icn3d 3.51.3 → 3.51.4

package/icn3d.js

@@ -101152,20 +101152,12 @@ class GetGraph {
        let thickness = me.htmlCls.coilValue;
        let prevChain = '', prevResName = '', prevResi = 0;
        // add chemicals as well
-       let residHash = {};
-       for(let i in atomSet) {
-           let atom = ic.atoms[i];
+       let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(atomSet);
+       for(let resid in residHash) {
+           let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
 
-           if(atom.chain != 'DUM' && (bAnyAtom || atom.het || (atom.name == "CA" && atom.elem == "C") || atom.name == "O3'" || atom.name == "O3*" || atom.name == "P")) {
-           // starting nucleotide have "P"
-           //if(atom.chain != 'DUM' &&(atom.name == "CA" || atom.name == "P")) {
-               let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
-               if(residHash.hasOwnProperty(resid)) {
-                   continue;
-               }
-               else {
-                   residHash[resid] = 1;
-               }
+           //if(atom.chain != 'DUM' && (bAnyAtom || atom.het || (atom.name == "CA" && atom.elem == "C") || atom.name == "O3'" || atom.name == "O3*" || atom.name == "P")) {
+           if(atom.chain != 'DUM') {
                let resName = me.utilsCls.residueName2Abbr(atom.resn) + atom.resi;
                if(labelType == 'chain' || labelType == 'structure') resName += '.' + atom.chain;
                if(labelType == 'structure') resName += '.' + atom.structure;
@@ -120659,6 +120651,7 @@ class DefinedSets {
                }
            }
        //}
+
        return residuesHash;
     }
     
@@ -122589,6 +122582,8 @@ class Selection {
     selectMainChains() { let ic = this.icn3d, me = ic.icn3dui;
         let currHAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
 
+        ic.opts.pk = 'atom';
+
         ic.hAtoms = ic.applyDisplayCls.selectMainChainSubset(currHAtoms);
 
         ic.hlUpdateCls.showHighlight();
@@ -122598,6 +122593,8 @@ class Selection {
     selectSideChains() { let ic = this.icn3d, me = ic.icn3dui;
         let currHAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
 
+        ic.opts.pk = 'atom';
+
         ic.hAtoms = this.getSideAtoms(currHAtoms);
         ic.hlUpdateCls.showHighlight();
     }
@@ -122619,6 +122616,8 @@ class Selection {
     selectMainSideChains() { let ic = this.icn3d, me = ic.icn3dui;
         let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.hAtoms);
 
+        ic.opts.pk = 'residue';
+
         ic.hAtoms = {};
         for(let resid in residHash) {
             ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, ic.residues[resid]);
@@ -122795,8 +122794,9 @@ class Selection {
             description = name;
         }
 
-        if(Object.keys(ic.selectedResidues).length > 0) {
-            if(ic.pk == 1) {
+        //if(Object.keys(ic.selectedResidues).length > 0) {
+            // if(ic.pk == 1) {
+            if(ic.opts.pk == 'atom') {
                 let bAtom = true;
                 this.selectResidueList(ic.hAtoms, name, description, undefined, undefined, bAtom);
                 //ic.hlUpdateCls.updateHlAll();
@@ -122823,7 +122823,7 @@ class Selection {
                     me.htmlCls.clickMenuCls.setLogCmd('select ' + ic.resid2specCls.residueids2spec(Object.keys(ic.selectedResidues)), true);
                 }
             }
-        }
+        //}
     }
 
     saveSelInCommand() { let ic = this.icn3d, me = ic.icn3dui;