icn3d 3.25.15 → 3.25.16

package/icn3d.js

@@ -35855,6 +35855,7 @@ class AnnoCddSite {
 
         for(let i = 0, il = dataArray.length; i < il; ++i) {
             //let data = (bSeq) ? dataArray[i][0] : dataArray[i];
+            // somehow Node.js returned data in dataArray[i]
             let data = (me.bNode) ? dataArray[i] : dataArray[i].value;
 
             if(!data) continue;
@@ -46832,8 +46833,10 @@ class AlignParser {
             let dataArray = await allPromise;
 
             let data2 = data;
-            let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
-            let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
+            // let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
+            // let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
+            let data3 = dataArray[0].value; //v3[0];
+            let data4 = dataArray[1].value; //v4[0];
 
             if(data3.atoms !== undefined && data4.atoms !== undefined) {
                 // ic.deferredOpm = $.Deferred(function() {
@@ -46995,7 +46998,8 @@ class AlignParser {
             
             let bFound = false;
             for(let i = 0, il = dataArray.length; i < il; ++i) {
-                let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
+                //let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
+                let opmdata = dataArray[i].value;
 
                 if(!opmdata) continue;
 
@@ -47155,7 +47159,8 @@ class ChainalignParser {
 
         // modify the previous trans and rotation matrix
         for(let i = 0, il = dataArray.length; i < il; ++i) {
-            let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
+            // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
+            let align = dataArray[i].value;//[0];
 
             let mmdbid_q = struArray[i];
             let index = indexArray[i];
@@ -47247,7 +47252,8 @@ class ChainalignParser {
              
         let bFoundAlignment = false;
         for(let i = 0, il = dataArray.length; i < il; ++i) {
-            let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
+            // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
+            let align = dataArray[i].value;//[0];
 
             let bEqualMmdbid = false;
             let bEqualChain = false;
@@ -47639,7 +47645,8 @@ class ChainalignParser {
         // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
         //var data2 = v2[0];
         // index = 0: the mmdb data of target
-        let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
+        // let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
+        let targetData = dataArray[0].value; //[0];
         let header = 'HEADER                                                        ' + mmdbid_t + '\n';
         if(isNaN(mmdbid_t) && mmdbid_t.length > 5) targetData = header + targetData;
 
@@ -47657,7 +47664,8 @@ class ChainalignParser {
         let queryDataArray = [];
 
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
-            let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
+            // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
+            let queryData = dataArray[index].value;//[0];
 
             let pos = chainidArray[index].indexOf('_');
             let mmdbid_q = chainidArray[index].substr(0, pos).toUpperCase();
@@ -47703,7 +47711,8 @@ class ChainalignParser {
                     ic.qt_start_end[index-1] = undefined;
                 }
                 else {
-                    let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
+                    // let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
+                    let align = dataArray[index2 - missedChainCnt].value;//[0];
 
                     let bEqualMmdbid = (mmdbid_q == mmdbid_t);
                     let bEqualChain = (chain_q == chain_t);
@@ -47921,7 +47930,8 @@ class ChainalignParser {
 
         let queryDataArray = [];
         for(let index = 0, indexl = structArray.length; index < indexl; ++index) {
-            let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
+            // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
+            let queryData = dataArray[index].value;//[0];
             let header = 'HEADER                                                        ' + structArray[index] + '\n';
             if(isNaN(structArray[index]) && structArray[index].length > 5) queryData = header + queryData;
 
@@ -50373,7 +50383,8 @@ class RealignParser {
       //var data2 = v2[0];
       for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
     //  for(let index = 1, indexl = dataArray.length; index < indexl; ++index) {
-          let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
+        //   let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
+          let data = dataArray[index].value;//[0];
           if(!data) continue;
 
           let fromStruct = chainidArray[index + 1].substr(0, chainidArray[index + 1].indexOf('_')); //.toUpperCase();
@@ -62187,14 +62198,15 @@ class Dssp {
         }
     }
 
-    async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
+    async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d; ic.icn3dui;
         //var dataArray =(struArray.length == 1) ? [data] : data;
 
         // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
         //var data2 = v2[0];
         for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
             //let ssHash = dataArray[index][0];
-            let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
+            //let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
+            let ssHash = dataArray[index].value;
 
             if(ssHash !== undefined && JSON.stringify(ssHash).indexOf('Oops there was a problem') === -1) {
               for(let chainNum in ic.chainsSeq) {
@@ -62476,16 +62488,17 @@ class Dssp {
             pdbAjaxArray.push(pdbAjax);
         }
 
-        // try {
+        try {
             let allPromise = Promise.allSettled(pdbAjaxArray);
             ic.pdbDataArray = await allPromise;
             await thisClass.parseRefPdbData(ic.pdbDataArray);
-        // }
-        // catch(err) {
-        //     if(!me.bNode) var aaa = 1; //alert("Error in retrieveing reference PDB data...");
-        //     //var aaa = 1; //alert("Error in retrieveing reference PDB data...");
-        //     return;
-        // }             
+        }
+        catch(err) {
+            if(!me.bNode) var aaa = 1; //alert("Error in retrieveing reference PDB data...");
+            //var aaa = 1; //alert("Error in retrieveing reference PDB data...");
+            return;
+        }       
+
         // }
         // }
     }
@@ -62562,12 +62575,13 @@ class Dssp {
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
                     let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
                     // ig strand for any subset will have the same k, use the number of residue to separate them
-                    let domainid = chainid + '-' + k + '_' + domainAtomsArray[k].length; 
+                    let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length; 
                     ic.domainid2pdb[domainid] = pdb_target;
 
                     for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
                         let struct2 = ic.defaultPdbId + index;
-                        let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
+                        //let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
+                        let pdb_query = dataArray[index].value; //[0];
                         let header = 'HEADER                                                        ' + struct2 + '\n';
                         pdb_query = header + pdb_query;
 
@@ -62581,7 +62595,7 @@ class Dssp {
             }
         }
 
-        // try {
+        try {
             let dataArray2 = [];
             let allPromise = Promise.allSettled(ajaxArray);
             dataArray2 = await allPromise;
@@ -62590,12 +62604,12 @@ class Dssp {
             await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
 
             /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
-        // }
-        // catch(err) {
-        //     if(!me.bNode) console.log("Error in aligning with TM-align...");
-        //     //console.log("Error in aligning with TM-align...");
-        //     return;
-        // }                       
+        }
+        catch(err) {
+            if(!me.bNode) console.log("Error in aligning with TM-align...");
+            //console.log("Error in aligning with TM-align...");
+            return;
+        }                       
     }
 
     async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
@@ -62619,7 +62633,8 @@ class Dssp {
         let minResidues = 20;
 
         for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
-            let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
+            //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
+            let queryData = dataArray[i].value; //[0];
 
             if(!queryData) {
                 if(!me.bNode) console.log("The alignment data for " + domainidpairArray[i] + " is unavailable...");
@@ -62711,7 +62726,8 @@ class Dssp {
                 let pdb_target = ic.domainid2pdb[domainid];
                 for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
                     let struct2 = ic.defaultPdbId + index;
-                    let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
+                    //let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
+                    let pdb_query = ic.pdbDataArray[index].value; //[0];
                     let header = 'HEADER                                                        ' + struct2 + '\n';
                     pdb_query = header + pdb_query;