moorhen 0.8.3 → 0.8.4

package/baby-gru/wasm/moorhen.worker.js

@@ -1 +1 @@
-"use strict";var Module={},ENVIRONMENT_IS_NODE="object"==typeof process&&"object"==typeof process.versions&&"string"==typeof process.versions.node;if(ENVIRONMENT_IS_NODE){var nodeWorkerThreads=require("worker_threads"),parentPort=nodeWorkerThreads.parentPort;parentPort.on("message",(e=>onmessage({data:e})));var fs=require("fs"),vm=require("vm");Object.assign(global,{self:global,require,Module,location:{href:__filename},Worker:nodeWorkerThreads.Worker,importScripts:e=>vm.runInThisContext(fs.readFileSync(e,"utf8"),{filename:e}),postMessage:e=>parentPort.postMessage(e),performance:global.performance||{now:Date.now}})}var initializedJS=!1;function assert(e,r){e||abort("Assertion failed: "+r)}function threadPrintErr(...e){var r=e.join(" ");ENVIRONMENT_IS_NODE?fs.writeSync(2,r+"\n"):console.error(r)}function threadAlert(...e){var r=e.join(" ");postMessage({cmd:"alert",text:r,threadId:Module._pthread_self()})}var out=()=>{throw"out() is not defined in worker.js."},err=threadPrintErr;self.alert=threadAlert;var dbg=threadPrintErr;function handleMessage(e){try{if("load"===e.data.cmd){let a=[];self.onmessage=e=>a.push(e),self.startWorker=e=>{Module=e,postMessage({cmd:"loaded"});for(let e of a)handleMessage(e);self.onmessage=handleMessage},Module.wasmModule=e.data.wasmModule;for(const r of e.data.handlers)Module[r]=(...e)=>{postMessage({cmd:"callHandler",handler:r,args:e})};if(Module.wasmMemory=e.data.wasmMemory,Module.buffer=Module.wasmMemory.buffer,Module.workerID=e.data.workerID,Module.ENVIRONMENT_IS_PTHREAD=!0,"string"==typeof e.data.urlOrBlob)importScripts(e.data.urlOrBlob);else{var r=URL.createObjectURL(e.data.urlOrBlob);importScripts(r),URL.revokeObjectURL(r)}createRSRModule(Module)}else if("run"===e.data.cmd){Module.__emscripten_thread_init(e.data.pthread_ptr,0,0,1),Module.__emscripten_thread_mailbox_await(e.data.pthread_ptr),assert(e.data.pthread_ptr),Module.establishStackSpace(),Module.PThread.receiveObjectTransfer(e.data),Module.PThread.threadInitTLS(),initializedJS||(Module.__embind_initialize_bindings(),initializedJS=!0);try{Module.invokeEntryPoint(e.data.start_routine,e.data.arg)}catch(e){if("unwind"!=e)throw e}}else"cancel"===e.data.cmd?Module._pthread_self()&&Module.__emscripten_thread_exit(-1):"setimmediate"===e.data.target||("checkMailbox"===e.data.cmd?initializedJS&&Module.checkMailbox():e.data.cmd&&(err(`worker.js received unknown command ${e.data.cmd}`),err(e.data)))}catch(e){throw err(`worker.js onmessage() captured an uncaught exception: ${e}`),e?.stack&&err(e.stack),Module.__emscripten_thread_crashed?.(),e}}Module.instantiateWasm=(e,r)=>{var a=Module.wasmModule;return Module.wasmModule=null,r(new WebAssembly.Instance(a,e))},self.onunhandledrejection=e=>{throw e.reason||e},self.onmessage=handleMessage;
+"use strict";var Module={},ENVIRONMENT_IS_NODE="object"==typeof process&&"object"==typeof process.versions&&"string"==typeof process.versions.node;if(ENVIRONMENT_IS_NODE){var nodeWorkerThreads=require("worker_threads"),parentPort=nodeWorkerThreads.parentPort;parentPort.on("message",(e=>onmessage({data:e})));var fs=require("fs");Object.assign(global,{self:global,require,Module,location:{href:__filename},Worker:nodeWorkerThreads.Worker,importScripts:e=>(0,eval)(fs.readFileSync(e,"utf8")+"//# sourceURL="+e),postMessage:e=>parentPort.postMessage(e),performance:global.performance||{now:Date.now}})}var initializedJS=!1;function assert(e,r){e||abort("Assertion failed: "+r)}function threadPrintErr(){var e=Array.prototype.slice.call(arguments).join(" ");ENVIRONMENT_IS_NODE?fs.writeSync(2,e+"\n"):console.error(e)}function threadAlert(){var e=Array.prototype.slice.call(arguments).join(" ");postMessage({cmd:"alert",text:e,threadId:Module._pthread_self()})}var out=()=>{throw"out() is not defined in worker.js."},err=threadPrintErr;self.alert=threadAlert;var dbg=threadPrintErr;function handleMessage(e){try{if("load"===e.data.cmd){let a=[];self.onmessage=e=>a.push(e),self.startWorker=e=>{Module=e,postMessage({cmd:"loaded"});for(let e of a)handleMessage(e);self.onmessage=handleMessage},Module.wasmModule=e.data.wasmModule;for(const r of e.data.handlers)Module[r]=(...e)=>{postMessage({cmd:"callHandler",handler:r,args:e})};if(Module.wasmMemory=e.data.wasmMemory,Module.buffer=Module.wasmMemory.buffer,Module.workerID=e.data.workerID,Module.ENVIRONMENT_IS_PTHREAD=!0,"string"==typeof e.data.urlOrBlob)importScripts(e.data.urlOrBlob);else{var r=URL.createObjectURL(e.data.urlOrBlob);importScripts(r),URL.revokeObjectURL(r)}createRSRModule(Module)}else if("run"===e.data.cmd){Module.__emscripten_thread_init(e.data.pthread_ptr,0,0,1),Module.__emscripten_thread_mailbox_await(e.data.pthread_ptr),assert(e.data.pthread_ptr),Module.establishStackSpace(),Module.PThread.receiveObjectTransfer(e.data),Module.PThread.threadInitTLS(),initializedJS||(Module.__embind_initialize_bindings(),initializedJS=!0);try{Module.invokeEntryPoint(e.data.start_routine,e.data.arg)}catch(e){if("unwind"!=e)throw e}}else"cancel"===e.data.cmd?Module._pthread_self()&&Module.__emscripten_thread_exit(-1):"setimmediate"===e.data.target||("checkMailbox"===e.data.cmd?initializedJS&&Module.checkMailbox():e.data.cmd&&(err(`worker.js received unknown command ${e.data.cmd}`),err(e.data)))}catch(e){throw err(`worker.js onmessage() captured an uncaught exception: ${e}`),e&&e.stack&&err(e.stack),Module.__emscripten_thread_crashed&&Module.__emscripten_thread_crashed(),e}}Module.instantiateWasm=(e,r)=>{var a=Module.wasmModule;return Module.wasmModule=null,r(new WebAssembly.Instance(a,e))},self.onunhandledrejection=e=>{throw e.reason||e},self.onmessage=handleMessage;

package/baby-gru/wasm/mtz_arraybuffer_worker.js

@@ -0,0 +1 @@
+var CCP4Module;importScripts("web_example.js"),createCCP4Module({print(e){postMessage(["output",e])},printErr(e){postMessage(["output",e])}}).then((function(e){CCP4Module=e})).catch((e=>{console.log("CCP4 problem :("),console.log(e)})),onmessage=function(e){var o=e.data[0];const l=new Uint8Array(o);var t=e.data[1];let a="FC",c="PHIC";void 0!==e.data[2]&&void 0!==e.data[3]&&(a=e.data[2],c=e.data[3]);try{CCP4Module.FS_createDataFile(".",t,l,!0,!0)}catch(e){}const n=CCP4Module.get_mtz_columns(t);console.log(n);for(let e=0;e<n.size();e+=2)console.log(n.get(e),n.get(e+1));console.log("Send",t,"to clipper");var r=CCP4Module.clipper_example_with_cols(t,a,c,2);console.log("In the worker..."),console.log(r),console.log(r.cell()),console.log(r.cell().a()),console.log(r.cell().b()),console.log(r.cell().c()),console.log(r.cell().alpha()),console.log(r.cell().beta()),console.log(r.cell().gamma()),CCP4Module.printMapStats(r);var s=new CCP4Module.CCP4MAPfile,C=new CCP4Module.Clipper_String("mapout.map");s.open_write(C),CCP4Module.exportXMapToMapFile(s,r),s.close_write(),console.log("Written",CCP4Module.clipperStringToString(C));var p=CCP4Module.FS.readFile(CCP4Module.clipperStringToString(C));postMessage(["result",p,t,l])};

package/baby-gru/wasm/mtz_worker.js

@@ -0,0 +1 @@
+var CCP4Module;importScripts("web_example.js"),createCCP4Module({print(e){postMessage(["output",e])},printErr(e){postMessage(["output",e])}}).then((function(e){CCP4Module=e})).catch((e=>{console.log("CCP4 problem :("),console.log(e)})),onmessage=function(e){var o=atob(e.data[0]),l=e.data[1];const t=new Array(o.length);for(let e=0;e<o.length;e++)t[e]=o.charCodeAt(e);const r=new Uint8Array(t);try{CCP4Module.FS_createDataFile(".",l,r,!0,!0)}catch(e){}console.log("Send",l,"to clipper");var n=CCP4Module.clipper_example(l);console.log("In the worker..."),console.log(n),console.log(n.cell()),console.log(n.cell().a()),CCP4Module.printMapStats(n);var a=new CCP4Module.CCP4MAPfile,p=new CCP4Module.Clipper_String("mapout.map");a.open_write(p),CCP4Module.exportXMapToMapFile(a,n),a.close_write(),console.log("Written",CCP4Module.clipperStringToString(p));var C=CCP4Module.FS.readFile(CCP4Module.clipperStringToString(p));postMessage(["result",C])};

package/baby-gru/wasm/nma_worker.js

@@ -0,0 +1 @@
+var CCP4Module;importScripts("web_example.js"),importScripts("papaparse.min.js"),createCCP4Module({print(e){postMessage(["output",e])},printErr(e){postMessage(["output",e])}}).then((function(e){CCP4Module=e})).catch((e=>{console.log("CCP4 problem :("),console.log(e)})),onmessage=function(e){new CCP4Module.VectorString;try{CCP4Module.FS_createDataFile(".",e.data[1],e.data[0],!0,!0)}catch(e){}var t=CCP4Module.calculate_normal_modes(e.data[1],1);const s=t.GetBValues(),o=s.size();let l=[],a=[];const p=CCP4Module.get_CA_bvalues_from_file(e.data[1]);let r;if(o>0){r=0;for(let e=0;e<o;e++)r+=s.get(e)/p.get(e);r/=o,r=1/r}else r=1;const u=CCP4Module.GetCorrelations(t,r);for(let e=0;e<o;e++)l.push({x:e+1,y:s.get(e)*r}),a.push({x:e+1,y:p.get(e)});const n=u.get_rows(),c=u.get_columns();let g={x:[],y:[],z:[]};for(let e=0;e<n;e++)for(let t=0;t<c;t++)g.x.push(e),g.y.push(t),g.z.push(u.get(e,t));postMessage(["corrMat",g]),postMessage(["bvalues",[l,a]]),postMessage(["result",0]);let C=CCP4Module.calculate_normal_modes(e.data[1],0);const d=CCP4Module.GetEigen(C).get(1),m=d.get_rows();d.get_columns(),postMessage(["output","Normal modes"]);let i=[];for(let e=6;e<m;e++)i.push(d.get(e,0));postMessage(["energies",i]);const M=CCP4Module.GetDisplacements(C),_=M.nModes(),f=M.nSteps();let h={modes:[]};for(let e=0;e<_;e++){h.modes.push({steps:[]});for(let t=0;t<f;t++){h.modes[e].steps.push({xyz:[]});const s=M.getDisplacements(e,t),o=s.size();for(let l=0;l<o;l++)h.modes[e].steps[t].xyz.push(s.get(l))}}postMessage(["displacements",h])};

package/baby-gru/wasm/papaparse.min.js

@@ -0,0 +1,2 @@
+/*! For license information please see papaparse.min.js.LICENSE.txt */
+!function(e,t){"function"==typeof define&&define.amd?define([],t):"object"==typeof module&&"undefined"!=typeof exports?module.exports=t():e.Papa=t()}(this,(function e(){"use strict";var t="undefined"!=typeof self?self:"undefined"!=typeof window?window:void 0!==t?t:{},i=!t.document&&!!t.postMessage,r=t.IS_PAPA_WORKER||!1,n={},s=0,a={parse:function(i,r){var o=(r=r||{}).dynamicTyping||!1;if(b(o)&&(r.dynamicTypingFunction=o,o={}),r.dynamicTyping=o,r.transform=!!b(r.transform)&&r.transform,r.worker&&a.WORKERS_SUPPORTED){var u=function(){if(!a.WORKERS_SUPPORTED)return!1;var i,r,o=(i=t.URL||t.webkitURL||null,r=e.toString(),a.BLOB_URL||(a.BLOB_URL=i.createObjectURL(new Blob(["var global = (function() { if (typeof self !== 'undefined') { return self; } if (typeof window !== 'undefined') { return window; } if (typeof global !== 'undefined') { return global; } return {}; })(); global.IS_PAPA_WORKER=true; ","(",r,")();"],{type:"text/javascript"})))),u=new t.Worker(o);return 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package/baby-gru/wasm/papaparse.min.js.LICENSE.txt

@@ -0,0 +1,6 @@
+/* @license
+Papa Parse
+v5.4.1
+https://github.com/mholt/PapaParse
+License: MIT
+*/

package/baby-gru/wasm/pdb_worker.js

@@ -0,0 +1 @@
+var CCP4Module,RDKit;function makeRequest(e,o){return new Promise((function(t,_){var c=new XMLHttpRequest;c.open(e,o,!0),c.onload=function(){this.status>=200&&this.status<300?t(c.response):_({status:this.status,statusText:c.statusText})},c.onerror=function(){_({status:this.status,statusText:c.statusText})},c.send()}))}function onlyUnique(e,o,t){return t.indexOf(e)===o}function getLoop(e,o){let t=o+".",_=!1,c=[],n=e.length;for(let o=0;o<n;o++){let n=e[o].replace(/(^\s+|\s+$)/g,"");if("loop_"===n||"_"===n.substring(0,1)&&n.substring(0,t.length)!==t){if(_)break;o<e.length&&e[o+1].substring(0,t.length)===t&&(_=!0)}else _&&c.push(n)}return c}function splitQuotedCIFString(e){return 0===e.length?[]:e.match(/(?:[^\s"]+|"[^"]*")+/g)}function addCIFAtomTypes(e,o){let t=[],_=getLoop(o.split("\n"),"_chem_comp_atom"),c=[];for(let e=0;e<_.length;e++)if("#"!==_[e].substr(0,1)&&""!==_[e].trim())if("_"===_[e].substr(0,1))t.push(_[e]);else{let o=splitQuotedCIFString(_[e]);if("."!==o[0]){let e={};for(let _=0;_<o.length;_++)e[t[_]]=o[_];c.push(e)}}return c}function addCIFBondTypes(e,o){let t=[],_=getLoop(o.split("\n"),"_chem_comp_bond"),c=[];for(let e=0;e<_.length;e++)if("#"!==_[e].substr(0,1)&&""!==_[e].trim())if("_"===_[e].substr(0,1))t.push(_[e]);else{let o=_[e].match(/(?:[^\s"]+|"[^"]*")+/g);if("."!==o[0]){let e={};for(let _=0;_<o.length;_++)e[t[_]]=o[_];void 0!==e["_chem_comp_bond.type"]&&e["_chem_comp_bond.type"].length>0&&void 0!==e["_chem_comp_bond.comp_id"]&&e["_chem_comp_bond.comp_id"].length>0&&void 0!==e["_chem_comp_bond.atom_id_1"]&&e["_chem_comp_bond.atom_id_1"].length>0&&void 0!==e["_chem_comp_bond.atom_id_2"]&&e["_chem_comp_bond.atom_id_2"].length>0?c.push(e):void 0!==e["_chem_comp_bond.value_order"]&&e["_chem_comp_bond.value_order"].length>0&&void 0!==e["_chem_comp_bond.comp_id"]&&e["_chem_comp_bond.comp_id"].length>0&&void 0!==e["_chem_comp_bond.atom_id_1"]&&e["_chem_comp_bond.atom_id_1"].length>0&&void 0!==e["_chem_comp_bond.atom_id_2"]&&e["_chem_comp_bond.atom_id_2"].length>0&&("Y"===e["_chem_comp_bond.pdbx_aromatic_flag"]?e["_chem_comp_bond.type"]="aromatic":"SING"===e["_chem_comp_bond.value_order"]||"SINGLE"===e["_chem_comp_bond.value_order"]?e["_chem_comp_bond.type"]="single":"DOUB"===e["_chem_comp_bond.value_order"]||"DOUBLE"===e["_chem_comp_bond.value_order"]?e["_chem_comp_bond.type"]="double":"TRIP"===e["_chem_comp_bond.value_order"]||"TRIPLE"===e["_chem_comp_bond.value_order"]?e["_chem_comp_bond.type"]="triple":e["_chem_comp_bond.type"]="single",c.push(e))}}return c}function dictToMolBlock(e,o){let t=addCIFAtomTypes(e,o),_=addCIFBondTypes(e,o),c=t.length,n=_.length,m=e+"\n  CCP4-MonomerLibrary-WebToCif\n\n";m+=("  "+c).slice(-3)+("  "+n).slice(-3)+"  0  0  0  0  0  0  0  0999 V2000\n";let i=0,l="";for(let e=0;e<c;e++){let o=parseFloat(t[e]["_chem_comp_atom.x"]),_=parseFloat(t[e]["_chem_comp_atom.y"]),c=parseFloat(t[e]["_chem_comp_atom.z"]);"."!=t[e]["_chem_comp_atom.charge"]&&"0"!=t[e]["_chem_comp_atom.charge"]&&(i++,l+=("   "+(e+1)).slice(-4)+("   "+t[e]["_chem_comp_atom.charge"]).slice(-4));let n=t[e]["_chem_comp_atom.type_symbol"];m+=("          "+o.toFixed(4)).slice(-10)+("          "+_.toFixed(4)).slice(-10)+("          "+c.toFixed(4)).slice(-10)+("   "+n).slice(-3)+"   0  0  0  0  0  0  0  0  0  0  0  0\n"}for(let e=0;e<n;e++){let o=t.find((o=>o["_chem_comp_atom.atom_id"]===_[e]["_chem_comp_bond.atom_id_1"])),c=t.find((o=>o["_chem_comp_atom.atom_id"]===_[e]["_chem_comp_bond.atom_id_2"])),n=t.indexOf(o),i=t.indexOf(c),l=("  "+(n+1)).slice(-3),s=("  "+(i+1)).slice(-3),p=1;!(["_chem_comp_bond.aromatic"]in _[e])||"y_XXX"!==_[e]["_chem_comp_bond.aromatic"]&&"Y_XXX"!==_[e]["_chem_comp_bond.aromatic"]?!(["_chem_comp_bond.type"]in _[e])||"TRIPLE"!==_[e]["_chem_comp_bond.type"]&&"triple"!==_[e]["_chem_comp_bond.type"]?!(["_chem_comp_bond.type"]in _[e])||"DOUBLE"!==_[e]["_chem_comp_bond.type"]&&"double"!==_[e]["_chem_comp_bond.type"]?!(["_chem_comp_bond.type"]in _[e])||"SINGLE"!==_[e]["_chem_comp_bond.type"]&&"single"!==_[e]["_chem_comp_bond.type"]?(console.log("Unknown bond type"),console.log(_[e])):p=1:p=2:p=3:p=4,m+=l+s+("  "+p).slice(-2)+" 0  0  0  0\n"}return i>0&&(m+="M  CHG"+("   "+i).slice(-3)+l+"\n"),m+="M  END",m}importScripts("web_example.js","RDKit_minimal.js"),createCCP4Module({print(e){postMessage(["output",e])},printErr(e){postMessage(["output",e])}}).then((function(e){CCP4Module=e})).catch((e=>{console.log("CCP4 problem :("),console.log(e)})),initRDKitModule({print(e){postMessage(["output",e])},printErr(e){postMessage(["output",e])}}).then((function(e){RDKit=e})).catch((e=>{console.log("RDKit problem :("),console.log(e)})),onmessage=function(e){let o=e.data[0],t=e.data[1];try{CCP4Module.FS_createDataFile(".",t,o,!0,!0)}catch(e){}let _=CCP4Module.get_annotated_glycans_hierarchical(t,!1,"undefined"),c={};c[t]=_,postMessage(["glycan_result",c]);let n=CCP4Module.mmdb2_example(t),m=[];for(let e=0;e<n.size();e++)m.push(n.get(e));let i=m.filter(onlyUnique),l=[];for(ilig=0;ilig<i.length;ilig++){let e=i[ilig],o="/monomers/"+e.toLowerCase()[0]+"/"+e.toUpperCase()+".cif";l.push(makeRequest("GET",o,!0))}let s={};l.length>0&&Promise.all(l).then((e=>{for(ilig=0;ilig<e.length;ilig++){let o=i[ilig],t=dictToMolBlock(o,e[ilig]),_=RDKit.get_mol(t),c=RDKit.get_mol(_.remove_hs()).get_smiles(),n=RDKit.get_mol(c);s[o]=n.get_svg()}postMessage(["result",s])})).catch((e=>{for(console.error(e),ilig=0;ilig<i.length;ilig++){let e=i[ilig];s[e]=""}postMessage(["result",s])}))};

package/baby-gru/wasm/smiles_to_pdb_worker.js

@@ -0,0 +1 @@
+var CCP4Module,RDKit;function makeRequest(o,e){return new Promise((function(t,_){var c=new XMLHttpRequest;c.open(o,e,!0),c.onload=function(){this.status>=200&&this.status<300?t(c.response):_({status:this.status,statusText:c.statusText})},c.onerror=function(){_({status:this.status,statusText:c.statusText})},c.send()}))}function onlyUnique(o,e,t){return t.indexOf(o)===e}function getLoop(o,e){let t=e+".",_=!1,c=[],n=o.length;for(let e=0;e<n;e++){let n=o[e].replace(/(^\s+|\s+$)/g,"");if("loop_"===n||"_"===n.substring(0,1)&&n.substring(0,t.length)!==t){if(_)break;e<o.length&&o[e+1].substring(0,t.length)===t&&(_=!0)}else _&&c.push(n)}return c}function splitQuotedCIFString(o){return 0===o.length?[]:o.match(/(?:[^\s"]+|"[^"]*")+/g)}function addCIFAtomTypes(o,e){let t=[],_=getLoop(e.split("\n"),"_chem_comp_atom"),c=[];for(let o=0;o<_.length;o++)if("#"!==_[o].substr(0,1)&&""!==_[o].trim())if("_"===_[o].substr(0,1))t.push(_[o]);else{let e=splitQuotedCIFString(_[o]);if("."!==e[0]){let o={};for(let _=0;_<e.length;_++)o[t[_]]=e[_];c.push(o)}}return c}function addCIFBondTypes(o,e){let t=[],_=getLoop(e.split("\n"),"_chem_comp_bond"),c=[];for(let o=0;o<_.length;o++)if("#"!==_[o].substr(0,1)&&""!==_[o].trim())if("_"===_[o].substr(0,1))t.push(_[o]);else{let e=_[o].match(/(?:[^\s"]+|"[^"]*")+/g);if("."!==e[0]){let o={};for(let _=0;_<e.length;_++)o[t[_]]=e[_];void 0!==o["_chem_comp_bond.type"]&&o["_chem_comp_bond.type"].length>0&&void 0!==o["_chem_comp_bond.comp_id"]&&o["_chem_comp_bond.comp_id"].length>0&&void 0!==o["_chem_comp_bond.atom_id_1"]&&o["_chem_comp_bond.atom_id_1"].length>0&&void 0!==o["_chem_comp_bond.atom_id_2"]&&o["_chem_comp_bond.atom_id_2"].length>0?c.push(o):void 0!==o["_chem_comp_bond.value_order"]&&o["_chem_comp_bond.value_order"].length>0&&void 0!==o["_chem_comp_bond.comp_id"]&&o["_chem_comp_bond.comp_id"].length>0&&void 0!==o["_chem_comp_bond.atom_id_1"]&&o["_chem_comp_bond.atom_id_1"].length>0&&void 0!==o["_chem_comp_bond.atom_id_2"]&&o["_chem_comp_bond.atom_id_2"].length>0&&("Y"===o["_chem_comp_bond.pdbx_aromatic_flag"]?o["_chem_comp_bond.type"]="aromatic":"SING"===o["_chem_comp_bond.value_order"]||"SINGLE"===o["_chem_comp_bond.value_order"]?o["_chem_comp_bond.type"]="single":"DOUB"===o["_chem_comp_bond.value_order"]||"DOUBLE"===o["_chem_comp_bond.value_order"]?o["_chem_comp_bond.type"]="double":"TRIP"===o["_chem_comp_bond.value_order"]||"TRIPLE"===o["_chem_comp_bond.value_order"]?o["_chem_comp_bond.type"]="triple":o["_chem_comp_bond.type"]="single",c.push(o))}}return c}function dictToMolBlock(o,e){let t=addCIFAtomTypes(o,e),_=addCIFBondTypes(o,e),c=t.length,n=_.length,m=o+"\n  CCP4-MonomerLibrary-WebToCif\n\n";m+=("  "+c).slice(-3)+("  "+n).slice(-3)+"  0  0  0  0  0  0  0  0999 V2000\n";let s=0,l="";for(let o=0;o<c;o++){let e=parseFloat(t[o]["_chem_comp_atom.x"]),_=parseFloat(t[o]["_chem_comp_atom.y"]),c=parseFloat(t[o]["_chem_comp_atom.z"]);"."!=t[o]["_chem_comp_atom.charge"]&&"0"!=t[o]["_chem_comp_atom.charge"]&&(s++,l+=("   "+(o+1)).slice(-4)+("   "+t[o]["_chem_comp_atom.charge"]).slice(-4));let n=t[o]["_chem_comp_atom.type_symbol"];m+=("          "+e.toFixed(4)).slice(-10)+("          "+_.toFixed(4)).slice(-10)+("          "+c.toFixed(4)).slice(-10)+("   "+n).slice(-3)+"   0  0  0  0  0  0  0  0  0  0  0  0\n"}for(let o=0;o<n;o++){let e=t.find((e=>e["_chem_comp_atom.atom_id"]===_[o]["_chem_comp_bond.atom_id_1"])),c=t.find((e=>e["_chem_comp_atom.atom_id"]===_[o]["_chem_comp_bond.atom_id_2"])),n=t.indexOf(e),s=t.indexOf(c),l=("  "+(n+1)).slice(-3),p=("  "+(s+1)).slice(-3),i=1;!(["_chem_comp_bond.aromatic"]in _[o])||"y_XXX"!==_[o]["_chem_comp_bond.aromatic"]&&"Y_XXX"!==_[o]["_chem_comp_bond.aromatic"]?!(["_chem_comp_bond.type"]in _[o])||"TRIPLE"!==_[o]["_chem_comp_bond.type"]&&"triple"!==_[o]["_chem_comp_bond.type"]?!(["_chem_comp_bond.type"]in _[o])||"DOUBLE"!==_[o]["_chem_comp_bond.type"]&&"double"!==_[o]["_chem_comp_bond.type"]?!(["_chem_comp_bond.type"]in _[o])||"SINGLE"!==_[o]["_chem_comp_bond.type"]&&"single"!==_[o]["_chem_comp_bond.type"]?(console.log("Unknown bond type"),console.log(_[o])):i=1:i=2:i=3:i=4,m+=l+p+("  "+i).slice(-2)+" 0  0  0  0\n"}return s>0&&(m+="M  CHG"+("   "+s).slice(-3)+l+"\n"),m+="M  END",m}importScripts("web_example.js","RDKit_minimal.js"),createCCP4Module({print(o){postMessage(["output",o])},printErr(o){postMessage(["output",o])}}).then((function(o){CCP4Module=o})).catch((o=>{console.log("CCP4 problem :("),console.log(o)})),initRDKitModule({print(o){postMessage(["output",o])},printErr(o){postMessage(["output",o])}}).then((function(o){RDKit=o})).catch((o=>{console.log("RDKit problem :("),console.log(o)})),onmessage=function(o){let e=[o.data[0]],t=[o.data[1]];console.log(e);let _={};e.length>0&&Promise.all(e).then((o=>{console.log("Do RDKit stuff");let e=RDKit.get_mol(o[0]),c=RDKit.get_mol(e.add_hs());console.log("Done get_mol"),_[t[0]]=c.get_svg(),console.log("Done get_svg"),postMessage(["result",_]),console.log("Done postMessage")})).catch((o=>{console.error(o),postMessage(["result",_])}))};

package/baby-gru/wasm/superpose_worker.js

@@ -0,0 +1 @@
+var CCP4Module;importScripts("web_example.js"),importScripts("papaparse.min.js"),createCCP4Module({print(t){postMessage(["output",t])},printErr(t){postMessage(["output",t])}}).then((function(t){CCP4Module=t})).catch((t=>{console.log("CCP4 problem :("),console.log(t)})),onmessage=function(t){var e=new CCP4Module.VectorString;e.push_back("gesamt");var a=new CCP4Module.VectorString;for(let s=0;s<t.data[0].length;s++){try{CCP4Module.FS_createDataFile(".",t.data[1][s],t.data[0][s],!0,!0)}catch(t){}e.push_back(t.data[1][s]),a.push_back("dummy")}e.push_back("-csv"),e.push_back("out.csv");var s=CCP4Module.gesamt(e),l=CCP4Module.FS.readFile("out.csv",{encoding:"utf8"});let r=Papa.parse(l).data;if(2==t.data[0].length){let e=!1,a=!1,s=[],l=[],p=-1;for(let t=0;t<r.length;t++){if(e&&t<p+4&&(l.push(parseFloat(r[t][0])),l.push(parseFloat(r[t][1])),l.push(parseFloat(r[t][2])),l.push(parseFloat(r[t][3]))),a){if(r[t][0].length>0){let e=parseFloat(r[t][0]),a=parseFloat(r[t][4].trim().split(" ")[r[t][4].trim().split(" ").length-1]);s.push({x:a,y:e})}if(r[t].length<5)break}4==r[t].length&&"Rx"===r[t][0].trim()&&"Ry"===r[t][1].trim()&&"Rz"===r[t][2].trim()&&"T"===r[t][3].trim()&&(e=!0,p=t),r[t].length>4&&"Dist [A]"===r[t][0].trim()&&"Query"===r[t][3].trim()&&"Target"===r[t][4].trim()&&(a=!0)}12==l.length&&(l.push(0),l.push(0),l.push(0),l.push(1));let o={};o.alignData=s,o.transformMatrices=[l],t.data.length>2&&(o.jobid=t.data[2]),postMessage(["csvResult",o])}else{let e=!1,a=!1,s=[],l=[],p=[],o=-1;for(let i=0;i<r.length;i++){if(e&&i<o+4&&(l.push(parseFloat(r[i][0])),l.push(parseFloat(r[i][1])),l.push(parseFloat(r[i][2])),l.push(parseFloat(r[i][3]))),12==l.length&&(l.push(0),l.push(0),l.push(0),l.push(1),p.push(l),l=[],e=!1),4==r[i].length&&"Rx"===r[i][0].trim()&&"Ry"===r[i][1].trim()&&"Rz"===r[i][2].trim()&&"T"===r[i][3].trim()&&(e=!0,o=i),a){if(r[i][0].length>0){let t=parseFloat(r[i][0]),e=parseFloat(r[i][1].trim().split(" ")[r[i][1].trim().split(" ").length-1]);s.push({x:e,y:t})}if(r[i].length<t.data[0].length+1)break}"Disp.[A]"===r[i][0].trim()&&i>2&&"RESIDUE ALIGNMENT"===r[i-2][0].trim()&&(a=!0)}let i={};i.transformMatrices=p,i.alignData=s,t.data.length>2&&(i.jobid=t.data[2]),postMessage(["csvResult",i])}postMessage(["result",s])};