icn3d 3.36.1 → 3.36.3

package/icn3d.js

@@ -56020,9 +56020,9 @@ class MmdbParser {
           let color =(molid2rescount[i].color === undefined) ? '#CCCCCC' : '#' +( '000000' + molid2rescount[i].color.toString( 16 ) ).slice( - 6 );
           let chainName =(molid2rescount[i].chain === undefined) ? '' : molid2rescount[i].chain.trim();
           // remove "_" in chain name
-          if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
+        //   if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
             chainName = chainName.replace(/_/g, '');
-          }
+        //   }
 
           if(chainNameHash[chainName] === undefined) {
               chainNameHash[chainName] = 1;
@@ -56268,8 +56268,8 @@ class BcifParser {
             // Iterate through every row in the table
             let db2Size = database_2.rowCount ;
             for (let i = 0; i < db2Size; ++i) {
-                let db_id = database_2.getColumn("database_id").getString(0);
-                let db_code = database_2.getColumn("database_code").getString(0);
+                let db_id = database_2.getColumn("database_id").getString(i);
+                let db_code = database_2.getColumn("database_code").getString(i);
 
                 if(db_id == "EMDB") {
                     emd = db_code;
@@ -56435,7 +56435,7 @@ class BcifParser {
 
         let bFull = (atomSize * 10 > ic.maxatomcnt) ? false : true;
 
-        let atom_hetatmArray, resnArray, elemArray, nameArray, chainArray, resiArray, resiOriArray, altArray, bArray, xArray, yArray, zArray, autochainArray = [];
+        let atom_hetatmArray, resnArray, elemArray, nameArray, chainArray, resiArray, resiOriArray, altArray, bArray, xArray, yArray, zArray, autochainArray, modelNumArray;
 
         if(!bNoCoord) {
             atom_hetatmArray = atom_site.getColumn("group_PDB");
@@ -56456,6 +56456,7 @@ class BcifParser {
             zArray = atom_site.getColumn("Cartn_z");
 
             autochainArray = atom_site.getColumn("label_asym_id");
+            modelNumArray = atom_site.getColumn("pdbx_PDB_model_num");
 
             // get the bond info
             let ligSeqHash = {}, prevAutochain = '';
@@ -56629,17 +56630,14 @@ class BcifParser {
             text += ", \"atoms\":[\n";
             prevResn = "";
             serial = 1;
-
-            let structure = atom_site.getColumn("pdbx_PDB_model_num").getString(0);
-
-            if(structure == "1") {
-                structure = bcifid;
-            }
-            else {
-                structure = bcifid + structure;
-            }
+            let structure = bcifid;
 
             for (let i = 0; i < atomSize; ++i) {
+                let modelNum = modelNumArray.getString(i);
+                if(modelNum != "1" && modelNum != "") {
+                    structure = bcifid + modelNum;
+                }
+
                 let atom_hetatm = atom_hetatmArray.getString(i);
                 let resn = resnArray.getString(i);
                 let elem = elemArray.getString(i);
@@ -56838,6 +56836,8 @@ class BcifParser {
         // print sequences
         text += ", \"sequences\":{";
         let bData = false;
+        // need to consider different models in NMR structures
+        // But this function is only used for meta data, 
         for(let chain in sChain) {
             let seq;
             if(ligSeqHash.hasOwnProperty(chain)) {
@@ -60771,9 +60771,9 @@ class LoadAtomData {
                   let chain = data.moleculeInfor[molid].chain.trim();
 
                   // remove "_" in chain name
-                  if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
+                //   if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
                     chain = chain.replace(/_/g, '');
-                  }
+                //   }
 
                   let chainid = pdbidTmp + '_' + chain;
 
@@ -60915,9 +60915,9 @@ class LoadAtomData {
             atm.chain = atm.chain.trim(); //.replace(/_/g, '');
 
             // remove "_" in chain name
-            if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
+            // if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
                 atm.chain = atm.chain.replace(/_/g, '');
-            }
+            // }
 
             // mmcif has pre-assigned structure in mmcifparser.cgi output
             if(type === 'mmdbid' || type === 'align') {
@@ -63849,13 +63849,13 @@ class LoadCIF {
         // if(!bMutation && !bAppend) {
         if(!bAppend) {
             ic.init();
-            moleculeNum = 1;
+            moleculeNum = 0; //1;
             serial = 0;
         }
         else {
             ic.oriNStru = (ic.structures) ? Object.keys(ic.structures).length : 0;
 
-            moleculeNum = ic.oriNStru + 1; //Object.keys(ic.structures).length + 1;
+            moleculeNum = ic.oriNStru; //ic.oriNStru + 1; //Object.keys(ic.structures).length + 1;
             // Concatenation of two pdbs will have several atoms for the same serial
             serial = (ic.atoms) ? Object.keys(ic.atoms).length : 0;
         }
@@ -63870,8 +63870,6 @@ class LoadCIF {
 
         let structure = id;
         let CSerial, prevCSerial, OSerial, prevOSerial;
-        
-        let bFirstAtom = true;
 
         let cifArray = (bText) ? bcifData.split('ENDMDL\n') : [bcifData];
 
@@ -64175,12 +64173,27 @@ class LoadCIF {
             let zArray = atom_site.getColumn("Cartn_z");
 
             let autochainArray = atom_site.getColumn("label_asym_id");
+            let modelNumArray = atom_site.getColumn("pdbx_PDB_model_num");
 
             // get the bond info
             let ligSeqHash = {}, prevAutochain = '';
             let prevResn;
             let sChain = {};
+            let prevModelNum = '';
             for (let i = 0; i < atomSize; ++i) {
+                let modelNum = modelNumArray.getString(i);
+                if(i > 0 && modelNum != prevModelNum) {
+                    ++moleculeNum;
+
+                    if(modelNum == "1") {
+                        structure = id;
+                    }
+                    else {
+                        structure = id + modelNum;
+                    }
+                }
+                prevModelNum = modelNum;
+
                 let atom_hetatm = atom_hetatmArray.getString(i);
                 let resn = resnArray.getString(i);
                 let elem = elemArray.getString(i);
@@ -64225,11 +64238,11 @@ class LoadCIF {
 
                 sChain[chain] = 1;
 
-                if(bFirstAtom) {
-                    structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
+                // if(bFirstAtom) {
+                //     structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
 
-                    bFirstAtom = false;
-                }
+                //     bFirstAtom = false;
+                // }
 
                 // "CA" has to appear before "O". Otherwise the cartoon of secondary structure will have breaks
                 // Concatenation of two pdbs will have several atoms for the same serial
@@ -67830,6 +67843,12 @@ class DefinedSets {
         let prevLabel = 'or';
 
         for(let i = 0, il = idArray.length; i < il; ++i) {
+            // replace 1CD8_A_1 with 1CD8_A1
+            let tmpArray = idArray[i].split('_');
+            if(tmpArray.length == 3 && !isNaN(tmpArray[2])) {
+                idArray[i] = tmpArray[0] + '_' + tmpArray[1] + tmpArray[2];
+            }
+
             if(idArray[i] === 'or' || idArray[i] === 'and' || idArray[i] === 'not') {
                 prevLabel = idArray[i];
                 continue;
@@ -69359,6 +69378,7 @@ class SelectByCommand {
            }
            else {
              chainStr = testStr.substr(periodPos + 1);
+
              //replace "A_1" with "A"
              chainStr = chainStr.replace(/_/g, '');
 
@@ -69486,7 +69506,6 @@ class SelectByCommand {
 
                      for(let l = 0, ll = residArray.length; l < ll; ++l) {
                         let residueId = residArray[l];
-
                         if(i === 0) {
                               residueHash[residueId] = 1;
                         }
@@ -82202,7 +82221,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.36.0';
+    this.REVISION = '3.36.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;