icn3d 3.31.2 → 3.31.3

package/icn3d.js

@@ -3577,20 +3577,20 @@ THREE.OrthographicTrackballControls.prototype = Object.create( THREE.EventDispat
 THREE.OrthographicTrackballControls.prototype.constructor = THREE.OrthographicTrackballControls;
 
 
-; var __CIFTools = function () {
-  'use strict';
+// ; var __CIFTools = function () {
+//   'use strict';
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
 var CIFTools;
 (function (CIFTools) {
     CIFTools.VERSION = { number: "1.1.7", date: "Oct 30 2018" };
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
+// var CIFTools;
+// (function (CIFTools) {
     var Utils;
     (function (Utils) {
         var ChunkedArray;
@@ -3728,7 +3728,7 @@ var CIFTools;
             ChunkedArray.create = create;
         })(ChunkedArray = Utils.ChunkedArray || (Utils.ChunkedArray = {}));
     })(Utils = CIFTools.Utils || (CIFTools.Utils = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
@@ -3738,9 +3738,9 @@ var CIFTools;
  * For the purposes of parsing numbers from the mmCIF data representations,
  * up to 4 times faster than JS parseInt/parseFloat.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Utils;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Utils;
     (function (Utils) {
         var FastNumberParsers;
         (function (FastNumberParsers) {
@@ -3820,13 +3820,13 @@ var CIFTools;
             FastNumberParsers.parseFloat = parseFloat;
         })(FastNumberParsers = Utils.FastNumberParsers || (Utils.FastNumberParsers = {}));
     })(Utils = CIFTools.Utils || (CIFTools.Utils = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Utils;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Utils;
     (function (Utils) {
         var __paddingSpaces = [];
         (function () {
@@ -3969,13 +3969,13 @@ var CIFTools;
             StringWriter.writeFloatPadRight = writeFloatPadRight;
         })(StringWriter = Utils.StringWriter || (Utils.StringWriter = {}));
     })(Utils = CIFTools.Utils || (CIFTools.Utils = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    "use strict";
+// var CIFTools;
+// (function (CIFTools) {
+//     "use strict";
     /**
      * Represents a column that is not present.
      */
@@ -4035,13 +4035,13 @@ var CIFTools;
         }
         Category.getVector = getVector;
     })(Category = CIFTools.Category || (CIFTools.Category = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    "use strict";
+// var CIFTools;
+// (function (CIFTools) {
+//     "use strict";
     var ParserResult;
     (function (ParserResult) {
         function error(message, line) {
@@ -4079,7 +4079,7 @@ var CIFTools;
         return ParserSuccess;
     }());
     CIFTools.ParserSuccess = ParserSuccess;
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
@@ -4123,8 +4123,8 @@ var CIFTools;
     in memory that is very efficient, fast and introduces a very minimal overhead.
 
  */
-var CIFTools;
-(function (CIFTools) {
+// var CIFTools;
+// (function (CIFTools) {
     var Text;
     (function (Text) {
         "use strict";
@@ -4348,13 +4348,13 @@ var CIFTools;
         }());
         Text.Column = Column;
     })(Text = CIFTools.Text || (CIFTools.Text = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Text;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Text;
     (function (Text) {
         "use strict";
         var TokenIndexBuilder;
@@ -4868,13 +4868,13 @@ var CIFTools;
         }
         Text.parse = parse;
     })(Text = CIFTools.Text || (CIFTools.Text = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Text;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Text;
     (function (Text) {
         "use strict";
         var StringWriter = CIFTools.Utils.StringWriter;
@@ -5114,12 +5114,12 @@ var CIFTools;
             }
         }
     })(Text = CIFTools.Text || (CIFTools.Text = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
+// var CIFTools;
+// (function (CIFTools) {
     var Binary;
     (function (Binary) {
         var MessagePack;
@@ -5335,13 +5335,13 @@ var CIFTools;
             MessagePack.decode = decode;
         })(MessagePack = Binary.MessagePack || (Binary.MessagePack = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         var MessagePack;
         (function (MessagePack) {
@@ -5629,13 +5629,13 @@ var CIFTools;
             }
         })(MessagePack = Binary.MessagePack || (Binary.MessagePack = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         var MessagePack;
         (function (MessagePack) {
@@ -5755,13 +5755,13 @@ var CIFTools;
             MessagePack.utf8ByteCount = utf8ByteCount;
         })(MessagePack = Binary.MessagePack || (Binary.MessagePack = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         /**
@@ -5963,13 +5963,13 @@ var CIFTools;
             }
         })(Decoder || (Decoder = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         var File = /** @class */ (function () {
@@ -6127,13 +6127,13 @@ var CIFTools;
             return MaskedStringColumn;
         }());
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         /**
@@ -6493,13 +6493,13 @@ var CIFTools;
             Encoder.stringArray = stringArray;
         })(Encoder = Binary.Encoder || (Binary.Encoder = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         Binary.VERSION = '0.3.0';
@@ -6534,13 +6534,13 @@ var CIFTools;
             Encoding.isSignedIntegerDataType = isSignedIntegerDataType;
         })(Encoding = Binary.Encoding || (Binary.Encoding = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         function checkVersions(min, current) {
@@ -6567,13 +6567,13 @@ var CIFTools;
         }
         Binary.parse = parse;
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         function encodeField(field, data, totalCount) {
@@ -6676,17 +6676,17 @@ var CIFTools;
         }());
         Binary.Writer = Writer;
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
-  return CIFTools;
-}
-if (typeof module === 'object' && typeof module.exports === 'object') {
-  module.exports = __CIFTools();
-} else if (typeof define === 'function' && define.amd) {
-  define(['require'], function(require) { return __CIFTools(); })
-} else {
-  var __target = !!window ? window : this;
-  __target.CIFTools = __CIFTools();
-}
+ })(CIFTools || (CIFTools = {}));
+//   return CIFTools;
+// }
+// if (typeof module === 'object' && typeof module.exports === 'object') {
+//   module.exports = __CIFTools();
+// } else if (typeof define === 'function' && define.amd) {
+//   define(['require'], function(require) { return __CIFTools(); })
+// } else {
+//   var __target = !!window ? window : this;
+//   __target.CIFTools = __CIFTools();
+// }
 
 
 'use strict';
@@ -16925,7 +16925,6 @@ class Events {
                 thisClass.setLogCmd('load mmcif file ' + $("#" + me.pre + "mmciffile").val(), false);
                 ic.molTitle = "";
 
-                /*
                 // let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
                 // //ic.bCid = undefined;
 
@@ -16943,19 +16942,6 @@ class Events {
                 ic.InputfileType = 'mmcif';
                 // await ic.mmcifParserCls.loadMmcifData(data); 
                 await ic.opmParserCls.loadOpmData(dataStr, undefined, undefined, 'mmcif', undefined, bText);
-                */
-
-                let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-
-                let dataObj = {'mmciffile': dataStr};
-                let data = await me.getAjaxPostPromise(url, dataObj, true);
-
-                //ic.initUI();
-                ic.init();
-                ic.bInputfile = true;
-                ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + data : data;
-                ic.InputfileType = 'mmcif';
-                await ic.mmcifParserCls.loadMmcifData(data); 
              };
              reader.readAsText(file);
            }
@@ -54482,7 +54468,6 @@ class MmcifParser {
         let url = "https://files.rcsb.org/download/" + mmcifid + ".cif";
         let data = await me.getAjaxPromise(url, 'text', true);
 
-        /*
         // url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
         // let dataObj = {'mmciffile': data};
         // let data2 = await me.getAjaxPostPromise(url, dataObj, true);
@@ -54495,13 +54480,6 @@ class MmcifParser {
 
         // await this.loadMmcifData(bcifJson, mmcifid);
         await ic.opmParserCls.loadOpmData(data, mmcifid, undefined, 'mmcif', undefined, bText);
-        */
-
-        url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-        let dataObj = {'mmciffile': data};
-        let data2 = await me.getAjaxPostPromise(url, dataObj, true);
-
-        await this.loadMmcifData(data2, mmcifid);
     }
 
     async downloadMmcifSymmetry(mmcifid, type) { let ic = this.icn3d, me = ic.icn3dui;
@@ -55196,8 +55174,6 @@ class BcifParser {
         await ic.opmParserCls.loadOpmData(bcifArrayBuffer, bcifid, undefined, 'bcif', undefined, bText);
     }
 
-    // For text mmCIF file, CIFTools library does not support atom_site.getColumn("Cartn_x").data,
-    // but just support atom_site.getColumn("Cartn_x").getFloat(i). So do not use "bText = true" for now.
     getBcifJson(bcifData, bcifid, bText, bNoCoord) { let ic = this.icn3d, me = ic.icn3dui;
         let text = "";
 
@@ -55260,25 +55236,25 @@ class BcifParser {
             // Retrieve the table corresponding to the struct_conf category, which delineates mainly helix
             let struct_conf = block.getCategory("_struct_conf");
 
-            let conf_type_idArray = struct_conf.getColumn("conf_type_id").data;
+            let conf_type_idArray = struct_conf.getColumn("conf_type_id");
 
-            let chain1Array = struct_conf.getColumn("beg_auth_asym_id").data;
-            let resi1Array = struct_conf.getColumn("beg_label_seq_id").data;
+            let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
+            let resi1Array = struct_conf.getColumn("beg_label_seq_id");
 
-            let chain2Array = struct_conf.getColumn("end_auth_asym_id").data;
-            let resi2Array = struct_conf.getColumn("end_label_seq_id").data;
+            let chain2Array = struct_conf.getColumn("end_auth_asym_id");
+            let resi2Array = struct_conf.getColumn("end_label_seq_id");
 
             // Iterate through every row in the struct_conf category table, where each row delineates an interatomic connection
             let confSize = struct_conf.rowCount;
             for (let i = 0; i < confSize; ++i) {
-                let conf_type_id = conf_type_idArray[i];
+                let conf_type_id = conf_type_idArray.getString(i);
 
-                let chain1 = chain1Array[i];
-                let resi1 = resi1Array[i];
+                let chain1 = chain1Array.getString(i);
+                let resi1 = resi1Array.getString(i);
                 let id1 = chain1 + "_" + resi1;
 
-                let chain2 = chain2Array[i];
-                let resi2 = resi2Array[i];
+                let chain2 = chain2Array.getString(i);
+                let resi2 = resi2Array.getString(i);
                 let id2 = chain2 + "_" + resi2;
 
                 let ss;
@@ -55310,23 +55286,23 @@ class BcifParser {
             // Retrieve the table corresponding to the struct_sheet_range category, which delineates mainly beta sheet
             let struct_sheet_range = block.getCategory("_struct_sheet_range");
 
-            let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id").data;
-            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id").data;
+            let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
+            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
 
-            let chain2Array = struct_sheet_range.getColumn("end_auth_asym_id").data;
-            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id").data;
+            let chain2Array = struct_sheet_range.getColumn("end_auth_asym_id");
+            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
 
             // Iterate through every row in the struct_sheet_range category table, where each row delineates an interatomic connection
             let sheetSize = struct_sheet_range.rowCount;
             for (let i = 0; i < sheetSize; ++i) {
-                let chain1 = chain1Array[i];
-                let resi1 = resi1Array[i];
+                let chain1 = chain1Array.getString(i);
+                let resi1 = resi1Array.getString(i);
                 let id1 = chain1 + "_" + resi1;
 
                 sSSBegin[id1] = 1;
 
-                let chain2 = chain2Array[i];
-                let resi2 = resi2Array[i];
+                let chain2 = chain2Array.getString(i);
+                let resi2 = resi2Array.getString(i);
                 let id2 = chain2 + "_" + resi2;
 
                 sSSEnd[id2] = 1;
@@ -55351,28 +55327,28 @@ class BcifParser {
             // Retrieve the table corresponding to the struct_conn category, which delineates connections1
             let struct_conn = block.getCategory("_struct_conn");
 
-            let conn_type_idArray = struct_conn.getColumn("conn_type_id").data;
+            let conn_type_idArray = struct_conn.getColumn("conn_type_id");
 
-            let chain1Array = struct_conn.getColumn("ptnr1_auth_asym_id").data;
-            let name1Array = struct_conn.getColumn("ptnr1_label_atom_id").data;
-            let resi1Array = struct_conn.getColumn("ptnr1_label_seq_id").data;
+            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 chain2Array = struct_conn.getColumn("ptnr2_auth_asym_id").data;
-            let name2Array = struct_conn.getColumn("ptnr2_label_atom_id").data;
-            let resi2Array = struct_conn.getColumn("ptnr2_label_seq_id").data;
+            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 connSize = struct_conn.rowCount;
             for (let i = 0; i < connSize; ++i) {
-                let conn_type_id = conn_type_idArray[i];
+                let conn_type_id = conn_type_idArray.getString(i);
 
-                let chain1 = chain1Array[i];
-                let name1 = name1Array[i];
-                let resi1 = resi1Array[i];
+                let chain1 = chain1Array.getString(i);
+                let name1 = name1Array.getString(i);
+                let resi1 = resi1Array.getString(i);
                 let id1 = chain1 + "_" + resi1 + "_" + name1;
 
-                let chain2 = chain2Array[i];
-                let name2 = name2Array[i];
-                let resi2 = resi2Array[i];
+                let chain2 = chain2Array.getString(i);
+                let name2 = name2Array.getString(i);
+                let resi2 = resi2Array.getString(i);
                 let id2 = chain2 + "_" + resi2 + "_" + name2;
 
                 // Verify that the linkage is covalent, as indicated by the conn_type_id attribute2
@@ -55413,40 +55389,40 @@ class BcifParser {
         let atom_hetatmArray, resnArray, elemArray, nameArray, chainArray, resiArray, resiOriArray, altArray, bArray, xArray, yArray, zArray, autochainArray = [];
 
         if(!bNoCoord) {
-            atom_hetatmArray = atom_site.getColumn("group_PDB").data;
-            resnArray = atom_site.getColumn("label_comp_id").data;
-            elemArray = atom_site.getColumn("type_symbol").data;
-            nameArray = atom_site.getColumn("label_atom_id").data;
+            atom_hetatmArray = atom_site.getColumn("group_PDB");
+            resnArray = atom_site.getColumn("label_comp_id");
+            elemArray = atom_site.getColumn("type_symbol");
+            nameArray = atom_site.getColumn("label_atom_id");
 
-            chainArray = atom_site.getColumn("auth_asym_id").data;
+            chainArray = atom_site.getColumn("auth_asym_id");
             
-            resiArray = atom_site.getColumn("label_seq_id").data;
-            resiOriArray = atom_site.getColumn("auth_seq_id").data;
-            altArray = atom_site.getColumn("label_alt_id").data;
+            resiArray = atom_site.getColumn("label_seq_id");
+            resiOriArray = atom_site.getColumn("auth_seq_id");
+            altArray = atom_site.getColumn("label_alt_id");
 
-            bArray = atom_site.getColumn("B_iso_or_equiv").data;
+            bArray = atom_site.getColumn("B_iso_or_equiv");
 
-            xArray = atom_site.getColumn("Cartn_x").data;
-            yArray = atom_site.getColumn("Cartn_y").data;
-            zArray = atom_site.getColumn("Cartn_z").data;
+            xArray = atom_site.getColumn("Cartn_x");
+            yArray = atom_site.getColumn("Cartn_y");
+            zArray = atom_site.getColumn("Cartn_z");
 
-            autochainArray = atom_site.getColumn("label_asym_id").data;
+            autochainArray = atom_site.getColumn("label_asym_id");
 
             // get the bond info
             let ligSeqHash = {}, prevAutochain = '';
             for (let i = 0; i < atomSize; ++i) {
-                let atom_hetatm = atom_hetatmArray[i];
-                let resn = resnArray[i];
-                let elem = elemArray[i];
-                let name = nameArray[i];
+                let atom_hetatm = atom_hetatmArray.getString(i);
+                let resn = resnArray.getString(i);
+                let elem = elemArray.getString(i);
+                let name = nameArray.getString(i);
         // use the chain name from author, and use seq id from standardized seq id
                 //let chain = atom_site.getColumn("label_asym_id").getString(i);
-                let chain = chainArray[i];
-                let resi = resiArray[i];
-                let oriResi = resiOriArray[i]; 
-                let alt = altArray[i];
+                let chain = chainArray.getString(i);
+                let resi = resiArray.getString(i);
+                let oriResi = resiOriArray.getString(i); 
+                let alt = altArray.getString(i);
 
-                let autochain = autochainArray[i];
+                let autochain = autochainArray.getString(i);
 
                 resi = oriResi;
 
@@ -55517,9 +55493,9 @@ class BcifParser {
                     }
                 }
 
-                let x = xArray[i];
-                let y = yArray[i];
-                let z = zArray[i];
+                let x = xArray.getFloat(i);
+                let y = yArray.getFloat(i);
+                let z = zArray.getFloat(i);
 
                 let id = serial.toString();
 
@@ -55615,18 +55591,18 @@ class BcifParser {
             }
 
             for (let i = 0; i < atomSize; ++i) {
-                let atom_hetatm = atom_hetatmArray[i];
-                let resn = resnArray[i];
-                let elem = elemArray[i];
-                let name = nameArray[i];
+                let atom_hetatm = atom_hetatmArray.getString(i);
+                let resn = resnArray.getString(i);
+                let elem = elemArray.getString(i);
+                let name = nameArray.getString(i);
         // use the chain name from author, and use seq id from standardized seq id
                 //let chain = atom_site.getColumn("label_asym_id").getString(i);
-                let chain = chainArray[i];
-                let resi = resiArray[i];
-                let oriResi = resiOriArray[i]; 
-                let alt = altArray[i];
+                let chain = chainArray.getString(i);
+                let resi = resiArray.getString(i);
+                let oriResi = resiOriArray.getString(i); 
+                let alt = altArray.getString(i);
 
-                let autochain = autochainArray[i];
+                let autochain = autochainArray.getString(i);
 
                 resi = oriResi;
 
@@ -55674,11 +55650,11 @@ class BcifParser {
                     // }
                 }
 
-                let b = bArray[i];
+                let b = bArray.getString(i);
 
-                let x = xArray[i];
-                let y = yArray[i];
-                let z = zArray[i];
+                let x = xArray.getFloat(i);
+                let y = yArray.getFloat(i);
+                let z = zArray.getFloat(i);
                 //int serial = parseInt(atom_site(i, "id"));
 
                 //let id = chain + "_" + resi + "_" + name;
@@ -55766,19 +55742,19 @@ class BcifParser {
         if(block.getCategory("_pdbx_poly_seq_scheme")) {
             let poly_seq_scheme = block.getCategory("_pdbx_poly_seq_scheme");
 
-            let resiArray = poly_seq_scheme.getColumn("seq_id").data;
-            let oriResiArray = poly_seq_scheme.getColumn("pdb_seq_num").data;
-            let resnArray = poly_seq_scheme.getColumn("mon_id").data;
-            let chainArray = poly_seq_scheme.getColumn("pdb_strand_id").data;
+            let resiArray = poly_seq_scheme.getColumn("seq_id");
+            let oriResiArray = poly_seq_scheme.getColumn("pdb_seq_num");
+            let resnArray = poly_seq_scheme.getColumn("mon_id");
+            let chainArray = poly_seq_scheme.getColumn("pdb_strand_id");
 
             let seqSize = poly_seq_scheme.rowCount;
             let prevChain = "";
             let seq = "";
             for (let i = 0; i < seqSize; ++i) {
-                resiArray[i];
-                let oriResi = oriResiArray[i];
-                let resn = resnArray[i];
-                let chain = chainArray[i];
+                resiArray.getString(i);
+                let oriResi = oriResiArray.getString(i);
+                let resn = resnArray.getString(i);
+                let chain = chainArray.getString(i);
 
                 if(chain != prevChain) {
                     if(i == 0) {
@@ -56207,19 +56183,16 @@ class OpmParser {
         if(type === 'mmtf') {
             await ic.bcifParserCls.parseBcifData(data, pdbid, bFull);
         }
-        else if(type === 'bcif') {
-            await ic.bcifParserCls.parseBcifData(data, pdbid, bFull);
-        }
         else 
         */
 
         if(type === 'mmcif' || type === 'bcif') {
-            if(type === 'mmcif') {
-                ic.loadAtomDataCls.loadAtomDataIn(data, data.mmcif, 'mmcifid', undefined, undefined);
-            }
-            else if(type === 'bcif') {
+            // if(type === 'mmcif') {
+            //     ic.loadAtomDataCls.loadAtomDataIn(data, data.mmcif, 'mmcifid', undefined, undefined);
+            // }
+            // else if(type === 'bcif') {
                 ic.loadCIFCls.loadCIF(data, pdbid, bText);
-            }
+            // }
 
             if(ic.emd !== undefined) {
               $("#" + ic.pre + "mapWrapper1").hide();
@@ -56235,7 +56208,7 @@ class OpmParser {
             if(Object.keys(ic.structures).length == 1) {
                 $("#" + ic.pre + "alternateWrapper").hide();
             }
-    
+/*    
             // load assembly info
             if(type === 'mmcif') {
                 let assembly =(data.assembly !== undefined) ? data.assembly : [];
@@ -56247,7 +56220,7 @@ class OpmParser {
                     }
                 }
             }
-        
+*/        
             if(ic.biomtMatrices !== undefined && ic.biomtMatrices.length > 1) {
                 $("#" + ic.pre + "assemblyWrapper").show();
     
@@ -56369,7 +56342,6 @@ class PdbParser {
             await this.loadPdbData(data, id, undefined, bAppend);
         }
         else if(type === 'mmcif') {
-            /*
             // let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
             // let dataObj = {'mmciffile': data};
             // let data2 = await me.getAjaxPostPromise(url, dataObj, true);
@@ -56381,12 +56353,6 @@ class PdbParser {
 
             // await ic.mmcifParserCls.loadMmcifData(bcifJson, undefined);
             await ic.opmParserCls.loadOpmData(data, undefined, undefined, 'mmcif', undefined, bText);
-            */
-
-            let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-            let dataObj = {'mmciffile': data};
-            let data2 = await me.getAjaxPostPromise(url, dataObj, true);
-            await ic.mmcifParserCls.loadMmcifData(data2, undefined);
         }
         else if(type === 'mol2') {
             await ic.mol2ParserCls.loadMol2Data(data);
@@ -62733,8 +62699,6 @@ class LoadCIF {
         this.icn3d = icn3d;
     }
 
-    // For text mmCIF file, CIFTools library does not support atom_site.getColumn("Cartn_x").data,
-    // but just support atom_site.getColumn("Cartn_x").getFloat(i). So do not use "bText = true" for now.
     loadCIF(bcifData, bcifid, bText, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
         let hAtoms = {};
 
@@ -62841,22 +62805,22 @@ class LoadCIF {
             // Retrieve the table corresponding to the struct_conf category, which delineates mainly helix
             let struct_conf = block.getCategory("_struct_conf");
         
-            let conf_type_idArray = struct_conf.getColumn("conf_type_id").data;
+            let conf_type_idArray = struct_conf.getColumn("conf_type_id");
         
-            let chain1Array = struct_conf.getColumn("beg_auth_asym_id").data;
-            let resi1Array = struct_conf.getColumn("beg_label_seq_id").data;
+            let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
+            let resi1Array = struct_conf.getColumn("beg_label_seq_id");
         
-            struct_conf.getColumn("end_auth_asym_id").data;
-            let resi2Array = struct_conf.getColumn("end_label_seq_id").data;
+            struct_conf.getColumn("end_auth_asym_id");
+            let resi2Array = struct_conf.getColumn("end_label_seq_id");
         
             // Iterate through every row in the struct_conf category table, where each row delineates an interatomic connection
             let confSize = struct_conf.rowCount;
             for (let i = 0; i < confSize; ++i) {
-                let conf_type_id = conf_type_idArray[i];
+                let conf_type_id = conf_type_idArray.getString(i);
             
-                let startChain = chain1Array[i];
-                let startResi = parseInt(resi1Array[i]);
-                let endResi = parseInt(resi2Array[i]);
+                let startChain = chain1Array.getString(i);
+                let startResi = parseInt(resi1Array.getString(i));
+                let endResi = parseInt(resi2Array.getString(i));
             
                 if(conf_type_id.substr(0, 4) == "HELX") {
                     for(let j = parseInt(startResi); j <= parseInt(endResi); ++j) {
@@ -62885,18 +62849,18 @@ class LoadCIF {
             // Retrieve the table corresponding to the struct_sheet_range category, which delineates mainly beta sheet
             let struct_sheet_range = block.getCategory("_struct_sheet_range");
         
-            let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id").data;
-            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id").data;
+            let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
+            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
         
-            struct_sheet_range.getColumn("end_auth_asym_id").data;
-            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id").data;
+            struct_sheet_range.getColumn("end_auth_asym_id");
+            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
         
             // Iterate through every row in the struct_sheet_range category table, where each row delineates an interatomic connection
             let sheetSize = struct_sheet_range.rowCount;
             for (let i = 0; i < sheetSize; ++i) {
-                let startChain = chain1Array[i];
-                let startResi = parseInt(resi1Array[i]);
-                let endResi = parseInt(resi2Array[i]);
+                let startChain = chain1Array.getString(i);
+                let startResi = parseInt(resi1Array.getString(i));
+                let endResi = parseInt(resi2Array.getString(i));
             
                 for(let j = startResi; j <= endResi; ++j) {
                     let resid = structure + "_" + startChain + "_" + j;
@@ -62916,28 +62880,28 @@ class LoadCIF {
             // Retrieve the table corresponding to the struct_conn category, which delineates connections1
             let struct_conn = block.getCategory("_struct_conn");
         
-            let conn_type_idArray = struct_conn.getColumn("conn_type_id").data;
+            let conn_type_idArray = struct_conn.getColumn("conn_type_id");
         
-            let chain1Array = struct_conn.getColumn("ptnr1_auth_asym_id").data;
-            let name1Array = struct_conn.getColumn("ptnr1_label_atom_id").data;
-            let resi1Array = struct_conn.getColumn("ptnr1_label_seq_id").data;
+            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 chain2Array = struct_conn.getColumn("ptnr2_auth_asym_id").data;
-            let name2Array = struct_conn.getColumn("ptnr2_label_atom_id").data;
-            let resi2Array = struct_conn.getColumn("ptnr2_label_seq_id").data;
+            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 connSize = struct_conn.rowCount;
             for (let i = 0; i < connSize; ++i) {
-                let conn_type_id = conn_type_idArray[i];
+                let conn_type_id = conn_type_idArray.getString(i);
             
-                let chain1 = chain1Array[i];
-                name1Array[i];
-                let resi1 = resi1Array[i];
+                let chain1 = chain1Array.getString(i);
+                name1Array.getString(i);
+                let resi1 = resi1Array.getString(i);
                 let id1 = structure + '_' + chain1 + "_" + resi1;
             
-                let chain2 = chain2Array[i];
-                name2Array[i];
-                let resi2 = resi2Array[i];
+                let chain2 = chain2Array.getString(i);
+                name2Array.getString(i);
+                let resi2 = resi2Array.getString(i);
                 let id2 = structure + '_' + chain2 + "_" + resi2;
             
                 // Verify that the linkage is covalent, as indicated by the conn_type_id attribute2
@@ -62969,31 +62933,31 @@ class LoadCIF {
             // Retrieve the table corresponding to the struct_oper_list category, which delineates assembly
             let struct_oper_list = block.getCategory("_pdbx_struct_oper_list");
         
-            let struct_oper_idArray = struct_oper_list.getColumn("id").data;
-            let m11Array = struct_oper_list.getColumn("matrix[1][1]").data;
-            let m12Array = struct_oper_list.getColumn("matrix[1][2]").data;
-            let m13Array = struct_oper_list.getColumn("matrix[1][3]").data;
-            let m14Array = struct_oper_list.getColumn("vector[1]").data;
+            let struct_oper_idArray = struct_oper_list.getColumn("id");
+            let m11Array = struct_oper_list.getColumn("matrix[1][1]");
+            let m12Array = struct_oper_list.getColumn("matrix[1][2]");
+            let m13Array = struct_oper_list.getColumn("matrix[1][3]");
+            let m14Array = struct_oper_list.getColumn("vector[1]");
         
-            let m21Array = struct_oper_list.getColumn("matrix[2][1]").data;
-            let m22Array = struct_oper_list.getColumn("matrix[2][2]").data;
-            let m23Array = struct_oper_list.getColumn("matrix[2][3]").data;
-            let m24Array = struct_oper_list.getColumn("vector[2]").data;
+            let m21Array = struct_oper_list.getColumn("matrix[2][1]");
+            let m22Array = struct_oper_list.getColumn("matrix[2][2]");
+            let m23Array = struct_oper_list.getColumn("matrix[2][3]");
+            let m24Array = struct_oper_list.getColumn("vector[2]");
         
-            let m31Array = struct_oper_list.getColumn("matrix[3][1]").data;
-            let m32Array = struct_oper_list.getColumn("matrix[3][2]").data;
-            let m33Array = struct_oper_list.getColumn("matrix[3][3]").data;
-            let m34Array = struct_oper_list.getColumn("vector[3]").data;
+            let m31Array = struct_oper_list.getColumn("matrix[3][1]");
+            let m32Array = struct_oper_list.getColumn("matrix[3][2]");
+            let m33Array = struct_oper_list.getColumn("matrix[3][3]");
+            let m34Array = struct_oper_list.getColumn("vector[3]");
         
             let assemblySize = struct_oper_list.rowCount;
             for (let i = 0; i < assemblySize; ++i) {
-                let struct_oper_id = struct_oper_idArray[i];
+                let struct_oper_id = struct_oper_idArray.getString(i);
                 if(struct_oper_id == "X0") continue;
 
                 if (ic.biomtMatrices[i] == undefined) ic.biomtMatrices[i] = new THREE.Matrix4().identity();
-                ic.biomtMatrices[i].set(m11Array[i], m12Array[i], m13Array[i], m14Array[i], 
-                    m21Array[i], m22Array[i], m23Array[i], m24Array[i], 
-                    m31Array[i], m32Array[i], m33Array[i], m34Array[i], 
+                ic.biomtMatrices[i].set(m11Array.getString(i), m12Array.getString(i), m13Array.getString(i), m14Array.getString(i), 
+                    m21Array.getString(i), m22Array.getString(i), m23Array.getString(i), m24Array.getString(i), 
+                    m31Array.getString(i), m32Array.getString(i), m33Array.getString(i), m34Array.getString(i), 
                     0, 0, 0, 1);
             }
         
@@ -63036,41 +63000,42 @@ class LoadCIF {
             ic.opts['nucleotides'] = 'o3 trace'; //nucleotide cartoon, o3 trace, schematic, lines, stick,
         }
 
-        let atom_hetatmArray = atom_site.getColumn("group_PDB").data;
-        let resnArray = atom_site.getColumn("label_comp_id").data;
-        let elemArray = atom_site.getColumn("type_symbol").data;
-        let nameArray = atom_site.getColumn("label_atom_id").data;
-    
-        let chainArray = atom_site.getColumn("auth_asym_id").data;
-    
-        let resiArray = atom_site.getColumn("label_seq_id").data;
-        let resiOriArray = atom_site.getColumn("auth_seq_id").data;
-        let altArray = atom_site.getColumn("label_alt_id").data;
-    
-        let bArray = atom_site.getColumn("B_iso_or_equiv").data;
-    
-        let xArray = atom_site.getColumn("Cartn_x").data;
-        let yArray = atom_site.getColumn("Cartn_y").data;
-        let zArray = atom_site.getColumn("Cartn_z").data;
-    
-        let autochainArray = atom_site.getColumn("label_asym_id").data;
+        let atom_hetatmArray = atom_site.getColumn("group_PDB");
+        let resnArray = atom_site.getColumn("label_comp_id");
+        let elemArray = atom_site.getColumn("type_symbol");
+        let nameArray = atom_site.getColumn("label_atom_id");
+
+        let chainArray = atom_site.getColumn("auth_asym_id");
+
+        let resiArray = atom_site.getColumn("label_seq_id");
+        let resiOriArray = atom_site.getColumn("auth_seq_id");
+        let altArray = atom_site.getColumn("label_alt_id");
+
+        let bArray = atom_site.getColumn("B_iso_or_equiv");
+
+        let xArray = atom_site.getColumn("Cartn_x");
+        let yArray = atom_site.getColumn("Cartn_y");
+        let zArray = atom_site.getColumn("Cartn_z");
+
+        let autochainArray = atom_site.getColumn("label_asym_id");
 
         // get the bond info
         let ligSeqHash = {}, prevAutochain = '';
         let prevResn;
         let sChain = {};
         for (let i = 0; i < atomSize; ++i) {
-            let atom_hetatm = atom_hetatmArray[i];
-            let resn = resnArray[i];
-            let elem = elemArray[i];
-            let atom = nameArray[i];
-            let chain = chainArray[i];
-            let resi = resiArray[i];
-            let oriResi = resiOriArray[i]; 
-            let alt = altArray[i];
-            let bFactor = bArray[i];
-
-            let autochain = autochainArray[i];
+            let atom_hetatm = atom_hetatmArray.getString(i);
+            let resn = resnArray.getString(i);
+            let elem = elemArray.getString(i);
+            let atom = nameArray.getString(i);
+            let chain = chainArray.getString(i);
+            let resi = resiArray.getString(i);
+            let oriResi = resiOriArray.getString(i); 
+            let alt = altArray.getString(i);
+            let bFactor = bArray.getString(i);
+
+            let autochain = autochainArray.getString(i);
+
 
             resi = oriResi;
 
@@ -63173,9 +63138,9 @@ class LoadCIF {
 
             //let chain_resi = chain + "_" + resi;
 
-            let x = xArray[i];
-            let y = yArray[i];
-            let z = zArray[i];
+            let x = xArray.getFloat(i);
+            let y = yArray.getFloat(i);
+            let z = zArray.getFloat(i);
             let coord = new THREE.Vector3(x, y, z);
 
             let atomDetails = {
@@ -63335,19 +63300,19 @@ class LoadCIF {
         if(block.getCategory("_pdbx_poly_seq_scheme")) {
             let poly_seq_scheme = block.getCategory("_pdbx_poly_seq_scheme");
 
-            let resiArray = poly_seq_scheme.getColumn("seq_id").data;
-            let oriResiArray = poly_seq_scheme.getColumn("pdb_seq_num").data;
-            let resnArray = poly_seq_scheme.getColumn("mon_id").data;
-            let chainArray = poly_seq_scheme.getColumn("pdb_strand_id").data;
+            let resiArray = poly_seq_scheme.getColumn("seq_id");
+            let oriResiArray = poly_seq_scheme.getColumn("pdb_seq_num");
+            let resnArray = poly_seq_scheme.getColumn("mon_id");
+            let chainArray = poly_seq_scheme.getColumn("pdb_strand_id");
 
             let seqSize = poly_seq_scheme.rowCount;
             let prevChain = "";
             let seqArray = [];
             for (let i = 0; i < seqSize; ++i) {
-                resiArray[i];
-                let oriResi = oriResiArray[i];
-                let resn = resnArray[i];
-                let chain = chainArray[i];
+                resiArray.getString(i);
+                let oriResi = oriResiArray.getString(i);
+                let resn = resnArray.getString(i);
+                let chain = chainArray.getString(i);
 
                 if(chain != prevChain && i > 0) {
                     mChainSeq[prevChain] = seqArray;
@@ -80293,7 +80258,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.31.0';
+    this.REVISION = '3.31.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;