icn3d 3.40.3 → 3.40.5

package/icn3d.js

@@ -10822,12 +10822,17 @@ class ClickMenu {
            //    var aaa = 1; //alert("The url is more than 4000 characters and may not work.");
            //}
            //else {
-               url = url.replace("icn3d/full.html?", "icn3d/full2.html?");
+               // url = url.replace("icn3d/full.html?", "icn3d/full2.html?");
+
+               url = url.replace(/icn3d\/full[_\d\.]*\.html\?/, "icn3d/full2.html?");
+
                url = url.replace("icn3d/?", "icn3d/full2.html?");
+
                url += '&closepopup=1';
                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
                window.open(url, urlTarget);
-               thisClass.setLogCmd('side by side | ' + url, true);
+               // thisClass.setLogCmd('side by side | ' + url, true);
+               thisClass.setLogCmd('side by side | ' + url, false);
            //}
         });
 
@@ -33249,7 +33254,6 @@ ElectronMap.prototype.fillvoxels = function(atoms, atomlist) { //(int seqinit,in
                     //this.vpAtomID[index] =(this.dataArray[index] >= 0) ? 1 : 0; // determine whether it's positive
                 }
             }
-            
         }
     }
 
@@ -59641,12 +59645,15 @@ class DensityCifParser {
        let thisClass = this;
 
        let url;
-       let detail = (me.utilsCls.isMobile() || me.cfg.notebook) ? 0 : 4; //4;
+       let detail = (me.utilsCls.isMobile() || me.cfg.notebook) ? 2 : 4; //0 : 4;
 
        //https://www.ebi.ac.uk/pdbe/densities/doc.html
        if(type == '2fofc' || type == 'fofc') {
-           detail = 0;
-           url = "https://www.ebi.ac.uk/pdbe/densities/x-ray/" + pdbid.toLowerCase() + "/cell?detail=" + detail;
+            //detail = 0;
+
+            //    url = "https://www.ebi.ac.uk/pdbe/densities/x-ray/" + pdbid.toLowerCase() + "/cell?detail=" + detail;
+            let min_max = ic.contactCls.getExtent(ic.atoms); 
+            url = "https://www.ebi.ac.uk/pdbe/volume-server/x-ray/" + pdbid.toLowerCase() + "/box/" + min_max[0][0] + "," + min_max[0][1] + "," + min_max[0][2] + "/" + min_max[1][0] + "," + min_max[1][1] + "," + min_max[1][2] + "?detail=" + detail;
        }
        else if(type == 'em') {
            url = "https://www.ebi.ac.uk/pdbe/densities/emd/" + emd.toLowerCase() + "/cell?detail=" + detail;
@@ -59719,6 +59726,33 @@ class DensityCifParser {
         // return sigma;
     }
 
+    setMatrix(density) { let ic = this.icn3d; ic.icn3dui;
+        let sampleCount = density.box.sampleCount;
+        let header = {xExtent: sampleCount[0], yExtent: sampleCount[1], zExtent: sampleCount[2], mean: density.valuesInfo.mean, sigma: density.valuesInfo.sigma, max: density.valuesInfo.max, min: density.valuesInfo.min};
+        for(let i = 0; i < density.data.length; ++i) {
+            density.data[i];
+        }
+
+        let origin = density.box.origin;
+        let dimensions = density.box.dimensions;
+        let basis = density.spacegroup.basis;
+        let scale = new THREE.Matrix4().makeScale(
+            dimensions[0] / (sampleCount[0] ),
+            dimensions[1] / (sampleCount[1] ),
+            dimensions[2] / (sampleCount[2] ));
+        let translate = new THREE.Matrix4().makeTranslation(origin[0], origin[1], origin[2]);
+        let fromFrac = new THREE.Matrix4().set(
+            basis.x[0], basis.y[0], basis.z[0], 0.0,
+            0.0, basis.y[1], basis.z[1], 0.0,
+            0.0, 0.0, basis.z[2], 0.0,
+            0.0, 0.0, 0.0, 1.0);
+
+        //var toFrac = new LiteMol.Visualization.THREE.Matrix4().getInverse(fromFrac);
+        let matrix = fromFrac.multiply(translate).multiply(scale);
+
+        return {matrix: matrix, header: header};
+    }
+
     parseChannels(densitydata, type, sigma) { let ic = this.icn3d; ic.icn3dui;
         let cif = this.BinaryParse(densitydata);
 
@@ -59728,92 +59762,35 @@ class DensityCifParser {
 
             // '2fofc'
             let density = twoDensity;
-            let sampleCount = density.box.sampleCount;
-            let header = {xExtent: sampleCount[0], yExtent: sampleCount[1], zExtent: sampleCount[2], mean: density.valuesInfo.mean, sigma: density.valuesInfo.sigma};
-            ic.mapData.header2 = header;
-
-            ic.mapData.data2 = density.data;
-            for(let i = 0; i < density.data.length; ++i) {
-                density.data[i];
-            }
-
-            let origin = density.box.origin;
-            let dimensions = density.box.dimensions;
-            let basis = density.spacegroup.basis;
-            let scale = new THREE.Matrix4().makeScale(
-                dimensions[0] / (sampleCount[0] ),
-                dimensions[1] / (sampleCount[1] ),
-                dimensions[2] / (sampleCount[2] ));
-            let translate = new THREE.Matrix4().makeTranslation(origin[0], origin[1], origin[2]);
-            let fromFrac = new THREE.Matrix4().set(
-                basis.x[0], basis.y[0], basis.z[0], 0.0,
-                0.0, basis.y[1], basis.z[1], 0.0,
-                0.0, 0.0, basis.z[2], 0.0,
-                0.0, 0.0, 0.0, 1.0);
-
-            //var toFrac = new LiteMol.Visualization.THREE.Matrix4().getInverse(fromFrac);
-            let matrix = fromFrac.multiply(translate).multiply(scale);
+            let result = this.setMatrix(density);
 
-            ic.mapData.matrix2 = matrix;
+            ic.mapData.matrix2 = result.matrix;
+            ic.mapData.header2 = result.header;
 
+            ic.mapData.data2 = density.data;
             ic.mapData.type2 = type;
             ic.mapData.sigma2 = sigma;
 
             // 'fofc'
             density = oneDensity;
-            sampleCount = density.box.sampleCount;
-            header = {xExtent: sampleCount[0], yExtent: sampleCount[1], zExtent: sampleCount[2], mean: density.valuesInfo.mean, sigma: density.valuesInfo.sigma};
-            ic.mapData.header = header;
+            result = this.setMatrix(density);
 
-            ic.mapData.data = density.data;
-
-            origin = density.box.origin;
-            dimensions = density.box.dimensions;
-            basis = density.spacegroup.basis;
-
-            scale = new THREE.Matrix4().makeScale(
-                dimensions[0] / (sampleCount[0] ),
-                dimensions[1] / (sampleCount[1] ),
-                dimensions[2] / (sampleCount[2] ));
-            translate = new THREE.Matrix4().makeTranslation(origin[0], origin[1], origin[2]);
-            fromFrac = new THREE.Matrix4().set(
-                basis.x[0], basis.y[0], basis.z[0], 0.0,
-                0.0, basis.y[1], basis.z[1], 0.0,
-                0.0, 0.0, basis.z[2], 0.0,
-                0.0, 0.0, 0.0, 1.0);
-            //var toFrac = new LiteMol.Visualization.THREE.Matrix4().getInverse(fromFrac);
-            matrix = fromFrac.multiply(translate).multiply(scale);
-            ic.mapData.matrix = matrix;
+            ic.mapData.matrix = result.matrix;
+            ic.mapData.header = result.header;
 
+            ic.mapData.data = density.data;
             ic.mapData.type = type;
             ic.mapData.sigma = sigma;
         }
         else if(type == 'em') {
             let density = this.getChannel(cif, 'EM');
 
-            let sampleCount = density.box.sampleCount;
-            let header = {xExtent: sampleCount[0], yExtent: sampleCount[1], zExtent: sampleCount[2], max: density.valuesInfo.max, min: density.valuesInfo.min};
-            ic.mapData.headerEm = header;
-
-            ic.mapData.dataEm = density.data;
+            let result = this.setMatrix(density);
 
-            let origin = density.box.origin;
-            let dimensions = density.box.dimensions;
-            let basis = density.spacegroup.basis;
-            let scale = new THREE.Matrix4().makeScale(
-                dimensions[0] / (sampleCount[0] ),
-                dimensions[1] / (sampleCount[1] ),
-                dimensions[2] / (sampleCount[2] ));
-            let translate = new THREE.Matrix4().makeTranslation(origin[0], origin[1], origin[2]);
-            let fromFrac = new THREE.Matrix4().set(
-                basis.x[0], basis.y[0], basis.z[0], 0.0,
-                0.0, basis.y[1], basis.z[1], 0.0,
-                0.0, 0.0, basis.z[2], 0.0,
-                0.0, 0.0, 0.0, 1.0);
-            //var toFrac = new LiteMol.Visualization.THREE.Matrix4().getInverse(fromFrac);
-            let matrix = fromFrac.multiply(translate).multiply(scale);
-            ic.mapData.matrixEm = matrix;
+            ic.mapData.matrixEm = result.matrix;
+            ic.mapData.headerEm = result.header;
 
+            ic.mapData.dataEm = density.data;
             ic.mapData.typeEm = type;
             ic.mapData.sigmaEm = sigma;
         }
@@ -72563,7 +72540,7 @@ class Dssp {
         // assign Ig types
         ic.ref2igtype = {};
 
-        ic.ref2igtype['ASF1A_2iijA_human'] = 'IgE';
+        ic.ref2igtype['ASF1A_2iijA_human'] = 'IgFN3-like';
         ic.ref2igtype['B2Microglobulin_7phrL_human_C1'] = 'IgC1';
         ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
         ic.ref2igtype['BTLA_2aw2A_human_Iset'] = 'IgI';
@@ -72598,7 +72575,7 @@ class Dssp {
         ic.ref2igtype['LAG3_7tzgD_human_V-n1'] = 'IgV';
         ic.ref2igtype['LaminAC_1ifrA_human'] = 'Lamin';
         ic.ref2igtype['MHCIa_7phrH_human_C1'] = 'IgC1';
-        ic.ref2igtype['MPT63_1lmiA_bacteria'] = 'IgE';
+        ic.ref2igtype['MPT63_1lmiA_bacteria'] = 'IgFN3-like';
         ic.ref2igtype['NaCaExchanger_2fwuA_dog_n2'] = 'IgFN3-like';
         ic.ref2igtype['NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = 'IgE';
         ic.ref2igtype['ORF7a_1xakA_virus'] = 'ORF';
@@ -72611,7 +72588,7 @@ class Dssp {
         ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC1';
         ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
         ic.ref2igtype['TCRa_6jxrm_human_V-n1'] = 'IgV';
-        ic.ref2igtype['TEAD1_3kysC_human'] = 'IgE';
+        ic.ref2igtype['TEAD1_3kysC_human'] = 'IgFN3-like';
         ic.ref2igtype['TP34_2o6cA_bacteria'] = 'IgE';
         ic.ref2igtype['TP47_1o75A_bacteria'] = 'IgE';
         ic.ref2igtype['Titin_4uowM_human_Iset-n152'] = 'IgI';
@@ -79006,6 +78983,8 @@ class SaveFile {
                  for(let i = 0, il = residueArray.length; i < il; ++i) {
                      let resid = residueArray[i];
                      let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                     if(!atom) continue;
+                     
                      let chainid = atom.structure + '_' + atom.chain;
                      let resnAbbr = me.utilsCls.residueName2Abbr(atom.resn);
                      let resName = resnAbbr + atom.resi;
@@ -82986,7 +82965,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.40.3';
+    this.REVISION = '3.40.5';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;