icn3d 3.25.5 → 3.25.7

package/icn3d.js

@@ -41923,9 +41923,9 @@ class ShowSeq {
         let index = 1, bStart = false;
         
         // 1. get the range of each strand excluding loops
-        let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0, resCntBfAnchor = 0;
+        let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0, resCntBfAnchor = 0, resCntAtAnchor = 0;
         if(!bCustom && !kabat_or_imgt) {
-            for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt, ++resCntBfAnchor) {
+            for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt, ++resCntBfAnchor, ++resCntAtAnchor) {
                 let currResi = ic.ParserUtilsCls.getResi(chnid, i);
                 let residueid = chnid + '_' + currResi;
                 refnumLabel = ic.resid2refnum[residueid];
@@ -41976,6 +41976,8 @@ class ShowSeq {
                                 if(lastTwo == 50) {
                                     strandArray[strandCnt].anchorRefnum = refnum;
                                     strandArray[strandCnt].resCntBfAnchor = resCntBfAnchor;
+
+                                    resCntAtAnchor = 0;
                                 }
 
                                 strandArray[strandCnt].strandPostfix = strandPostfix; // a in A1250a
@@ -41990,12 +41992,22 @@ class ShowSeq {
                             }
                             else {
                                 if(strandHash[currStrand + postfix]) {
-                                    strandArray[strandCnt - 1].endResi = currResi;
-                                    strandArray[strandCnt - 1].endRefnum = refnum; // 1250a
-
                                     if(lastTwo == 50) {
                                         strandArray[strandCnt - 1].anchorRefnum = refnum;
                                         strandArray[strandCnt - 1].resCntBfAnchor = resCntBfAnchor;
+
+                                        // update
+                                        strandArray[strandCnt - 1].startRefnum = strandArray[strandCnt - 1].anchorRefnum - strandArray[strandCnt - 1].resCntBfAnchor;
+
+                                        resCntAtAnchor = 0;
+                                    }
+
+                                    strandArray[strandCnt - 1].endResi = currResi;
+                                    strandArray[strandCnt - 1].endRefnum = refnum; // 1250a
+                                    strandArray[strandCnt - 1].resCntAtAnchor = resCntAtAnchor;
+
+                                    if(strandArray[strandCnt - 1].anchorRefnum) {
+                                        strandArray[strandCnt - 1].endRefnum = strandArray[strandCnt - 1].anchorRefnum + strandArray[strandCnt - 1].resCntAtAnchor;
                                     }
 
                                     resCnt = 0;
@@ -42010,16 +42022,20 @@ class ShowSeq {
 
             // 2. remove strands with less than 3 residues
             for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
-                if(strandArray[i].endRefnum - strandArray[i].startRefnum < 3 - 1) { // remove the strand
+                if(strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
+                    if(i != il - 1) { // modify 
+                        strandArray[i + 1].loopResCnt += strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
+                    }
+
                     strandArray.splice(i, 1);
                 }
             }
-
+            
             // 3. assign refnumLabel for each resid
             strandCnt = 0;
             let loopCnt = 0;
 
-            let bNterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
+            let bNterminal = true, bCterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
             bStart = false;
             let refnumInStrand = 0;
             if(strandArray.length > 0) {
@@ -42094,6 +42110,7 @@ class ShowSeq {
                         }
                         else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
                             bNterminal = false;
+                            //bCterminal = true; // The next will be C-terminal
 
                             if(strandArray[strandCnt].anchorRefnum) { // use anchor to name refnum
                                 if(currResi == strandArray[strandCnt].startResi) {
@@ -42120,14 +42137,28 @@ class ShowSeq {
                         else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {     
                             ic.residIgLoop[residueid] = 1;    
 
-                            // C-terminal
-                            if(!ic.resid2refnum[residueid]) {
-                                break;
+                            if(!bCterminal) {
+                                refnumLabelNoPostfix = undefined;
+                                refnumLabel = undefined;
                             }
                             else {
-                                currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
-                                refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
-                                refnumLabel = refnumLabelNoPostfix  + strandArray[strandCnt].strandPostfix; 
+                                // C-terminal
+                                if(!ic.resid2refnum[residueid]) {
+                                    //break;
+
+                                    bCterminal = false;
+                                    //bNterminal = true; // The next will be N-terminal
+
+                                    refnumLabelNoPostfix = undefined;
+                                    refnumLabel = undefined;
+                                }
+                                else {
+                                    bCterminal = true;
+
+                                    currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
+                                    refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
+                                    refnumLabel = refnumLabelNoPostfix  + strandArray[strandCnt].strandPostfix; 
+                                }
                             }
                         }
                     }
@@ -55404,11 +55435,13 @@ class LoadPDB {
         }
     }
 
-    setSsbond() { let ic = this.icn3d; ic.icn3dui;
+    setSsbond(chainidHash) { let ic = this.icn3d; ic.icn3dui;
         // get all Cys residues
         let structure2cys_resid = {};
 
         for(let chainid in ic.chainsSeq) {
+            if(chainidHash && !chainidHash.hasOwnProperty(chainid)) continue;
+
             let seq = ic.chainsSeq[chainid];
             let structure = chainid.substr(0, chainid.indexOf('_'));