moorhen 0.0.1

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

@@ -0,0 +1 @@
+"use strict";var Module={};var ENVIRONMENT_IS_NODE=typeof process=="object"&&typeof process.versions=="object"&&typeof process.versions.node=="string";if(ENVIRONMENT_IS_NODE){var nodeWorkerThreads=require("worker_threads");var parentPort=nodeWorkerThreads.parentPort;parentPort.on("message",data=>onmessage({data:data}));var fs=require("fs");Object.assign(global,{self:global,require:require,Module:Module,location:{href:__filename},Worker:nodeWorkerThreads.Worker,importScripts:function(f){(0,eval)(fs.readFileSync(f,"utf8")+"//# sourceURL="+f)},postMessage:function(msg){parentPort.postMessage(msg)},performance:global.performance||{now:function(){return Date.now()}}})}var initializedJS=false;var pendingNotifiedProxyingQueues=[];function assert(condition,text){if(!condition)abort("Assertion failed: "+text)}function threadPrintErr(){var text=Array.prototype.slice.call(arguments).join(" ");if(ENVIRONMENT_IS_NODE){fs.writeSync(2,text+"\n");return}console.error(text)}function threadAlert(){var text=Array.prototype.slice.call(arguments).join(" ");postMessage({cmd:"alert",text:text,threadId:Module["_pthread_self"]()})}var out=()=>{throw"out() is not defined in worker.js."};var err=threadPrintErr;self.alert=threadAlert;Module["instantiateWasm"]=(info,receiveInstance)=>{var instance=new WebAssembly.Instance(Module["wasmModule"],info);receiveInstance(instance);Module["wasmModule"]=null;return instance.exports};self.onunhandledrejection=e=>{throw e.reason??e};self.onmessage=e=>{try{if(e.data.cmd==="load"){Module["wasmModule"]=e.data.wasmModule;for(const handler of e.data.handlers){Module[handler]=function(){postMessage({cmd:"callHandler",handler:handler,args:[...arguments]})}}Module["wasmMemory"]=e.data.wasmMemory;Module["buffer"]=Module["wasmMemory"].buffer;Module["ENVIRONMENT_IS_PTHREAD"]=true;if(typeof e.data.urlOrBlob=="string"){importScripts(e.data.urlOrBlob)}else{var objectUrl=URL.createObjectURL(e.data.urlOrBlob);importScripts(objectUrl);URL.revokeObjectURL(objectUrl)}createRSRModule(Module).then(function(instance){Module=instance})}else if(e.data.cmd==="run"){Module["__performance_now_clock_drift"]=performance.now()-e.data.time;Module["__emscripten_thread_init"](e.data.pthread_ptr,0,0,1);assert(e.data.pthread_ptr);Module["establishStackSpace"]();Module["PThread"].receiveObjectTransfer(e.data);Module["PThread"].threadInitTLS();if(!initializedJS){Module["__embind_initialize_bindings"]();pendingNotifiedProxyingQueues.forEach(queue=>{Module["executeNotifiedProxyingQueue"](queue)});pendingNotifiedProxyingQueues=[];initializedJS=true}try{Module["invokeEntryPoint"](e.data.start_routine,e.data.arg)}catch(ex){if(ex!="unwind"){if(ex instanceof Module["ExitStatus"]){if(Module["keepRuntimeAlive"]()){err("Pthread 0x"+Module["_pthread_self"]().toString(16)+" called exit(), staying alive due to noExitRuntime.")}else{err("Pthread 0x"+Module["_pthread_self"]().toString(16)+" called exit(), calling _emscripten_thread_exit.");Module["__emscripten_thread_exit"](ex.status)}}else{throw ex}}else{err("Pthread 0x"+Module["_pthread_self"]().toString(16)+" completed its main entry point with an `unwind`, keeping the worker alive for asynchronous operation.")}}}else if(e.data.cmd==="cancel"){if(Module["_pthread_self"]()){Module["__emscripten_thread_exit"](-1)}}else if(e.data.target==="setimmediate"){}else if(e.data.cmd==="processProxyingQueue"){if(initializedJS){Module["executeNotifiedProxyingQueue"](e.data.queue)}else{pendingNotifiedProxyingQueues.push(e.data.queue)}}else if(e.data.cmd){err("worker.js received unknown command "+e.data.cmd);err(e.data)}}catch(ex){err("worker.js onmessage() captured an uncaught exception: "+ex);if(ex&&ex.stack)err(ex.stack);if(Module["__emscripten_thread_crashed"]){Module["__emscripten_thread_crashed"]()}throw ex}};

package/baby-gru/wasm/mtz_arraybuffer_worker.js

@@ -0,0 +1,59 @@
+var CCP4Module;
+
+importScripts('web_example.js');
+
+createCCP4Module({print(t){postMessage(["output",t])},printErr(t){postMessage(["output",t]);}})
+    .then(function(CCP4Mod) {
+             CCP4Module = CCP4Mod;
+            })
+.catch((e) => {
+        console.log("CCP4 problem :(");
+        console.log(e);
+        });
+
+onmessage = function(e) {
+    var arrayBuffer = e.data[0];
+    const byteArray = new Uint8Array(arrayBuffer);
+    var selectedFileName = e.data[1];
+
+    let f_col = "FC";
+    let phi_col = "PHIC";
+    if(e.data[2]!==undefined && e.data[3]!==undefined){
+        f_col = e.data[2];
+        phi_col = e.data[3];
+    }
+
+    try {
+        CCP4Module.FS_createDataFile(".", selectedFileName, byteArray, true, true);
+    } catch(e) {
+    }
+
+    //FIXME - This is not used. It is intended to allow auto-open mtz
+    const header_info = CCP4Module.get_mtz_columns(selectedFileName);
+    console.log(header_info);
+    for(let ih=0;ih<header_info.size();ih+=2){
+        console.log(header_info.get(ih),header_info.get(ih+1));
+    }
+
+    console.log("Send",selectedFileName,"to clipper");
+    var result = CCP4Module.clipper_example_with_cols(selectedFileName,f_col,phi_col,2.0);
+    console.log("In the worker...");
+    console.log(result);
+    console.log(result.cell());
+    console.log(result.cell().a());
+    console.log(result.cell().b());
+    console.log(result.cell().c());
+    console.log(result.cell().alpha());
+    console.log(result.cell().beta());
+    console.log(result.cell().gamma());
+    CCP4Module.printMapStats(result);
+    var fout = new CCP4Module.CCP4MAPfile();
+    var outpath = new CCP4Module.Clipper_String("mapout.map");
+    fout.open_write(outpath);
+    CCP4Module.exportXMapToMapFile(fout,result);
+    fout.close_write();
+    console.log("Written",CCP4Module.clipperStringToString(outpath));
+    var mapasstr = CCP4Module.FS.readFile(CCP4Module.clipperStringToString(outpath));
+    postMessage(["result",mapasstr,selectedFileName,byteArray]);
+
+}

package/baby-gru/wasm/mtz_worker.js

@@ -0,0 +1,45 @@
+var CCP4Module;
+
+importScripts('web_example.js');
+
+createCCP4Module({print(t){postMessage(["output",t])},printErr(t){postMessage(["output",t]);}})
+    .then(function(CCP4Mod) {
+             CCP4Module = CCP4Mod;
+            })
+.catch((e) => {
+        console.log("CCP4 problem :(");
+        console.log(e);
+        });
+
+onmessage = function(e) {
+    var byteCharacters = atob(e.data[0]);
+    var selectedFileName = e.data[1];
+
+    const byteNumbers = new Array(byteCharacters.length);
+    for (let i = 0; i < byteCharacters.length; i++) {
+        byteNumbers[i] = byteCharacters.charCodeAt(i);
+    }
+    const byteArray = new Uint8Array(byteNumbers);
+
+    try {
+        CCP4Module.FS_createDataFile(".", selectedFileName, byteArray, true, true);
+    } catch(e) {
+    }
+
+    console.log("Send",selectedFileName,"to clipper");
+    var result = CCP4Module.clipper_example(selectedFileName);
+    console.log("In the worker...");
+    console.log(result);
+    console.log(result.cell());
+    console.log(result.cell().a());
+    CCP4Module.printMapStats(result);
+    var fout = new CCP4Module.CCP4MAPfile();
+    var outpath = new CCP4Module.Clipper_String("mapout.map");
+    fout.open_write(outpath);
+    CCP4Module.exportXMapToMapFile(fout,result);
+    fout.close_write();
+    console.log("Written",CCP4Module.clipperStringToString(outpath));
+    var mapasstr = CCP4Module.FS.readFile(CCP4Module.clipperStringToString(outpath));
+    postMessage(["result",mapasstr]);
+
+}

package/baby-gru/wasm/nma_worker.js

@@ -0,0 +1,103 @@
+var CCP4Module;
+
+importScripts('web_example.js');
+importScripts('papaparse.min.js');
+
+createCCP4Module({print(t){postMessage(["output",t])},printErr(t){postMessage(["output",t]);}})
+    .then(function(CCP4Mod) {
+             CCP4Module = CCP4Mod;
+            })
+.catch((e) => {
+        console.log("CCP4 problem :(");
+        console.log(e);
+        });
+
+onmessage = function(e) {
+
+    var args = new CCP4Module.VectorString();
+
+    try {
+        CCP4Module.FS_createDataFile(".", e.data[1], e.data[0], true, true);
+    } catch(e) {
+        //This happens when we supply sme file name on subsequent calls to this function?:w
+    }
+
+    var nma = CCP4Module.calculate_normal_modes(e.data[1],1);
+
+    const bvalc = nma.GetBValues();
+    const nbval = bvalc.size();
+
+    let bvals = [];
+    let bvals_exptl = [];
+
+    const bval_exptl =  CCP4Module.get_CA_bvalues_from_file(e.data[1]);
+    let norm;
+    if(nbval>0){
+        norm = 0.0;
+        for(let i=0;i<nbval;i++){
+            const theo_bval = bvalc.get(i);
+            const expr_bval = bval_exptl.get(i);
+            norm += theo_bval/expr_bval;
+        }
+        norm /= nbval;
+        norm = 1/norm;
+    }else{
+        norm = 1.0;
+    }
+
+    const norm_matrix = CCP4Module.GetCorrelations(nma,norm);
+
+//FIXME - (possible) x should be sequence number?
+    for(let i=0;i<nbval;i++){
+        bvals.push({x:i+1,y:bvalc.get(i)*norm});
+        bvals_exptl.push({x:i+1,y:bval_exptl.get(i)});
+    }
+
+    const nrows = norm_matrix.get_rows();
+    const ncols = norm_matrix.get_columns();
+    let corrMat = {x:[],y:[],z:[]};
+    for(let i=0;i<nrows;i++){
+        for(let j=0;j<ncols;j++){
+            corrMat.x.push(i);
+            corrMat.y.push(j);
+            corrMat.z.push(norm_matrix.get(i,j));
+        }
+    }
+
+    let result = 0;
+    
+    postMessage(["corrMat",corrMat]);
+    postMessage(["bvalues",[bvals,bvals_exptl]]);
+    postMessage(["result",result]);
+
+    let nma_anm = CCP4Module.calculate_normal_modes(e.data[1],0);
+    const eigens = CCP4Module.GetEigen(nma_anm);
+    const evalMat = eigens.get(1);
+    const nrows_e = evalMat.get_rows();
+    const ncols_e = evalMat.get_columns();
+    postMessage(["output","Normal modes"]);
+    let energies = [];
+ 
+    for(let i=6;i<nrows_e;i++){
+        energies.push(evalMat.get(i,0));
+    }
+
+    postMessage(["energies",energies]);
+    const displacements = CCP4Module.GetDisplacements(nma_anm);
+    const nModes = displacements.nModes();
+    const nSteps = displacements.nSteps();
+
+    let dispMessage = {modes:[]};
+    for(let imode=0;imode<nModes;imode++){
+        dispMessage.modes.push({steps:[]});
+        for(let istep=0;istep<nSteps;istep++){
+            dispMessage.modes[imode].steps.push({xyz:[]});
+            const disp = displacements.getDisplacements(imode,istep);
+            const dispSize = disp.size();
+            for(let idisp=0;idisp<dispSize;idisp++){
+                dispMessage.modes[imode].steps[istep].xyz.push(disp.get(idisp));
+            }
+        }
+    }
+    postMessage(["displacements",dispMessage]);
+}

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

@@ -0,0 +1,7 @@
+/* @license
+Papa Parse
+v5.3.2
+https://github.com/mholt/PapaParse
+License: MIT
+*/
+!function(e,t){"function"==typeof define&&define.amd?define([],t):"object"==typeof module&&"undefined"!=typeof exports?module.exports=t():e.Papa=t()}(this,function s(){"use strict";var f="undefined"!=typeof self?self:"undefined"!=typeof window?window:void 0!==f?f:{};var n=!f.document&&!!f.postMessage,o=n&&/blob:/i.test((f.location||{}).protocol),a={},h=0,b={parse:function(e,t){var i=(t=t||{}).dynamicTyping||!1;M(i)&&(t.dynamicTypingFunction=i,i={});if(t.dynamicTyping=i,t.transform=!!M(t.transform)&&t.transform,t.worker&&b.WORKERS_SUPPORTED){var r=function(){if(!b.WORKERS_SUPPORTED)return!1;var e=(i=f.URL||f.webkitURL||null,r=s.toString(),b.BLOB_URL||(b.BLOB_URL=i.createObjectURL(new Blob(["(",r,")();"],{type:"text/javascript"})))),t=new f.Worker(e);var i,r;return t.onmessage=_,t.id=h++,a[t.id]=t}();return r.userStep=t.step,r.userChunk=t.chunk,r.userComplete=t.complete,r.userError=t.error,t.step=M(t.step),t.chunk=M(t.chunk),t.complete=M(t.complete),t.error=M(t.error),delete 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t=[],i=!0,r=!1;this.pause=function(){u.prototype.pause.apply(this,arguments),this._input.pause()},this.resume=function(){u.prototype.resume.apply(this,arguments),this._input.resume()},this.stream=function(e){this._input=e,this._input.on("data",this._streamData),this._input.on("end",this._streamEnd),this._input.on("error",this._streamError)},this._checkIsFinished=function(){r&&1===t.length&&(this._finished=!0)},this._nextChunk=function(){this._checkIsFinished(),t.length?this.parseChunk(t.shift()):i=!0},this._streamData=v(function(e){try{t.push("string"==typeof e?e:e.toString(this._config.encoding)),i&&(i=!1,this._checkIsFinished(),this.parseChunk(t.shift()))}catch(e){this._streamError(e)}},this),this._streamError=v(function(e){this._streamCleanUp(),this._sendError(e)},this),this._streamEnd=v(function(){this._streamCleanUp(),r=!0,this._streamData("")},this),this._streamCleanUp=v(function(){this._input.removeListener("data",this._streamData),this._input.removeListener("end",this._streamEnd),this._input.removeListener("error",this._streamError)},this)}function i(m){var a,o,h,r=Math.pow(2,53),n=-r,s=/^\s*-?(\d+\.?|\.\d+|\d+\.\d+)([eE][-+]?\d+)?\s*$/,u=/^(\d{4}-[01]\d-[0-3]\dT[0-2]\d:[0-5]\d:[0-5]\d\.\d+([+-][0-2]\d:[0-5]\d|Z))|(\d{4}-[01]\d-[0-3]\dT[0-2]\d:[0-5]\d:[0-5]\d([+-][0-2]\d:[0-5]\d|Z))|(\d{4}-[01]\d-[0-3]\dT[0-2]\d:[0-5]\d([+-][0-2]\d:[0-5]\d|Z))$/,t=this,i=0,f=0,d=!1,e=!1,l=[],c={data:[],errors:[],meta:{}};if(M(m.step)){var 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package/baby-gru/wasm/pdb_worker.js

@@ -0,0 +1,282 @@
+var CCP4Module;
+var RDKit;
+
+importScripts('web_example.js','RDKit_minimal.js');
+
+createCCP4Module({print(t){postMessage(["output",t])},printErr(t){postMessage(["output",t]);}})
+    .then(function(CCP4Mod) {
+             CCP4Module = CCP4Mod;
+            })
+.catch((e) => {
+        console.log("CCP4 problem :(");
+        console.log(e);
+        });
+
+initRDKitModule({print(t){postMessage(["output",t])},printErr(t){postMessage(["output",t]);}})
+    .then(function(RDKitMod) {
+             RDKit = RDKitMod;
+            })
+.catch((e) => {
+        console.log("RDKit problem :(");
+        console.log(e);
+        });
+
+function makeRequest (method, url) {
+  return new Promise(function (resolve, reject) {
+    var xhr = new XMLHttpRequest();
+    xhr.open(method, url, true);
+    xhr.onload = function () {
+      if (this.status >= 200 && this.status < 300) {
+        resolve(xhr.response);
+      } else {
+        reject({
+          status: this.status,
+          statusText: xhr.statusText
+        });
+      }
+    };
+    xhr.onerror = function () {
+      reject({
+        status: this.status,
+        statusText: xhr.statusText
+      });
+    };
+    xhr.send();
+  });
+}
+
+function onlyUnique(value, index, self) {
+  return self.indexOf(value) === index;
+}
+
+function getLoop(lines,loopName_in){
+    let loopName = loopName_in+".";
+    let inWantedLoop = false;
+    let loopLines = [];
+    let len = lines.length;
+    for(let il=0;il<len;il++){
+        let l = lines[il].replace(/(^\s+|\s+$)/g,'');
+        if(l === "loop_"||(l.substring(0,1)==="_"&&l.substring(0,loopName.length)!==loopName)){
+            if(inWantedLoop){
+                break;
+            }else{
+                if(il<lines.length){
+                    if(lines[il+1].substring(0,loopName.length) === loopName){
+                        inWantedLoop = true;
+                    }
+                }
+            }
+        }else{
+            if(inWantedLoop){
+                loopLines.push(l);
+            }
+        }
+    }
+    return loopLines;
+}
+
+function splitQuotedCIFString(stringToSplit){
+    if(stringToSplit.length===0) return [];
+    return stringToSplit.match(/(?:[^\s"]+|"[^"]*")+/g);
+}
+
+function addCIFAtomTypes(resname,cif) {
+
+    let ener_lib_lines = cif.split("\n");
+    let libAtomTypes = [];
+    let libAtomLines = getLoop(ener_lib_lines,"_chem_comp_atom");
+    let atoms = [];
+    for(let il=0;il<libAtomLines.length;il++){
+        // We are only interested in atom_id and type_energy, so we do not worry about float and int types.
+        if(libAtomLines[il].substr(0,1)==="#"||libAtomLines[il].trim()===""){
+            continue;
+        } else if(libAtomLines[il].substr(0,1)==="_"){
+            libAtomTypes.push(libAtomLines[il]);
+        } else {
+            let split = splitQuotedCIFString(libAtomLines[il]);
+            if(split[0]!=="."){
+                let atom = {};
+                for(let iprop=0;iprop<split.length;iprop++){
+                    atom[libAtomTypes[iprop]] = split[iprop];
+                }
+                atoms.push(atom);
+            }
+        }
+    }
+    return atoms;
+}
+
+function addCIFBondTypes(resname,cif) {
+    let ener_lib_lines = cif.split("\n");
+    let libAtomTypes = [];
+    let libAtomLines = getLoop(ener_lib_lines,"_chem_comp_bond");
+    let bonds = [];
+    for(let il=0;il<libAtomLines.length;il++){
+        // We are only interested in bond_id, atom_id and type, so we do not worry about float and int types.
+        if(libAtomLines[il].substr(0,1)==="#"||libAtomLines[il].trim()===""){
+            continue;
+        } else if(libAtomLines[il].substr(0,1)==="_"){
+            libAtomTypes.push(libAtomLines[il]);
+        } else {
+            let split = libAtomLines[il].match(/(?:[^\s"]+|"[^"]*")+/g);
+            if(split[0]!=="."){
+                let bond = {};
+                for(let iprop=0;iprop<split.length;iprop++){
+                    bond[libAtomTypes[iprop]] = split[iprop];
+                }
+                if(typeof(bond["_chem_comp_bond.type"])!=="undefined"&&bond["_chem_comp_bond.type"].length>0&&typeof(bond["_chem_comp_bond.comp_id"])!=="undefined"&&bond["_chem_comp_bond.comp_id"].length>0&&typeof(bond["_chem_comp_bond.atom_id_1"])!=="undefined"&&bond["_chem_comp_bond.atom_id_1"].length>0&&typeof(bond["_chem_comp_bond.atom_id_2"])!=="undefined"&&bond["_chem_comp_bond.atom_id_2"].length>0){
+                    bonds.push(bond);
+                } else if(typeof(bond["_chem_comp_bond.value_order"])!=="undefined"&&bond["_chem_comp_bond.value_order"].length>0&&typeof(bond["_chem_comp_bond.comp_id"])!=="undefined"&&bond["_chem_comp_bond.comp_id"].length>0&&typeof(bond["_chem_comp_bond.atom_id_1"])!=="undefined"&&bond["_chem_comp_bond.atom_id_1"].length>0&&typeof(bond["_chem_comp_bond.atom_id_2"])!=="undefined"&&bond["_chem_comp_bond.atom_id_2"].length>0){
+                    if(bond["_chem_comp_bond.pdbx_aromatic_flag"]==="Y"){
+                        bond["_chem_comp_bond.type"] = "aromatic";
+                    } else if(bond["_chem_comp_bond.value_order"]==="SING"||bond["_chem_comp_bond.value_order"]==="SINGLE"){
+                        bond["_chem_comp_bond.type"] = "single";
+                    } else if(bond["_chem_comp_bond.value_order"]==="DOUB"||bond["_chem_comp_bond.value_order"]==="DOUBLE"){
+                        bond["_chem_comp_bond.type"] = "double";
+                    } else if(bond["_chem_comp_bond.value_order"]==="TRIP"||bond["_chem_comp_bond.value_order"]==="TRIPLE"){
+                        bond["_chem_comp_bond.type"] = "triple";
+                    } else {
+                        bond["_chem_comp_bond.type"] = "single";
+                    }
+                    bonds.push(bond);
+                }
+            }
+        }
+    }
+
+    return bonds;
+}
+
+function dictToMolBlock(name,dictLines){
+
+    let atoms = addCIFAtomTypes(name,dictLines);
+    let bonds = addCIFBondTypes(name,dictLines);
+
+    let nAtoms = atoms.length;
+    let nBonds = bonds.length;
+
+    let nAtomsString = ("  " + nAtoms).slice(-3);
+    let nBondsString = ("  " + nBonds).slice(-3);
+
+    let molblock = name+`
+  CCP4-MonomerLibrary-WebToCif
+
+`
+
+    molblock += nAtomsString+nBondsString+"  0  0  0  0  0  0  0  0999 V2000\n"
+    let ncharged = 0;
+    let chargeStr = "";
+    for(let iat=0;iat<nAtoms;iat++){
+        let x = parseFloat(atoms[iat]["_chem_comp_atom.x"]);
+        let y = parseFloat(atoms[iat]["_chem_comp_atom.y"]);
+        let z = parseFloat(atoms[iat]["_chem_comp_atom.z"]);
+        if(atoms[iat]["_chem_comp_atom.charge"]!="."&&atoms[iat]["_chem_comp_atom.charge"]!="0"){
+            ncharged++;
+            chargeStr += ("   "+(iat+1)).slice(-4)+("   "+atoms[iat]["_chem_comp_atom.charge"]).slice(-4);
+        }
+        let symbol =  atoms[iat]["_chem_comp_atom.type_symbol"];
+        let xString = ("          "+x.toFixed(4)).slice(-10)
+        let yString = ("          "+y.toFixed(4)).slice(-10)
+        let zString = ("          "+z.toFixed(4)).slice(-10)
+        let symbolString = ("   "+symbol).slice(-3);
+        molblock += xString+yString+zString+symbolString+"   0  0  0  0  0  0  0  0  0  0  0  0\n";
+    }
+
+    for(let ib=0;ib<nBonds;ib++){
+        let atom1 = atoms.find(obj => {
+                return obj["_chem_comp_atom.atom_id"] === bonds[ib]["_chem_comp_bond.atom_id_1"]
+        })
+        let atom2 = atoms.find(obj => {
+                return obj["_chem_comp_atom.atom_id"] === bonds[ib]["_chem_comp_bond.atom_id_2"]
+        })
+        let idx1 = atoms.indexOf(atom1);
+        let idx2 = atoms.indexOf(atom2);
+        let atom1String = ("  " + (idx1+1)).slice(-3);
+        let atom2String = ("  " + (idx2+1)).slice(-3);
+        let bondType = 1;
+        //FIXME - I am not sure this is handled by RDKit.
+        if(["_chem_comp_bond.aromatic"] in bonds[ib] && (bonds[ib]["_chem_comp_bond.aromatic"]==='y_XXX'||bonds[ib]["_chem_comp_bond.aromatic"]==='Y_XXX')){
+            bondType = 4;
+        } else if(["_chem_comp_bond.type"] in bonds[ib] && (bonds[ib]["_chem_comp_bond.type"]==='TRIPLE'||bonds[ib]["_chem_comp_bond.type"]==='triple')) {
+            bondType = 3;
+        } else if(["_chem_comp_bond.type"] in bonds[ib] && (bonds[ib]["_chem_comp_bond.type"]==='DOUBLE'||bonds[ib]["_chem_comp_bond.type"]==='double')) {
+            bondType = 2;
+        } else if(["_chem_comp_bond.type"] in bonds[ib] && (bonds[ib]["_chem_comp_bond.type"]==='SINGLE'||bonds[ib]["_chem_comp_bond.type"]==='single')) {
+            bondType = 1;
+        } else {
+            console.log("Unknown bond type");
+            console.log(bonds[ib]);
+        }
+        let bondTypeString = ("  " + (bondType)).slice(-2);
+
+        molblock += atom1String+atom2String+bondTypeString+" 0  0  0  0\n";
+    }
+
+    if(ncharged>0){
+        molblock += "M  CHG"+(("   "+ncharged).slice(-3))+chargeStr+"\n";
+    }
+    molblock += "M  END";
+
+    return molblock;
+
+}
+
+onmessage = function(e) {
+    let contents = e.data[0];
+    let selectedFileName = e.data[1];
+
+    try {
+        CCP4Module.FS_createDataFile(".", selectedFileName, contents, true, true);
+    } catch(e) {
+    }
+
+    let svgTree = CCP4Module.get_annotated_glycans_hierarchical(selectedFileName,false,"undefined");
+    let glycanResult = {};
+    glycanResult[selectedFileName] = svgTree;
+    postMessage(["glycan_result",glycanResult]);
+
+    let result = CCP4Module.mmdb2_example(selectedFileName);
+    let resultJS = [];
+    for(let ir=0;ir<result.size();ir++){
+        resultJS.push(result.get(ir));
+    }
+
+    let unique = resultJS.filter(onlyUnique);
+
+    //let ligandServer = "http://192.168.1.242:8000/";
+    let ligandServer = "/monomers/";
+
+    let promises = [];
+
+    for(ilig=0;ilig<unique.length;ilig++){
+        let ligType = unique[ilig];
+        let theUrl = ligandServer+ligType.toLowerCase()[0]+"/"+ligType.toUpperCase()+".cif";
+        promises.push(makeRequest('GET',theUrl,true));
+    }
+
+    let svgResult = {};
+
+    if(promises.length>0){
+        Promise.all(promises).then((values) => {
+             for(ilig=0;ilig<values.length;ilig++){
+                 let ligType = unique[ilig];
+                 let ligandlines = values[ilig];
+                 let molblock = dictToMolBlock(ligType,ligandlines);
+                 let mol = RDKit.get_mol(molblock);
+                 let mol2 = RDKit.get_mol(mol.remove_hs());
+                 let smiles = mol2.get_smiles();
+                 let mol3 = RDKit.get_mol(smiles);
+                 svgResult[ligType] = mol3.get_svg();
+             }
+             postMessage(["result",svgResult]);
+        }).catch((error) => {
+             console.error(error);
+             for(ilig=0;ilig<unique.length;ilig++){
+                 let ligType = unique[ilig];
+                 svgResult[ligType] = "";
+             }
+             postMessage(["result",svgResult]);
+        });
+    }
+
+}