icn3d 3.51.0 → 3.51.1

package/icn3d.js

@@ -84127,18 +84127,30 @@ class ApplyClbonds {
             if(clbondArray === undefined) {
                 break;
             }
-            for(let i = 0, il = clbondArray.length; i < il; i = i + 2) {
-                let resid1 = clbondArray[i];
-                let resid2 = clbondArray[i+1];
 
-                let atom1 = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid1]);
-                let atom2 = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid2]);
+            let clusterArray = this.clusterLinkedNodes(clbondArray);
+
+            for(let i = 0, il = clusterArray.length; i < il; ++i) {
+                let rootResid = 0;
+                for(let j = 0, jl = clusterArray[i].length; j < jl; ++j) {
+                    let resid = clusterArray[i][j];
+                    let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
 
-                if((ic.proteins.hasOwnProperty(atom1.serial) || ic.nucleotides.hasOwnProperty(atom1.serial)) && ic.chemicals.hasOwnProperty(atom2.serial)) {
-                    ic.residues[resid1] = me.hashUtilsCls.unionHash(ic.residues[resid1], ic.residues[resid2]);
+                    if(ic.proteins.hasOwnProperty(atom.serial) || ic.nucleotides.hasOwnProperty(atom.serial)) {
+                        rootResid = resid;
+                        break;
+                    }
                 }
-                else if((ic.proteins.hasOwnProperty(atom2.serial) || ic.nucleotides.hasOwnProperty(atom2.serial)) && ic.chemicals.hasOwnProperty(atom1.serial)) {
-                    ic.residues[resid2] = me.hashUtilsCls.unionHash(ic.residues[resid2], ic.residues[resid1]);
+
+                if(rootResid) {
+                    for(let j = 0, jl = clusterArray[i].length; j < jl; ++j) {
+                        let resid = clusterArray[i][j];
+                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+
+                        if(ic.chemicals.hasOwnProperty(atom.serial)) {
+                            ic.residues[rootResid] = me.hashUtilsCls.unionHash(ic.residues[rootResid], ic.residues[resid]);
+                        }
+                    }
                 }
             }
         }
@@ -84146,6 +84158,45 @@ class ApplyClbonds {
       return ic.residuesHashClbonds;
     }
 
+    clusterLinkedNodes(clbondArray) {  let ic = this.icn3d; ic.icn3dui;
+        const parent = new Map();
+
+        // Find the root of a node, with path compression
+        function find(node) {
+            if (!parent.has(node)) parent.set(node, node);
+            if (parent.get(node) !== node) {
+            parent.set(node, find(parent.get(node))); // path compression
+            }
+            return parent.get(node);
+        }
+
+        // Union two nodes into the same cluster
+        function union(a, b) {
+            const rootA = find(a);
+            const rootB = find(b);
+            if (rootA !== rootB) parent.set(rootA, rootB);
+        }
+
+        // Process all pairs
+        // for (const [a, b] of pairs) {
+        //     union(a, b);
+        // }
+        
+        for(let i = 0, il = clbondArray.length; i < il; i = i + 2) {
+            union(clbondArray[i], clbondArray[i+1]);
+        }
+
+        // Group nodes by their root
+        const clusters = new Map();
+        for (const node of parent.keys()) {
+            const root = find(node);
+            if (!clusters.has(root)) clusters.set(root, []);
+            clusters.get(root).push(node);
+        }
+
+        return Array.from(clusters.values());
+    }
+
     applyClbondsOptions_base(type) { let ic = this.icn3d, me = ic.icn3dui;
          // only apply to displayed atoms
          let atomHash = me.hashUtilsCls.cloneHash(ic.chemicals);
@@ -84248,6 +84299,9 @@ class ApplyMissingRes {
             let bStart = false;
             let startResid, currResid, prevResid;
             let bCurrCoord, bPrevCoord = false;
+
+            if(!ic.chainsSeq[chainid]) continue;
+            
             for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
                 currResid = chainid + '_' + ic.chainsSeq[chainid][i].resi;
 
@@ -107248,11 +107302,11 @@ class BcifParser {
 
             let chain1Array = struct_conn.getColumn("ptnr1_auth_asym_id");
             let name1Array = struct_conn.getColumn("ptnr1_label_atom_id");
-            let resi1Array = struct_conn.getColumn("ptnr1_label_seq_id");
+            let resi1Array = struct_conn.getColumn("ptnr1_auth_seq_id");
 
             let chain2Array = struct_conn.getColumn("ptnr2_auth_asym_id");
             let name2Array = struct_conn.getColumn("ptnr2_label_atom_id");
-            let resi2Array = struct_conn.getColumn("ptnr2_label_seq_id");
+            let resi2Array = struct_conn.getColumn("ptnr2_auth_seq_id");
 
             let connSize = struct_conn.rowCount;
             for (let i = 0; i < connSize; ++i) {
@@ -107444,7 +107498,7 @@ class BcifParser {
                 else {
                     // bond between this atom and all other atom in the same residue
                     for(let j in mResi2Atoms[currResi]) { // j is atom.id
-                        if(this.hasCovalentBond(atom, mResi2Atoms[currResi][j], para)) {
+                        if(this.hasCovalentBond2(atom, mResi2Atoms[currResi][j], para)) {
                             if(!mId2Set.hasOwnProperty(atom.id)) mId2Set[atom.id] = {};
                             if(!mId2Set.hasOwnProperty(mResi2Atoms[currResi][j].id)) mId2Set[mResi2Atoms[currResi][j].id] = {};
                             mId2Set[atom.id][mResi2Atoms[currResi][j].id] = 1;
@@ -107457,7 +107511,7 @@ class BcifParser {
 
                 // bond between N and previous C
                 if(name == "N" && prevC.id != "") {
-                    if(this.hasCovalentBond(atom, prevC, para)) {
+                    if(this.hasCovalentBond2(atom, prevC, para)) {
                         if(!mId2Set.hasOwnProperty(atom.id)) mId2Set[atom.id] = {};
                         if(!mId2Set.hasOwnProperty(prevC.id)) mId2Set[prevC.id] = {};
                         mId2Set[atom.id][prevC.id] = 1;
@@ -107798,7 +107852,7 @@ class BcifParser {
         return text;
     }
 
-    hasCovalentBond(atom1, atom2, para) { let ic = this.icn3d; ic.icn3dui;
+    hasCovalentBond2(atom1, atom2, para) { let ic = this.icn3d; ic.icn3dui;
         let r = this.mElem2Radius[atom1.elem] + this.mElem2Radius[atom2.elem];
 
         let dx = (atom1.x - atom2.x);
@@ -116072,6 +116126,10 @@ class LoadPDB {
     setResidMapping() { let ic = this.icn3d; ic.icn3dui;
         // set ic.ncbi2resid and ic.resid2ncbi
         for(let chainid in ic.chainsSeq) {
+            if(!ic.chainsSeq[chainid]) {
+                continue;
+            }
+
             for(let j = 0, jl = ic.chainsSeq[chainid].length; j < jl; ++j) {
                 // NCBI residue number starts from 1 and increases continuously
                 let residNCBI = chainid + '_' + (j+1).toString();
@@ -116421,6 +116479,7 @@ class LoadCIF {
                 chain1Array = resi1Array = resi2Array = [];
             }
 
+            // let vBonds = [];
             if(block.getCategory("_struct_conn")) {
                 ic.bSsbondProvided = true;
 
@@ -116431,11 +116490,13 @@ class LoadCIF {
             
                 let chain1Array = struct_conn.getColumn("ptnr1_auth_asym_id");
                 let name1Array = struct_conn.getColumn("ptnr1_label_atom_id");
-                let resi1Array = struct_conn.getColumn("ptnr1_label_seq_id");
+                let resi1Array = struct_conn.getColumn("ptnr1_auth_seq_id");
+                // let resn1Array = struct_conn.getColumn("ptnr1_auth_comp_id");
             
                 let chain2Array = struct_conn.getColumn("ptnr2_auth_asym_id");
                 let name2Array = struct_conn.getColumn("ptnr2_label_atom_id");
-                let resi2Array = struct_conn.getColumn("ptnr2_label_seq_id");
+                let resi2Array = struct_conn.getColumn("ptnr2_auth_seq_id");
+                // let resn2Array = struct_conn.getColumn("ptnr2_auth_comp_id");
             
                 let connSize = struct_conn.rowCount;
                 for (let i = 0; i < connSize; ++i) {
@@ -116444,21 +116505,24 @@ class LoadCIF {
                     let chain1 = chain1Array.getString(i);
                     name1Array.getString(i);
                     let resi1 = resi1Array.getString(i);
+                    // let resn1 = resn1Array.getString(i);
                     let id1 = structure + '_' + chain1 + "_" + resi1;
+
+                    // let chain1Tmp = (me.parasCls.residueAbbrev.hasOwnProperty(resn1)) ? chain1 : resn1;
+                    // let bondId1 = chain1Tmp + "_" + resi1 + "_" + name1;
                 
                     let chain2 = chain2Array.getString(i);
                     name2Array.getString(i);
                     let resi2 = resi2Array.getString(i);
+                    // let resn2 = resn2Array.getString(i);
                     let id2 = structure + '_' + chain2 + "_" + resi2;
-                
-                    // Verify that the linkage is covalent, as indicated by the conn_type_id attribute2
-                
-                    // if (conn_type_id == "covale") {
-                    //     vBonds.push(id1);
-                    //     vBonds.push(id2);
-                    // }
-                    
-                    if(conn_type_id == "disulf") {
+
+                    // let chain2Tmp = (me.parasCls.residueAbbrev.hasOwnProperty(resn2)) ? chain2 : resn2;
+                    // let bondId2 = chain2Tmp + "_" + resi2 + "_" + name2;
+
+                    // Verify that the linkage is covalent, as indicated by the conn_type_id attribute2 
+                    if (conn_type_id == "covale") ;
+                    else if(conn_type_id == "disulf") {
                         if(ic.ssbondpnts[structure] === undefined) ic.ssbondpnts[structure] = [];
 
                         ic.ssbondpnts[structure].push(id1);
@@ -116591,6 +116655,7 @@ class LoadCIF {
             let nameArray = atom_site.getColumn("label_atom_id");
             let entiyidArray = atom_site.getColumn("label_entity_id");
 
+            // check 3QUM
             let chainArray = atom_site.getColumn("auth_asym_id");
 
             let resiArray = atom_site.getColumn("label_seq_id");
@@ -116612,7 +116677,6 @@ class LoadCIF {
             let sChain = {};
             let prevModelNum = '';
             if(!ic.molid2chain) ic.molid2chain = {};
-            
             for (let i = 0; i < atomSize; ++i) {
                 let modelNum = modelNumArray.getString(i);
                 if(i > 0 && modelNum != prevModelNum) {
@@ -116640,7 +116704,6 @@ class LoadCIF {
 
                 let autochain = autochainArray.getString(i);
 
-
                 resi = oriResi;
 
                 let molecueType;
@@ -116659,7 +116722,7 @@ class LoadCIF {
                     }
                     else {
                         molecueType = "ligand"; // ligands or ions
-                        chain = resn;
+                        if(chain == "?" || chain == ".") chain = resn; // check 3QUM
                     }
                 }
                 if(chain === '') chain = 'A';
@@ -116749,6 +116812,8 @@ class LoadCIF {
                 let z = zArray.getFloat(i);
                 let coord = new Vector3$1(x, y, z);
 
+                let id = serial.toString();
+
                 let atomDetails = {
                     het: (atom_hetatm == "HETATM"), // optional, used to determine chemicals, water, ions, etc
                     serial: serial,         // required, unique atom id
@@ -116905,6 +116970,30 @@ class LoadCIF {
             ic.residues[residueNum] = residuesTmp;
             if(ic.chains[chainNum] === undefined) ic.chains[chainNum] = {};
             ic.chains[chainNum] = me.hashUtilsCls.unionHash2Atoms(ic.chains[chainNum], chainsTmp, ic.atoms);
+/*
+            /// add the defined bonds
+            for(let i = 0; i < vBonds.length; i = i + 2) {
+                let id1 = mName2Serial[vBonds[i]];
+                let id2 = mName2Serial[vBonds[i+1]];
+
+                if(!mId2Set.hasOwnProperty(id1)) mId2Set[id1] = {};
+                if(!mId2Set.hasOwnProperty(id2)) mId2Set[id2] = {};
+                mId2Set[id1][id2] = 1;
+                mId2Set[id2][id1] = 1;
+            }
+
+            for(let id in mId2Set) {
+                let sConnId = mId2Set[id];
+                let vConnId = Object.keys(sConnId);
+                let serial = parseInt(id);
+                
+                for(let j = 0, jl = vConnId.length; j < jl; ++j) {
+                    if(vConnId[j] === 'undefined' || !ic.atoms[serial]) continue;
+                    if(!ic.atoms[serial].bonds) ic.atoms[serial].bonds = [];
+                    ic.atoms[serial].bonds.push(parseInt(vConnId[j]));
+                }
+            }
+*/
 
             // clear memory
             atom_hetatmArray = resnArray = elemArray = nameArray = chainArray = resiArray = resiOriArray 
@@ -117076,6 +117165,41 @@ class LoadCIF {
             }
         }
 
+        // check the bonds between chemicals and all other atoms
+        let processedChemicals = {};
+        for(let i in ic.chemicals) {
+            console.log(" i = ", i, " processedChemicals = ", processedChemicals);
+            if(processedChemicals.hasOwnProperty(i)) continue;
+
+            let atom = ic.atoms[i];
+            let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
+
+            let radius = 4;
+            let residueAtoms = ic.residues[resid];
+            let otherAtoms = me.hashUtilsCls.exclHash(ic.atoms, residueAtoms);
+            let neighborAtoms = ic.contactCls.getAtomsWithinAtom(otherAtoms, residueAtoms, radius);
+
+            for(let j in residueAtoms) {
+                let startAtom = ic.atoms[j];
+                for(let k in neighborAtoms) {
+                    let neighborAtom = ic.atoms[k];
+                    let neighborResid = neighborAtom.structure + '_' + neighborAtom.chain + '_' + neighborAtom.resi;
+                    if(resid === neighborResid) continue;
+
+                    if(me.utilsCls.hasCovalentBond(startAtom, neighborAtom)) {
+                        // Handle covalent bond
+                        if(!startAtom.bonds) startAtom.bonds = [];
+                        if(!neighborAtom.bonds) neighborAtom.bonds = []; 
+                    
+                        startAtom.bonds.push(neighborAtom.serial);
+                        neighborAtom.bonds.push(startAtom.serial);
+                    }
+                }
+            }
+
+            processedChemicals = me.hashUtilsCls.unionHash(processedChemicals, ic.residues[resid]);
+        }
+
         ic.pmin = pmin;
         ic.pmax = pmax;