moorhen 0.0.1

package/baby-gru/wasm/smiles_to_pdb_worker.js

@@ -0,0 +1,252 @@
+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 name = e.data[1];
+
+    let promises = [contents];
+    let names = [name];
+
+    console.log(promises);
+
+    let svgResult = {};
+
+    if(promises.length>0){
+        Promise.all(promises).then((values) => {
+            console.log("Do RDKit stuff");
+            let mol2 = RDKit.get_mol(values[0]);
+            let mol3 = RDKit.get_mol(mol2.add_hs());
+            console.log("Done get_mol");
+            svgResult[names[0]] = mol3.get_svg();
+            console.log("Done get_svg");
+            postMessage(["result",svgResult]);
+            console.log("Done postMessage");
+        }).catch((error) => {
+             console.error(error);
+             postMessage(["result",svgResult]);
+        });
+    }
+
+
+}

package/baby-gru/wasm/superpose_worker.js

@@ -0,0 +1,144 @@
+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();
+    //Do not add program name for superpose, only gesamt. I probably should have had the programs behave the same.
+    args.push_back("gesamt");
+    var sels = new CCP4Module.VectorString();
+
+    for(let ifile=0;ifile<e.data[0].length;ifile++){
+        try {
+            CCP4Module.FS_createDataFile(".", e.data[1][ifile], e.data[0][ifile], true, true);
+        } catch(e) {
+            //This happens when we supply sme file name on subsequent calls to this function?:w
+        }
+        args.push_back(e.data[1][ifile]);
+        sels.push_back("dummy"); // TODO: Selections are not dealt with yet
+    }
+
+    //var result = CCP4Module.superpose(args,sels);
+    //Do not do this with superpose!
+    args.push_back("-csv");
+    args.push_back("out.csv");
+    var result = CCP4Module.gesamt(args);
+    var csv_out = CCP4Module.FS.readFile("out.csv", { encoding: 'utf8' });
+    var json_out = Papa.parse(csv_out);
+    
+    /*
+    //Testing, belongs elsewhere
+    var bessel = CCP4Module.gsl_sf_bessel_J0(5.0);
+    var hg = CCP4Module.gsl_cdf_hypergeometric_P(4, 7, 19, 13);
+    console.log(bessel);
+    console.log(hg);
+    */
+
+    let csv_data = json_out["data"];
+    if(e.data[0].length==2){ // TODO: I haven't thought about parsing multi-align csv yet.
+        let inTransformation = false;
+        let inAlign = false;
+        let alignData = [];
+        let transformMatrix = [];
+        let iTransform = -1;
+        for(let ij=0;ij<csv_data.length;ij++){
+            if(inTransformation&&ij<iTransform+4){
+                transformMatrix.push(parseFloat(csv_data[ij][0]));
+                transformMatrix.push(parseFloat(csv_data[ij][1]));
+                transformMatrix.push(parseFloat(csv_data[ij][2]));
+                transformMatrix.push(parseFloat(csv_data[ij][3]));
+            }
+            if(inAlign){
+                if(csv_data[ij][0].length>0){
+                    let y = parseFloat(csv_data[ij][0]);
+                    let x = parseFloat(csv_data[ij][4].trim().split(" ")[csv_data[ij][4].trim().split(" ").length-1]);
+                    alignData.push({x:x,y:y});
+                }
+                if(csv_data[ij].length<5){
+                    break;
+                }
+            }
+            if(csv_data[ij].length==4 && csv_data[ij][0].trim()==="Rx" && csv_data[ij][1].trim()==="Ry" && csv_data[ij][2].trim()==="Rz"&& csv_data[ij][3].trim()==="T"){
+                inTransformation = true;
+                iTransform = ij;
+            }
+            if(csv_data[ij].length>4 && csv_data[ij][0].trim()==="Dist [A]" && csv_data[ij][3].trim()==="Query" && csv_data[ij][4].trim()==="Target"){
+                inAlign = true;
+            }
+        }
+        if(transformMatrix.length==12){
+            transformMatrix.push(0.0);
+            transformMatrix.push(0.0);
+            transformMatrix.push(0.0);
+            transformMatrix.push(1.0);
+        }
+        let cvsResult = {};
+        cvsResult["alignData"] = alignData;
+        cvsResult["transformMatrices"] = [transformMatrix];
+        if(e.data.length>2){
+            cvsResult["jobid"] = e.data[2];
+        }
+        postMessage(["csvResult",cvsResult]);
+    } else {
+        let inTransformation = false;
+        let inAlign = false;
+        let alignData = [];
+        let transformMatrix = [];
+        let transformMatrices = [];
+        let iTransform = -1;
+        for(let ij=0;ij<csv_data.length;ij++){
+            if(inTransformation&&ij<iTransform+4){
+                transformMatrix.push(parseFloat(csv_data[ij][0]));
+                transformMatrix.push(parseFloat(csv_data[ij][1]));
+                transformMatrix.push(parseFloat(csv_data[ij][2]));
+                transformMatrix.push(parseFloat(csv_data[ij][3]));
+            }
+            if(transformMatrix.length==12){
+                transformMatrix.push(0.0);
+                transformMatrix.push(0.0);
+                transformMatrix.push(0.0);
+                transformMatrix.push(1.0);
+                transformMatrices.push(transformMatrix);
+                transformMatrix = [];
+                inTransformation = false;
+            }
+            if(csv_data[ij].length==4 && csv_data[ij][0].trim()==="Rx" && csv_data[ij][1].trim()==="Ry" && csv_data[ij][2].trim()==="Rz"&& csv_data[ij][3].trim()==="T"){
+                inTransformation = true;
+                iTransform = ij;
+            }
+            if(inAlign){
+                if(csv_data[ij][0].length>0){
+                    let y = parseFloat(csv_data[ij][0]);
+                    let x = parseFloat(csv_data[ij][1].trim().split(" ")[csv_data[ij][1].trim().split(" ").length-1]);
+                    alignData.push({x:x,y:y});
+                }
+                if(csv_data[ij].length<e.data[0].length+1){
+                    break;
+                }
+            }
+            if(csv_data[ij][0].trim()==="Disp.[A]"&&ij>2&&csv_data[ij-2][0].trim()==="RESIDUE ALIGNMENT"){
+                inAlign = true;
+            }
+        }
+        let cvsResult = {};
+        cvsResult["transformMatrices"] = transformMatrices;
+        cvsResult["alignData"] = alignData;
+        if(e.data.length>2){
+            cvsResult["jobid"] = e.data[2];
+        }
+        postMessage(["csvResult",cvsResult]);
+    }
+
+    postMessage(["result",result]);
+}