icn3d 3.25.4 → 3.25.6

package/icn3d.js

@@ -42010,7 +42010,11 @@ 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);
                 }
             }
@@ -42098,6 +42102,10 @@ class ShowSeq {
                             if(strandArray[strandCnt].anchorRefnum) { // use anchor to name refnum
                                 if(currResi == strandArray[strandCnt].startResi) {
                                     refnumInStrand = strandArray[strandCnt].anchorRefnum - strandArray[strandCnt].resCntBfAnchor;
+                                    strandArray[strandCnt].startRefnum = refnumInStrand;
+                                }
+                                else if(currResi == strandArray[strandCnt].endResi) {
+                                    strandArray[strandCnt].endRefnum = refnumInStrand;
                                 }
 
                                 refnumLabelNoPostfix = strandArray[strandCnt].strand + refnumInStrand;
@@ -55400,11 +55408,13 @@ 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('_'));
 
@@ -62310,7 +62320,7 @@ if(!me.bNode) {
                     prevStrand = (refnumLabel) ? refnumLabel.replace(new RegExp(refnum,'g'), '') : undefined;
 
                     ic.resid2refnum[resid] = refnumLabel;
-
+console.log(resid + " " + refnumLabel);
                     // final reference numbers will be assign in ic.showSeqCls.showRefNum()
 
                     // if(!ic.refnum2residArray.hasOwnProperty(refnum)) {