icn3d 3.35.0 → 3.35.1

package/icn3d.js

@@ -37305,7 +37305,6 @@ class HBond {
     //"threshold" is the maximum distance of hydrogen bonds and has the unit of angstrom.
     calculateChemicalHbonds(startAtoms, targetAtoms, threshold, bSaltbridge, type, bInternal) { let ic = this.icn3d, me = ic.icn3dui;
         if(Object.keys(startAtoms).length === 0 || Object.keys(targetAtoms).length === 0) return;
-
         ic.resid2Residhash = {};
 
         let atomHbond = {};
@@ -37399,6 +37398,7 @@ class HBond {
                 && (atom.name === 'N' || atom.name === 'O') && (atomHbond[j].name === 'O' || atomHbond[j].name === 'N') ) {
 
                 if(atom.name === atomHbond[j].name) continue;
+
                 if(atom.structure == atomHbond[j].structure && atom.chain == atomHbond[j].chain && Math.abs(atom.resi - atomHbond[j].resi) <= 1) continue; // peptide bond
 
                 // protein backbone hydrogen
@@ -50714,11 +50714,12 @@ class ShowInter {
         let firstSetAtoms, complement;
         firstSetAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray2);
         complement = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-        ic.firstAtomObjCls.getFirstAtomObj(firstSetAtoms);
+        // let firstAtom = ic.firstAtomObjCls.getFirstAtomObj(firstSetAtoms);
 
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
             // let selectedAtoms = ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
             let selectedAtoms = ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.hash2Atoms(complement, ic.atoms), me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
+
             let commanddesc;
             if(bSaltbridge) {
                 ic.resid2ResidhashSaltbridge = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
@@ -51156,6 +51157,7 @@ class ViewInterPairs {
            if(!threshold || isNaN(threshold)) threshold = ic.tsHbond;
            if(!bHbondCalc) {
                ic.hAtoms = me.hashUtilsCls.cloneHash(prevHatoms);
+
                ic.showInterCls.showHbonds(threshold, nameArray2, nameArray, bHbondCalc, undefined, type);
            }
            hAtoms = me.hashUtilsCls.unionHash(hAtoms, ic.hAtoms);
@@ -63800,6 +63802,7 @@ class LoadCIF {
         let id = (bcifid) ? bcifid : ic.defaultPdbId;
 
         let structure = id;
+        let CSerial, prevCSerial, OSerial, prevOSerial;
         
         let bFirstAtom = true;
 
@@ -64249,19 +64252,23 @@ class LoadCIF {
                     ssend: false            // optional, used to show the end of secondary structures
                 };
 
-                if(!atomDetails.het && atomDetails.name === 'C') ;
-                if(!atomDetails.het && atomDetails.name === 'O') ;
+                if(!atomDetails.het && atomDetails.name === 'C') {
+                    CSerial = serial;
+                }
+                if(!atomDetails.het && atomDetails.name === 'O') {
+                    OSerial = serial;
+                }
 
                 // from DSSP C++ code
-                // if(!atomDetails.het && atomDetails.name === 'N' && prevCSerial !== undefined && prevOSerial !== undefined) {
-                //     let dist = ic.atoms[prevCSerial].coord.distanceTo(ic.atoms[prevOSerial].coord);
+                if(!atomDetails.het && atomDetails.name === 'N' && prevCSerial !== undefined && prevOSerial !== undefined) {
+                    let dist = ic.atoms[prevCSerial].coord.distanceTo(ic.atoms[prevOSerial].coord);
 
-                //     let x2 = atomDetails.coord.x + (ic.atoms[prevCSerial].coord.x - ic.atoms[prevOSerial].coord.x) / dist;
-                //     let y2 = atomDetails.coord.y + (ic.atoms[prevCSerial].coord.y - ic.atoms[prevOSerial].coord.y) / dist;
-                //     let z2 = atomDetails.coord.z + (ic.atoms[prevCSerial].coord.z - ic.atoms[prevOSerial].coord.z) / dist;
+                    let x2 = atomDetails.coord.x + (ic.atoms[prevCSerial].coord.x - ic.atoms[prevOSerial].coord.x) / dist;
+                    let y2 = atomDetails.coord.y + (ic.atoms[prevCSerial].coord.y - ic.atoms[prevOSerial].coord.y) / dist;
+                    let z2 = atomDetails.coord.z + (ic.atoms[prevCSerial].coord.z - ic.atoms[prevOSerial].coord.z) / dist;
 
-                //     atomDetails.hcoord = new THREE.Vector3(x2, y2, z2);
-                // }
+                    atomDetails.hcoord = new THREE.Vector3(x2, y2, z2);
+                }
 
                 ic.atoms[serial] = atomDetails;
 
@@ -64333,6 +64340,8 @@ class LoadCIF {
 
                     // different chain
                     if(chainNum !== prevChainNum) {
+                        prevCSerial = undefined;
+                        prevOSerial = undefined;
 
                         // a chain could be separated in two sections
                         if(serial !== 1 && prevChainNum !== '') {
@@ -64354,6 +64363,8 @@ class LoadCIF {
                         ic.chainsSeq[chainNum].push(resObject);
                     }
                     else {
+                        prevCSerial = CSerial;
+                        prevOSerial = OSerial;
 
                         let resObject = {};
                         resObject.resi = resi;