moorhen 0.0.1

package/baby-gru/wasm/crystallography_worker.js

@@ -0,0 +1,610 @@
+// FIXME - Handle mmCIF, data cif, monomers(?)
+// FIXME - We may not want multiple modules (CCP4Module,RSRModule) since files have to be loaded into FS of each one.
+// FIXME - Does not seem to work in Safari. Importing moorhen.js is *not possible* in a thread on Safari, because it uses
+//         Workers internally to do the threading. And Safari does not support nested Workers, not even in technology preview.
+
+let currentTaskName = "";
+function rsrPrint(t){
+    postMessage({
+        messageTag: "output",
+        result: t,
+        taskName: currentTaskName
+    })
+}
+
+let CCP4Module;
+let RSRModule;
+let molecules_container = null;
+
+importScripts('./web_example.js');
+importScripts('./pako.js');
+
+createCCP4Module({print: rsrPrint,printErr: rsrPrint})
+    .then(function(CCP4Mod) {
+             CCP4Module = CCP4Mod;
+            })
+.catch((e) => {
+        console.log("CCP4 problem :(");
+        console.log(e);
+        });
+
+importScripts('./moorhen.js');
+
+const Lib = {
+    locateFile: (file) => file,
+    onRuntimeInitialized: () => {
+        console.log('onRuntimeInitialized');
+    },
+    mainScriptUrlOrBlob: "./moorhen.js",
+    print: rsrPrint,
+    printErr: rsrPrint,
+};
+
+createRSRModule(Lib)
+    .then(function(CCP4Mod) {
+             RSRModule = CCP4Mod;
+             molecules_container = new RSRModule.molecules_container_js();
+             molecules_container.geometry_init_standard();
+             molecules_container.fill_rotamer_probability_tables();
+             console.log("##################################################");
+             console.log(molecules_container);
+             console.log("##################################################");
+            })
+.catch((e) => {
+        console.log("RSR problem :(");
+        console.log(e);
+        });
+
+
+let dataObjects = {pdbFiles:{}, mtzFiles:{}, cifFiles:{}};
+let dataObjectsNames = {pdbFiles:{}, mtzFiles:{}, cifFiles:{}, ramaInfo:{}, bvalInfo:{}, mol_cont_idx:{}, map_cont_idx:{}, densityFitInfo:{}, rotamersInfo:{}};
+
+function guid(){
+    var d = Date.now();
+    var uuid = 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'.replace(/[xy]/g, function(c) {
+        var r = (d + Math.random()*16)%16 | 0;
+        d = Math.floor(d/16);
+        return (c==='x' ? r : (r&0x3|0x8)).toString(16);
+    });
+    return uuid;
+}
+
+//TODO 
+// * Make files loaded from PDB available to MiniRSR/Flip and Ramachandran plot. Do not know why they are not ...
+// * Create method to get Rama data from a PDB file, 
+// * Change dataObjectsNames to globalCache or something
+// * Add Rama data to the globalCache
+
+function updateDataObjectsNames(){
+    postMessage({
+        messageTag: "dataObjectsNames",
+        result: dataObjectsNames,
+    })
+}
+
+function downLoadFiles(files){
+    let CIFfiles = [];
+    let gzCIFfiles = [];
+    let PDBfiles = [];
+    let gzPDBfiles = [];
+    let MTZfiles = [];
+
+    for(let x=0;x<files.length;x++){
+        if(files[x].endsWith(".mtz")){
+            MTZfiles.push(files[x]);
+        } else if(files[x].endsWith(".pdb")||files[x].endsWith(".ent")){
+            PDBfiles.push(files[x]);
+        } else if(files[x].endsWith(".cif")){
+            CIFfiles.push(files[x]);
+        } else if(files[x].endsWith(".pdb.gz")||files[x].endsWith(".ent.gz")){
+            gzPDBfiles.push(files[x]);
+        } else if(files[x].endsWith(".cif.gz")){
+            gzCIFfiles.push(files[x]);
+        } else {
+            console.log("Unknown file suffix");
+        }
+    }
+
+    console.log(gzCIFfiles);
+
+    Promise.all(gzCIFfiles.map(function(url) {
+        return fetch(url).then(resp => resp.blob()).then(data => [url, data]);
+    })).then(results => {
+        for(ires=0;ires<results.length;ires++){
+            const thisResult = results[ires];
+            console.log(thisResult);
+            const key = guid();
+            //Now gunzip, etc...
+        }
+    })
+
+    /*
+    Promise.all(gzPDBfiles.map(function(file) {
+      return fetch(file).then(resp => resp.blob())
+        .then(data => [file, data]);
+    })).then(function(results){
+        for(ires=0;ires<results.length;ires++){
+            const thisResult = results[ires];
+            console.log(thisResult);
+            const key = guid();
+            CCP4Module.FS_createDataFile(".", key + ".pdb", thisResult[1], true, true);
+            RSRModule.FS_createDataFile(".", key + ".pdb", thisResult[1], true, true);
+            //TODO - parsePDB is now in a react-app/src. How do I get at it from here?
+            //const dataSplit = thisResult[1].split("\n");
+            //const hierarchy = parsePDB(dataSplit,name);
+            //dataObjects.pdbFiles[key] = {hierarchy:hierarchy, fileName:key + ".pdb", originalFileName:thisResult[0], contents:thisResult[1]};
+            dataObjects.pdbFiles[key] = {fileName:key + ".pdb", originalFileName:thisResult[0], contents:thisResult[1]};
+            dataObjectsNames.pdbFiles[key] = {fileName:key + ".pdb", originalFileName:thisResult[0]};
+        }
+        updateShareArrayBuffer();
+    }) .catch(function(err) {
+        console.log(err);
+    });
+    */
+
+
+}
+
+function loadFiles(files){
+
+    let PDBfiles = [];
+    let MTZfiles = [];
+
+    for(let x=0;x<files.length;x++){
+        if(files[x].name.endsWith(".mtz")){
+            MTZfiles.push(files[x]);
+        } else if(files[x].name.endsWith(".pdb")||files[x].name.endsWith(".ent")){
+            PDBfiles.push(files[x]);
+        }
+    }
+
+    Promise.all(PDBfiles.map(function(file) {
+      return file.text()
+        .then(data => [file.name, data]);
+    })).then(function(results){
+        for(ires=0;ires<results.length;ires++){
+            const thisResult = results[ires];
+            const key = guid();
+            CCP4Module.FS_createDataFile(".", key + ".pdb", thisResult[1], true, true);
+            RSRModule.FS_createDataFile(".", key + ".pdb", thisResult[1], true, true);
+            //TODO - parsePDB is now in a react-app/src. How do I get at it from here?
+            //const dataSplit = thisResult[1].split("\n");
+            //const hierarchy = parsePDB(dataSplit,name);
+            //dataObjects.pdbFiles[key] = {hierarchy:hierarchy, fileName:key + ".pdb", originalFileName:thisResult[0], contents:thisResult[1]};
+            dataObjects.pdbFiles[key] = {fileName:key + ".pdb", originalFileName:thisResult[0], contents:thisResult[1]};
+            dataObjectsNames.pdbFiles[key] = {fileName:key + ".pdb", originalFileName:thisResult[0]};
+            const result = molecules_container.read_pdb(key + ".pdb");
+            dataObjectsNames.mol_cont_idx[key] = result;
+        }
+        updateDataObjectsNames();
+    }) .catch(function(err) {
+        console.log(err);
+    });
+
+
+    Promise.all(MTZfiles.map(function(file) {
+      return file.arrayBuffer()
+        .then(data => [file.name, data]);
+    })).then(function(results){
+        for(ires=0;ires<results.length;ires++){
+            const thisResult = results[ires];
+            const key = guid();
+            const byteArray = new Uint8Array(thisResult[1]);
+            CCP4Module.FS_createDataFile(".", key + ".mtz", byteArray, true, true);
+            RSRModule.FS_createDataFile(".", key + ".mtz", byteArray, true, true);
+            dataObjects.mtzFiles[key] = {fileName:key + ".mtz", originalFileName:thisResult[0], contents:byteArray};
+            dataObjectsNames.mtzFiles[key] = {fileName:key + ".mtz", originalFileName:thisResult[0]};
+            //TODO - work out what columns to use ...
+            const f = "FC";
+            const phi = "PHIC";
+            const wt = "";
+            const use_wt = false;
+            const is_diff = false;
+            const result = molecules_container.read_mtz(key + ".mtz",f,phi,wt,use_wt,is_diff);
+            dataObjectsNames.map_cont_idx[key] = result;
+        }
+        updateDataObjectsNames();
+    }).catch(function(err) {
+        console.log(err);
+    });
+
+}
+
+
+function getDensityFit(e) {
+    console.log(e.data);
+    const jobId = e.data.jobId;
+    const pdbin = dataObjects.pdbFiles[e.data.pdbinKey].fileName;
+    const chainId = e.data["chainId"];
+    const hklin = dataObjects.mtzFiles[e.data.hklinKey].fileName;
+    const imol_model = dataObjectsNames.mol_cont_idx[e.data.pdbinKey];
+    const imol_map = dataObjectsNames.map_cont_idx[e.data.hklinKey];
+    console.log(imol_model,imol_map);
+    const result = molecules_container.density_fit_analysis(imol_model, imol_map);
+    console.log(result);
+    const index_for_chain = result.get_index_for_chain(chainId);
+    console.log(index_for_chain);
+    console.log(result.cviv.get(index_for_chain));
+    const resInfo = result.cviv.get(index_for_chain).rviv;
+    console.log(resInfo);
+    console.log(resInfo.size());
+    let resInfoJS = [];
+    for(let ir=0;ir<resInfo.size();ir++){
+        const CPPchainId = resInfo.get(ir).residue_spec.chain_id;
+        const seqNum = resInfo.get(ir).residue_spec.res_no;
+        const value = resInfo.get(ir).distortion;
+        const insCode = resInfo.get(ir).residue_spec.ins_code;
+        //FIXME - It would be nice to know.
+        const restype = "UNK";
+        const jsres = {chainId:CPPchainId,insCode:insCode,seqNum:seqNum,restype:restype,density_fit:1./value};
+        resInfoJS.push(jsres);
+    }
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "result",
+        result: resInfoJS,
+        taskName: currentTaskName
+    })
+}
+
+function getBVals(e) {
+    console.log(e.data);
+    const jobId = e.data.jobId;
+    const pdbin = dataObjects.pdbFiles[e.data.pdbinKey].fileName;
+    const chainId = e.data["chainId"];
+    const result = RSRModule.getBVals(pdbin,chainId);
+    let resInfo = [];
+    for(let ir=0;ir<result.size();ir++){
+        const cppres = result.get(ir);
+        //TODO - Is there a nicer way to do this?
+        const jsres = {chainId:cppres.chainId,insCode:cppres.insCode,seqNum:cppres.seqNum,restype:cppres.restype,bval:cppres.property};
+        resInfo.push(jsres);
+    }
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "result",
+        result: resInfo,
+        taskName: currentTaskName
+    })
+}
+
+function getRama(e) {
+    console.log(e.data);
+    const jobId = e.data.jobId;
+    const pdbin = dataObjects.pdbFiles[e.data.pdbinKey].fileName;
+    const chainId = e.data["chainId"];
+    const result = RSRModule.getRamachandranData(pdbin,chainId);
+    console.log(result);
+    let resInfo = [];
+    for(let ir=0;ir<result.size();ir++){
+        const cppres = result.get(ir);
+        //TODO - Is there a nicer way to do this?
+        const jsres = {chainId:cppres.chainId,insCode:cppres.insCode,seqNum:cppres.seqNum,restype:cppres.restype,phi:cppres.phi,psi:cppres.psi,isOutlier:cppres.isOutlier,is_pre_pro:cppres.is_pre_pro};
+        resInfo.push(jsres);
+    }
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "result",
+        result: resInfo,
+        taskName: currentTaskName
+    })
+}
+
+function drawMesh(simpleMesh,e) {
+    const nVertices = molecules_container.count_simple_mesh_vertices(simpleMesh);
+    const vertices = simpleMesh.vertices;
+    const nVerticesDirect = vertices.size();
+    const triangles = simpleMesh.triangles;
+    const nTriangles = triangles.size();
+    let totIdxs = [];
+    let totPos = [];
+    let totNorm = [];
+    let totCol = [];
+    for(let i=0;i<triangles.size();i++){
+        const idxs = triangles.get(i).point_id;
+        totIdxs.push(...idxs);
+    }
+    for(let i=0;i<vertices.size();i++){
+        const vert = vertices.get(i);
+        totPos.push(...vert.pos);
+        totNorm.push(...vert.normal);
+        totCol.push(...vert.color);
+    }
+    const cubeInfo = {prim_types:[["TRIANGLES"]],idx_tri:[[totIdxs]],vert_tri:[[totPos]],norm_tri:[[totNorm]],col_tri:[[totCol]]};
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "result",
+        result: cubeInfo,
+        taskName: currentTaskName
+    })
+}
+
+function drawDodos(e) {
+
+    //This is not yet used
+    //const chainId = e.data["chainId"];
+
+    const idx = dataObjectsNames.mol_cont_idx[e.data.pdbinKey];
+    const simpleMesh = molecules_container.get_rotamer_dodecs(idx);
+    drawMesh(simpleMesh,e);
+}
+
+function drawRamaBalls(e) {
+
+    //This is not yet used
+    //const chainId = e.data["chainId"];
+
+    const idx = dataObjectsNames.mol_cont_idx[e.data.pdbinKey];
+    const simpleMesh = molecules_container.ramachandran_validation_markup_mesh(idx);
+    drawMesh(simpleMesh,e);
+}
+
+function drawCube(e) {
+    const simpleMesh = molecules_container.test_origin_cube();
+    drawMesh(simpleMesh,e);
+}
+
+
+function getRotamers(e) {
+    const jobId = e.data.jobId;
+    const pdbin = dataObjects.pdbFiles[e.data.pdbinKey].fileName;
+    const chainId = e.data["chainId"];
+
+    const rotamersMap = RSRModule.getRotamersMap();
+
+    let rotamersInfo = [];
+    const residueList = RSRModule.getResidueListForChain(pdbin,chainId);
+    const residueSpecList = RSRModule.getResidueSpecListForChain(pdbin,chainId);
+    for(let i=0;i<residueList.size();i++){
+        const resRot = rotamersMap.get(residueList.get(i));
+        if(resRot){
+            let irot = 0;
+            let resRots = [];
+            for(irot=0;irot<resRot.size();irot++){
+                const rotamer = resRot.get(irot);
+                const chi1 = rotamer.get_chi(1);
+                const chi2 = rotamer.get_chi(2);
+                const chi3 = rotamer.get_chi(3);
+                const chi4 = rotamer.get_chi(4);
+                resRots.push([chi1,chi2,chi3,chi4]);
+            }
+            rotamersInfo.push({chainId:chainId,seqNum:residueSpecList.get(i).res_no,insCode:residueSpecList.get(i).ins_code,restype:residueList.get(i),data:resRots});
+        } else {
+            rotamersInfo.push({chainId:chainId,seqNum:residueSpecList.get(i).res_no,insCode:residueSpecList.get(i).ins_code,restype:residueList.get(i),data:[]});
+        }
+    }
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "result",
+        result: rotamersInfo,
+        taskName: currentTaskName
+    })
+}
+
+function autoFitRotamer(e) {
+
+    const jobId = e.data.jobId;
+
+    const pdbin = dataObjects.pdbFiles[e.data.pdbinKey].fileName;
+    const chainId = e.data["chainId"];
+    const resno = e.data["resno"];
+    const pdbout = jobId+"out.pdb";
+    const imol_model = dataObjectsNames.mol_cont_idx[e.data.pdbinKey];
+    const imol_map = dataObjectsNames.map_cont_idx[e.data.hklinKey];
+
+    const resultMolCont = molecules_container.auto_fit_rotamer(imol_model,chainId,resno,"","",imol_map)
+
+    const write_result = molecules_container.writePDBASCII(dataObjectsNames.mol_cont_idx[e.data.pdbinKey],pdbout);
+    console.log("result of which is",resultMolCont,write_result);
+    var pdb_out = RSRModule.FS.readFile(pdbout, { encoding: 'utf8' });
+
+    //postMessage(["result",result,currentTaskName]);
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "result",
+        result: resultMolCont,
+        taskName: currentTaskName
+    })
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "pdb_out",
+        jobId: jobId,
+        result: pdb_out,
+        taskName: currentTaskName
+    })
+}
+
+function flipPeptide(e) {
+
+    const jobId = e.data.jobId;
+
+    const pdbin = dataObjects.pdbFiles[e.data.pdbinKey].fileName;
+    const chainId = e.data["chainId"];
+    const resno = e.data["resnoFlip"];
+    const pdbout = jobId+"out.pdb";
+
+    const resSpec = new RSRModule.residue_spec_t(chainId,resno,"");
+
+    /*
+    var result = RSRModule.flipPeptide(pdbin,resSpec,pdbout);
+    var pdb_out = RSRModule.FS.readFile(pdbout, { encoding: 'utf8' });
+    */
+
+    console.log("Should in fact call molecules_container.flipPeptide_rs with", dataObjectsNames.mol_cont_idx[e.data.pdbinKey]);
+    const resultMolCont = molecules_container.flipPeptide_rs(dataObjectsNames.mol_cont_idx[e.data.pdbinKey],resSpec,"");
+    const write_result = molecules_container.writePDBASCII(dataObjectsNames.mol_cont_idx[e.data.pdbinKey],pdbout);
+    console.log("result of which is",resultMolCont,write_result);
+    var pdb_out = RSRModule.FS.readFile(pdbout, { encoding: 'utf8' });
+
+    //postMessage(["result",result,currentTaskName]);
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "result",
+        result: resultMolCont,
+        taskName: currentTaskName
+    })
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "pdb_out",
+        jobId: jobId,
+        result: pdb_out,
+        taskName: currentTaskName
+    })
+}
+
+function miniRSR(e) {
+
+    console.log(e.data);
+
+    const jobId = e.data.jobId;
+
+    var args = new RSRModule.VectorString();
+    args.push_back("mini_rsr");
+
+    //mini_rsr --pdbin /Users/stuart/CCP4MG_DOWNLOAD/5a3h.pdb --hklin /Users/stuart/CCP4MG_DOWNLOAD/5a3h_final.mtz --pdbout mini_rsr_out.pdb --resno-start 27 --resno-end 37 --chain-id A --debug
+
+    args.push_back("--pdbin");
+    args.push_back(dataObjects.pdbFiles[e.data.pdbinKey].fileName);
+
+    args.push_back("--hklin");
+    args.push_back(dataObjects.mtzFiles[e.data.hklinKey].fileName);
+
+    args.push_back("--pdbout");
+    args.push_back(jobId+"out.pdb");
+
+    args.push_back("--resno-start");
+    args.push_back((e.data["resnoStart"]).toString());
+    args.push_back("--resno-end");
+    args.push_back((e.data["resnoEnd"]).toString());
+    args.push_back("--chain-id");
+    args.push_back(e.data["chainId"]);
+
+    args.push_back("--debug");
+
+    console.log("Calling");
+
+    var result = RSRModule.mini_rsr(args);
+    var pdb_out = RSRModule.FS.readFile(jobId+"out.pdb", { encoding: 'utf8' });
+    //TODO We need to store pdb_out! (and cache with updateShareArrayBuffer)
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "result",
+        result: result,
+        taskName: currentTaskName
+    })
+    postMessage({
+        messageId: e.data.messageId,
+        messageTag: "pdb_out",
+        jobId: jobId,
+        result: pdb_out,
+        taskName: currentTaskName
+    })}
+
+
+onmessage = function(e) {
+
+    switch(e.data.method){
+        case "loadFile":
+            console.log("Load file(s)",e.data.files);
+            loadFiles(e.data.files);
+            break;
+        case "loadUrl":
+            console.log("Download file(s)",e.data.urls);
+            downLoadFiles(e.data.urls);
+            break;
+        case "get_rama":
+            currentTaskName = "get_rama";
+            getRama(e);
+            currentTaskName = "";
+            break;
+        case "flip_peptide":
+            console.log("Do peptide-flip in cryst worker ...");
+            currentTaskName = "flip_peptide";
+            flipPeptide(e);
+            currentTaskName = "";
+            break;
+        case "mini_rsr":
+            console.log("Do mini-rsr in cryst worker ...");
+            currentTaskName = "mini_rsr";
+            miniRSR(e);
+            currentTaskName = "";
+            break;
+        case "auto_fit_rotamer":
+            console.log("Do auto-fit rotamer in cryst worker ...");
+            currentTaskName = "mini_rsr";
+            autoFitRotamer(e);
+            currentTaskName = "";
+            break;
+        case "get_bvals":
+            currentTaskName = "get_bvals";
+            getBVals(e);
+            currentTaskName = "";
+            break;
+        case "density_fit":
+            currentTaskName = "density_fit";
+            getDensityFit(e);
+            currentTaskName = "";
+            break;
+        case "get_xyz":
+            currentTaskName = "get_xyz";
+            const pdbRegex = /.pdb$/;
+            const pdbKeys = Object.keys(dataObjectsNames.pdbFiles);
+            let theData_id;
+            if(e.data.resInfo.molKey){
+                theData_id = e.data.resInfo.molKey
+            } else {
+                for(let iobj=0;iobj<pdbKeys.length;iobj++){
+                    const data_id = pdbKeys[iobj];
+                    const name = dataObjectsNames.pdbFiles[data_id].originalFileName;
+                    const shortName = name.replace(pdbRegex,"");
+                    if(shortName===e.data.resInfo.molName){
+                        console.log("Use",data_id,dataObjects.pdbFiles[data_id]);
+                        theData_id = data_id;
+                        break;
+                    }
+                }
+            }
+            if(theData_id){
+                let result;
+                if(e.data.resInfo.seqNum){
+                    //FIXME - this is almost certainly dodgy. Ignoring insCode is probably a bad idea.
+                    result = CCP4Module.getXYZSeqNumInsCode(dataObjects.pdbFiles[theData_id].fileName,e.data.resInfo.chain,e.data.resInfo.seqNum,"");
+                } else {
+                    result = CCP4Module.getXYZResNo(dataObjects.pdbFiles[theData_id].fileName,e.data.resInfo.chain,e.data.resInfo.resNo);
+                }
+                if(result.size()===3){
+                    postMessage({
+                        messageId: e.data.messageId,
+                        messageTag: "result",
+                        result: [-result.get(0),-result.get(1),-result.get(2)],
+                        taskName: currentTaskName
+                    })
+                }
+            }
+            currentTaskName = "";
+            break;
+        case "get_rotamers":
+            currentTaskName = "rotamers";
+            getRotamers(e);
+            currentTaskName = "";
+            break;
+        case "draw_cube":
+            currentTaskName = "draw_cube";
+            drawCube(e);
+            currentTaskName = "";
+            break;
+        case "rotamer_dodecs":
+            currentTaskName = "rotamer_dodecs";
+            drawDodos(e);
+            currentTaskName = "";
+            break;
+        case "rama_balls":
+            currentTaskName = "rama_balls";
+            drawRamaBalls(e);
+            currentTaskName = "";
+            break;
+        default:
+            console.log("default, do nothing",e.data.method);
+    }
+
+}

package/baby-gru/wasm/mini_rsr_worker.js

@@ -0,0 +1,72 @@
+var CCP4Module;
+
+importScripts('./mini-rsr-web.js');
+
+const Lib = {
+    locateFile: (file) => file,
+    onRuntimeInitialized: () => {
+        console.log('onRuntimeInitialized');
+    },
+    mainScriptUrlOrBlob: "./mini-rsr-web.js",
+    print(t){postMessage(["output",t])},
+    printErr(t){postMessage(["output",t])},
+};
+
+createRSRModule(Lib)
+    .then(function(CCP4Mod) {
+             CCP4Module = CCP4Mod;
+            })
+.catch((e) => {
+        console.log("CCP4 problem :(");
+        console.log(e);
+        });
+
+onmessage = function(e) {
+
+    console.log(e.data);
+
+    const jobId = e.data.jobId;
+
+    var args = new CCP4Module.VectorString();
+    args.push_back("mini_rsr");
+
+    //mini_rsr --pdbin /Users/stuart/CCP4MG_DOWNLOAD/5a3h.pdb --hklin /Users/stuart/CCP4MG_DOWNLOAD/5a3h_final.mtz --pdbout mini_rsr_out.pdb --resno-start 27 --resno-end 37 --chain-id A --debug
+
+    //try {
+        CCP4Module.FS_createDataFile(".", jobId+e.data["pdbinName"], e.data["pdbinData"], true, true);
+    //} catch(e) {
+        //This happens when we supply same file name on subsequent calls to this function?
+    //}
+    args.push_back("--pdbin");
+    args.push_back(jobId+e.data["pdbinName"]);
+
+    //try {
+        CCP4Module.FS_createDataFile(".", jobId+e.data["hklinName"], e.data["hklinData"], true, true);
+    //} catch(e) {
+        //This happens when we supply same file name on subsequent calls to this function?
+    //}
+    args.push_back("--hklin");
+    args.push_back(jobId+e.data["hklinName"]);
+
+    args.push_back("--pdbout");
+    args.push_back(jobId+"out.pdb");
+
+    args.push_back("--resno-start");
+    args.push_back((e.data["resnoStart"]).toString());
+    args.push_back("--resno-end");
+    args.push_back((e.data["resnoEnd"]).toString());
+    args.push_back("--chain-id");
+    args.push_back(e.data["chainId"]);
+
+    args.push_back("--debug");
+
+    console.log(args);
+    var result = CCP4Module.mini_rsr(args);
+    var pdb_out = CCP4Module.FS.readFile(jobId+"out.pdb", { encoding: 'utf8' });
+    CCP4Module.FS_unlink(jobId+e.data["pdbinName"])
+    CCP4Module.FS_unlink(jobId+e.data["hklinName"])
+    CCP4Module.FS_unlink(jobId+"out.pdb")
+
+    postMessage(["result",result]);
+    postMessage(["pdb_out",pdb_out,jobId]);
+}