,a),o.delete(),t.delete()},privateerValidationToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){for(var o=e.get(t),s=[],n=o.torsions,i=n.size(),c=0;c<i;c++)s.push(n.get(c));n.delete();var _={torsions:s,svg:o.svg.replace(/: *32/g,""),id:o.id.replace(/: *32/g,""),chain:o.chain,wurcs:o.wurcs,glyconnect_id:o.glyconnect_id,glytoucan_id:o.glytoucan_id,torsion_err:o.torsion_err,anomer_err:o.anomer_err,conformation_err:o.conformation_err,puckering_err:o.puckering_err,chirality_err:o.chirality_err};r.push(_)}return e.delete(),r},headerInfoAsJSObject=function(e){var r=e.author_lines,a=stringArrayToJSArray(r),t=e.compound_lines,o=stringArrayToJSArray(t),s=e.journal_lines,n=stringArrayToJSArray(s);return{title:e.title,author_lines:a,compound_lines:o,journal_lines:n}},doCootCommand=function(e){var r=e.returnType,a=e.command,t=e.commandArgs,o=e.messageId,s=e.myTimeStamp,n=e.message;try{var i=void 0;switch(a){case"shim_new_positions_for_residue_atoms":i=new_positions_for_residue_atoms.apply(void 0,t);break;case"shim_read_mtz":i=read_mtz.apply(void 0,t);break;case"shim_auto_read_mtz":i=auto_read_mtz.apply(void 0,t);break;case"shim_read_ccp4_map":i=read_ccp4_map.apply(void 0,t);break;case"shim_associate_data_mtz_file_with_map":i=associate_data_mtz_file_with_map.apply(void 0,t);break;case"shim_replace_map_by_mtz_from_file":i=replace_map_by_mtz_from_file.apply(void 0,t);break;case"shim_set_bond_colours":i=setUserDefinedBondColours.apply(void 0,t);break;case"shim_export_map_as_gltf":i=export_map_as_gltf.apply(void 0,t);break;case"shim_export_molecule_as_gltf":i=export_molecule_as_gltf.apply(void 0,t);break;case"shim_export_molecular_represenation_as_gltf":i=export_molecular_represenation_as_gltf.apply(void 0,t);break;case"parse_mon_lib_list_cif":i=parseMonLibListCif.apply(void 0,t);break;default:i=molecules_container[a].apply(molecules_container,t)}var c=void 0;switch(r){case"header_info_t":c=headerInfoAsJSObject(i);break;case"texture_as_floats_t":c=textureAsFloatsToJSTextureAsFloats(i);break;case"fit_ligand_info_array":c=fitLigandInfoArrayToJSArray(i);break;case"string_array_array":c=stringArrayArrayToJSArray(i);break;case"instanced_mesh_perm":c=instancedMeshToMeshData(i,!0);break;case"histogram_info_t":c=histogramInfoToJSData(i);break;case"symmetry":c=symmetryToJSData(i);break;case"mmrrcc_stats":c=mmrrccStatsToJSArray(i);break;case"colour_rules":c=colourRulesToJSArray(i);break;case"instanced_mesh_perfect_spheres":c=instancedMeshToMeshData(i,!1,!0);break;case"instanced_mesh":c=instancedMeshToMeshData(i,!1,!1,5);break;case"mesh_perm3":c=simpleMeshToMeshData(i,!0,!0);break;case"mesh_perm":c=simpleMeshToMeshData(i,!0);break;case"mesh":c=simpleMeshToMeshData(i);break;case"lit_lines_mesh":c=simpleMeshToLineMeshData(i,!0);break;case"lines_mesh":c=simpleMeshToLineMeshData(i,!1);break;case"float_array":c=floatArrayToJSArray(i);break;case"int_array":c=intArrayToJSArray(i);break;case"auto_read_mtz_info_array":c=autoReadMtzInfoVectToJSArray(i);break;case"map_molecule_centre_info_t":c=mapMoleculeCentreInfoToJSObject(i);break;case"string_array":c=stringArrayToJSArray(i);break;case"residue_specs":c=residueSpecToJSArray(i);break;case"atom_specs":c=atomSpecToJSArray(i);break;case"ramachandran_data":c=ramachandranDataToJSArray(i,e.chainID);break;case"validation_data":c=validationDataToJSArray(i,e.chainID);break;case"interesting_places_data":c=interestingPlaceDataToJSArray(i);break;case"superpose_results":c=SuperposeResultsToJSArray(i);break;case"generic_3d_lines_bonds_box":c=linesBoxToJSArray(i);break;case"vector_hbond":c=vectorHBondToJSArray(i);break;case"status_instanced_mesh_pair":c={status:i.first,mesh:instancedMeshToMeshData(i.second,!1,!1,5)};break;case"string_string_pair_vector":c=stringPairVectorToJSArray(i);break;case"void":c=null;break;case"vector_pair_clipper_coord_float":c=vectorPairClipperCoordFloatToJSArray(i);break;case"vector_pair_string_int":c=vectorPairStringIntToJSArray(i);break;case"privateer_results":c=privateerValidationToJSArray(i);break;default:c=i}try{i.delete()}catch(e){}return{messageId:o,messageSendTime:Date.now(),command:a,consoleMessage:"Completed ".concat(a," in ").concat(Date.now()-s," ms"),result:{status:"Completed",result:c}}}catch(e){return{messageId:o,myTimeStamp:s,message:n,consoleMessage:"EXCEPTION RAISED IN ".concat(a,", ").concat(e),result:{status:"Exception"}}}};onmessage=function(e){if("CootInitialize"===e.data.message)createRSRModule({onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"moorhen.js",print,printErr:print}).then((function(r){postMessage({consoleMessage:"Initialized molecules_container",message:e.data.message,messageId:e.data.messageId}),(molecules_container=new(cootModule=r).molecules_container_js(!1)).set_use_gemmi(!1),molecules_container.set_show_timings(!1),molecules_container.set_refinement_is_verbose(!1),molecules_container.fill_rotamer_probability_tables(),molecules_container.set_map_sampling_rate(1.7),molecules_container.set_map_is_contoured_with_thread_pool(!0),molecules_container.set_max_number_of_threads(3),cootModule.FS.mkdir("COOT_BACKUP")})).catch((function(e){print(e)})),createCCP4Module({onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"web_example.js",print,printErr:print}).then((function(e){ccp4Module=e})).catch((function(e){print(e)}));else if("close"===e.data.message)null==molecules_container||molecules_container.delete(),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Closed molecules container",message:e.data.message,result:{}});else if("get_mtz_data"===e.data.message){var r=cootModule.FS.readFile(e.data.fileName,{encoding:"binary"});postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched mtz data for map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mtzData:r}})}else if("get_map"===e.data.message){var a=guid(),t="./".concat(a,".map");molecules_container.writeCCP4Map(e.data.molNo,t);var o=cootModule.FS.readFile(t,{encoding:"binary"});cootModule.FS_unlink(t),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched map of map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mapData:o.buffer}})}else if("delete_file_name"===e.data.message){var s=cootModule.FS_unlink(e.data.fileName);postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,messageTag:"result",result:s})}else if("coot_command_list"===e.data.message){var n=e.data.commandList.map((function(r){return doCootCommand(__assign(__assign({},e.data),r))}));postMessage({messageId:e.data.messageId,resultList:n})}if("coot_command"===e.data.message){s=doCootCommand(e.data);postMessage(s)}};

package/{baby-gru → public}/CootWorker.ts

@@ -1,6 +1,6 @@
-import { libcootApi } from "../../src/types/libcoot"
-import { emscriptem } from "../../src/types/emscriptem"
-import { privateer } from "../../src/types/privateer";
+import { libcootApi } from "../src/types/libcoot"
+import { emscriptem } from "../src/types/emscriptem"
+import { privateer } from "../src/types/privateer";
 
 // @ts-ignore
 importScripts('./moorhen.js')
@@ -24,7 +24,24 @@ const guid = () => {
 // @ts-ignore
 let print = (stuff) => {
     console.log(stuff)
-    postMessage({ consoleMessage: JSON.stringify(stuff) })
+}
+
+const parseMonLibListCif = (fileContents: string): libcootApi.compoundInfo[] => {
+    const table = cootModule.parse_mon_lib_list_cif(fileContents)
+    const tableSize = table.size()
+
+    let result: libcootApi.compoundInfo[] = []
+    for (let i = 0; i < tableSize; i++) {
+        const compound = table.get(i)
+        result.push({
+            three_letter_code: compound.three_letter_code,
+            // @ts-ignore
+            name: compound.name.replaceAll("'", "").toLowerCase()
+        })
+    }
+
+    table.delete()
+    return result
 }
 
 const instancedMeshToMeshData = (instanceMesh: libcootApi.InstancedMeshT, perm: boolean, toSpheres: boolean = false, maxZSize: number = 10000.): libcootApi.InstancedMeshJS => {
@@ -226,7 +243,7 @@ const instancedMeshToMeshData = (instanceMesh: libcootApi.InstancedMeshT, perm:
     }
 }
 
-const simpleMeshToMeshData = (simpleMesh: libcootApi.SimpleMeshT, perm: boolean = false): libcootApi.SimpleMeshJS => {
+const simpleMeshToMeshData = (simpleMesh: libcootApi.SimpleMeshT, perm: boolean = false, keepNorm: boolean = false): libcootApi.SimpleMeshJS => {
 
     const print_timing = false
     const ts = performance.now()
@@ -246,7 +263,11 @@ const simpleMeshToMeshData = (simpleMesh: libcootApi.SimpleMeshT, perm: boolean
     cootModule.getColoursFromSimpleMesh2(simpleMesh,totCol_C)
 
     if (perm){
-        cootModule.getReversedNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
+        if(keepNorm){
+            cootModule.getReversedNormalsFromSimpleMesh3(simpleMesh,totNorm_C)
+        } else {
+            cootModule.getReversedNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
+        }
         cootModule.getPermutedTriangleIndicesFromSimpleMesh2(simpleMesh,totIdxs_C)
     } else {
         cootModule.getNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
@@ -956,12 +977,12 @@ const read_ccp4_map = (mapData: ArrayBufferLike, name: string, isDiffMap: boolea
     return molNo
 }
 
-const setUserDefinedBondColours = (imol: number, colours: { cid: string; rgb: [number, number, number] }[], applyColourToNonCarbonAtoms: boolean = false) => {
-    let colourMap = new cootModule.MapIntFloat3()
+const setUserDefinedBondColours = (imol: number, colours: { cid: string; rgba: [number, number, number, number] }[], applyColourToNonCarbonAtoms: boolean = false) => {
+    let colourMap = new cootModule.MapIntFloat4()
     let indexedResiduesVec = new cootModule.VectorStringUInt_pair()
     
     colours.forEach((colour, index) => {
-        colourMap.set(index + 51, colour.rgb)
+        colourMap.set(index + 51, colour.rgba)
         const i = { first: colour.cid, second: index + 51 }
         indexedResiduesVec.push_back(i)
     })
@@ -1016,7 +1037,25 @@ const privateerValidationToJSArray = (results: emscriptem.vector<privateer.Resul
 
     results.delete();
     return data;
+}
+
+const headerInfoAsJSObject = (result: libcootApi.headerInfo): libcootApi.headerInfoJS => {
+
+    const authorLines = result.author_lines
+    const author_lines: string[] = stringArrayToJSArray(authorLines)
+
+    const compoundLines = result.compound_lines
+    const compound_lines: string[] = stringArrayToJSArray(compoundLines)
+
+    const journalLines = result.journal_lines
+    const journal_lines: string[] = stringArrayToJSArray(journalLines)
 
+    return {
+        title: result.title,
+        author_lines,
+        compound_lines,
+        journal_lines
+    }
 }
 
 const doCootCommand = (messageData: { 
@@ -1054,7 +1093,7 @@ const doCootCommand = (messageData: {
                 cootResult = replace_map_by_mtz_from_file(...commandArgs as [number, ArrayBufferLike, { F: string; PHI: string; }])
                 break
             case 'shim_set_bond_colours':
-                cootResult = setUserDefinedBondColours(...commandArgs as [number, { cid: string; rgb: [number, number, number] }[], boolean])
+                cootResult = setUserDefinedBondColours(...commandArgs as [number, { cid: string; rgba: [number, number, number, number] }[], boolean])
                 break
             case 'shim_export_map_as_gltf':
                 cootResult = export_map_as_gltf(...commandArgs as [number, number, number, number, number, number])
@@ -1065,6 +1104,9 @@ const doCootCommand = (messageData: {
             case 'shim_export_molecular_represenation_as_gltf':
                 cootResult = export_molecular_represenation_as_gltf(...commandArgs as [number, string, string, string])
                 break
+            case "parse_mon_lib_list_cif":
+                cootResult =  parseMonLibListCif(...commandArgs as [string])
+                break
             default:
                 cootResult = molecules_container[command](...commandArgs)
                 break
@@ -1072,6 +1114,9 @@ const doCootCommand = (messageData: {
 
         let returnResult;
         switch (returnType) {
+            case 'header_info_t':
+                returnResult = headerInfoAsJSObject(cootResult)
+                break
             case 'texture_as_floats_t':
                 returnResult = textureAsFloatsToJSTextureAsFloats(cootResult)
                 break;
@@ -1102,6 +1147,9 @@ const doCootCommand = (messageData: {
             case 'instanced_mesh':
                 returnResult = instancedMeshToMeshData(cootResult, false, false, 5)
                 break;
+            case 'mesh_perm3':
+                returnResult = simpleMeshToMeshData(cootResult, true, true)
+                break;
             case 'mesh_perm':
                 returnResult = simpleMeshToMeshData(cootResult, true)
                 break;

package/public/manifest.json

@@ -0,0 +1,25 @@
+{
+  "short_name": "Moorhen",
+  "name": "Moorhen",
+  "icons": [
+    {
+      "src": "favicon.ico",
+      "sizes": "64x64 32x32 24x24 16x16",
+      "type": "image/x-icon"
+    },
+    {
+      "src": "logo192.png",
+      "type": "image/png",
+      "sizes": "192x192"
+    },
+    {
+      "src": "logo512.png",
+      "type": "image/png",
+      "sizes": "512x512"
+    }
+  ],
+  "start_url": ".",
+  "display": "standalone",
+  "theme_color": "#000000",
+  "background_color": "#ffffff"
+}

package/{baby-gru → public}/moorhen.css

@@ -127,21 +127,21 @@ div.darkly text.end-label {fill:#FFF !important;}
 
 .rama-validation-tool-container-row {
   width: 100%;
-  margin: 0;
+  margin: 0 !important;
   padding: 0;
   height: 100%;
 }
 
 .big-validation-tool-container-row {
   width: 100%;
-  margin: 0;
+  margin: 0 !important;
   padding: 0;
   height: calc(100% - 6rem);
 }
 
 .small-validation-tool-container-row {
   width: 100%;
-  margin: 0;
+  margin: 0 !important;
   padding: 0;
   height: calc(100% - 19rem);
 }
@@ -223,6 +223,21 @@ div.darkly text.end-label {fill:#FFF !important;}
   justify-content: center;
 }
 
+.moorhen-sidebar-div {
+  box-shadow: 0px 3px 5px -1px rgba(0,0,0,0.2),0px 6px 10px 0px rgba(0,0,0,0.14),0px 1px 18px 0px rgba(0,0,0,0.12);
+  width: 14rem;
+  min-height: 3rem;
+  height: fit-content;
+  overflow-y: auto;
+  overflow-x: hidden;
+  padding: 0.5rem;
+  display: flex;
+  border-radius: 0.5rem;
+  align-items: center;
+  align-content: center;
+  justify-content: center;
+}
+
 .moorhen-tooltip {
   display: flex;
   z-index: 9999;