icn3d 3.54.3 → 3.54.5

package/icn3d.js

@@ -2557,7 +2557,147 @@ var CIFTools;
             }
             return result(file);
         }
+        /**
+         * Small-molecule / crystallographic ("core") CIF support, e.g. files from COD.
+         * Core CIF uses underscore names (_atom_site_label, _atom_site_fract_x) and fractional
+         * coordinates, while iCn3D's loadCIF expects mmCIF names (_atom_site.label_atom_id)
+         * and Cartesian coordinates. Without conversion getCategory("_atom_site") returns undefined.
+         * This converts such a file to a minimal mmCIF text before it is parsed.
+         */
+        function isCoreCif(data) {
+            return /^\s*_atom_site_fract_x\b/m.test(data) && !/^\s*_atom_site\./m.test(data);
+        }
+        // tokenize one CIF text keeping quotes; returns {tags:[...], loops:[{cols, rows}], singles:{}}
+        function coreTokens(data) {
+            var tokens = [], lines = data.split(/\r?\n/), i, line, m, re = /'([^']*)'(?=\s|$)|"([^"]*)"(?=\s|$)|(\S+)/g;
+            for (i = 0; i < lines.length; i++) {
+                line = lines[i];
+                if (line.charAt(0) === ';') { // multi-line text field, skip it
+                    i++;
+                    while (i < lines.length && lines[i].charAt(0) !== ';') i++;
+                    tokens.push({ v: '?', t: 'text' });
+                    continue;
+                }
+                re.lastIndex = 0;
+                while ((m = re.exec(line)) !== null) {
+                    if (m[3] !== undefined && m[3].charAt(0) === '#') break; // comment
+                    tokens.push(m[3] !== undefined ? { v: m[3] } : { v: (m[1] !== undefined ? m[1] : m[2]), t: 'quoted' });
+                }
+            }
+            return tokens;
+        }
+        function coreToNumber(s) {
+            var v = parseFloat(String(s).replace(/\(\d+\)$/, '')); // 0.7556(3) -> 0.7556
+            return isNaN(v) ? 0 : v;
+        }
+        // symmetry operator like "1/2-x,y,1/2+z" -> function(frac) -> frac
+        function coreSymop(str) {
+            var parts = str.replace(/\s+/g, '').toLowerCase().split(','), rows = [], p, k, re = /([+-]?)(?:(\d+(?:\.\d+)?)(?:\/(\d+))?|([xyz]))/g, m, row, c;
+            if (parts.length !== 3) return null;
+            for (p = 0; p < 3; p++) {
+                row = [0, 0, 0, 0]; // x y z const
+                re.lastIndex = 0;
+                while ((m = re.exec(parts[p])) !== null) {
+                    c = (m[1] === '-') ? -1 : 1;
+                    if (m[4]) { row['xyz'.indexOf(m[4])] += c; }
+                    else { row[3] += c * parseFloat(m[2]) / (m[3] ? parseFloat(m[3]) : 1); }
+                }
+                rows.push(row);
+            }
+            return function (f) {
+                var out = [];
+                for (k = 0; k < 3; k++) out.push(rows[k][0] * f[0] + rows[k][1] * f[1] + rows[k][2] * f[2] + rows[k][3]);
+                return out;
+            };
+        }
+        function convertCoreCif(data) {
+            var tk = coreTokens(data), i = 0, n = tk.length, single = {}, loops = [], name = 'data_core', t, cols, rows, cur;
+            function isTag(x) { return x && !x.t && x.v.charAt(0) === '_'; }
+            while (i < n) {
+                t = tk[i];
+                if (!t.t && /^data_/i.test(t.v)) { name = t.v; i++; }
+                else if (!t.t && /^loop_$/i.test(t.v)) {
+                    i++; cols = []; rows = [];
+                    while (i < n && isTag(tk[i])) cols.push(tk[i++].v.toLowerCase());
+                    cur = [];
+                    while (i < n && !isTag(tk[i]) && !(/^(loop_|data_)/i.test(tk[i].v) && !tk[i].t)) {
+                        cur.push(tk[i++].v);
+                        if (cur.length === cols.length) { rows.push(cur); cur = []; }
+                    }
+                    loops.push({ cols: cols, rows: rows });
+                }
+                else if (isTag(t)) { single[t.v.toLowerCase()] = (tk[i + 1] ? tk[i + 1].v : '?'); i += 2; }
+                else i++;
+            }
+            var atoms = null, symops = [], l, c;
+            for (l = 0; l < loops.length; l++) {
+                if (loops[l].cols.indexOf('_atom_site_fract_x') >= 0) atoms = loops[l];
+                c = loops[l].cols.indexOf('_symmetry_equiv_pos_as_xyz');
+                if (c < 0) c = loops[l].cols.indexOf('_space_group_symop_operation_xyz');
+                if (c >= 0) loops[l].rows.forEach(function (r) { var f = coreSymop(r[c]); if (f) symops.push(f); });
+            }
+            if (!atoms) return null;
+            if (!symops.length) symops.push(coreSymop('x,y,z'));
+
+            // orthogonalization matrix (a along x, c* along z)
+            var a = coreToNumber(single['_cell_length_a']), b = coreToNumber(single['_cell_length_b']), cc = coreToNumber(single['_cell_length_c']);
+            var al = coreToNumber(single['_cell_angle_alpha'] || 90) * Math.PI / 180, be = coreToNumber(single['_cell_angle_beta'] || 90) * Math.PI / 180, ga = coreToNumber(single['_cell_angle_gamma'] || 90) * Math.PI / 180;
+            var cosa = Math.cos(al), cosb = Math.cos(be), cosg = Math.cos(ga), sing = Math.sin(ga);
+            var vol = Math.sqrt(1 - cosa * cosa - cosb * cosb - cosg * cosg + 2 * cosa * cosb * cosg);
+            function toCart(f) {
+                return [a * f[0] + b * cosg * f[1] + cc * cosb * f[2],
+                        b * sing * f[1] + cc * (cosa - cosb * cosg) / sing * f[2],
+                        cc * vol / sing * f[2]];
+            }
+            var col = {}; atoms.cols.forEach(function (x, k) { col[x] = k; });
+            function get(r, key) { return (col[key] === undefined) ? '?' : r[col[key]]; }
+
+            var out = [name, '#', '_entry.id ' + name.substr(5), '#'];
+            // core CIF "_cell_length_a" -> mmCIF "_cell.length_a" so iCn3D can parse the unit cell
+            Object.keys(single).forEach(function (key) {
+                if (/^_cell_/.test(key)) out.push(key.replace(/^_cell_/, '_cell.') + ' ' + String(single[key]).replace(/\(\d+\)$/, ''));
+            });
+            out.push('#');
+            out.push(
+                'loop_', '_atom_site.group_PDB', '_atom_site.id', '_atom_site.type_symbol', '_atom_site.label_atom_id', '_atom_site.label_alt_id',
+                '_atom_site.label_comp_id', '_atom_site.label_asym_id', '_atom_site.label_entity_id', '_atom_site.label_seq_id',
+                '_atom_site.Cartn_x', '_atom_site.Cartn_y', '_atom_site.Cartn_z', '_atom_site.occupancy', '_atom_site.B_iso_or_equiv',
+                '_atom_site.auth_seq_id', '_atom_site.auth_asym_id', '_atom_site.pdbx_PDB_model_num');
+            var serial = 0, seen = [], r, s, f, g, k, dup, j, sym, el, lab, cart;
+            for (r = 0; r < atoms.rows.length; r++) {
+                var row = atoms.rows[r];
+                if (get(row, '_atom_site_calc_flag') === 'dum') continue; // dummy atoms
+                f = [coreToNumber(get(row, '_atom_site_fract_x')), coreToNumber(get(row, '_atom_site_fract_y')), coreToNumber(get(row, '_atom_site_fract_z'))];
+                lab = get(row, '_atom_site_label');
+                sym = get(row, '_atom_site_type_symbol'); if (sym === '?') sym = lab;
+                el = (sym.match(/^[A-Za-z]{1,2}/) || ['X'])[0];
+                el = el.charAt(0).toUpperCase() + el.substr(1).toLowerCase();
+                var mySeen = [];
+                for (s = 0; s < symops.length; s++) {
+                    g = symops[s](f).map(function (v) { return v - Math.floor(v + 1e-6); });
+                    dup = false;
+                    for (j = 0; j < mySeen.length; j++) {
+                        if (Math.abs(mySeen[j][0] - g[0]) < 1e-3 && Math.abs(mySeen[j][1] - g[1]) < 1e-3 && Math.abs(mySeen[j][2] - g[2]) < 1e-3) { dup = true; break; }
+                    }
+                    if (dup) continue;
+                    mySeen.push(g);
+                    cart = toCart(g);
+                    out.push(['HETATM', ++serial, el, lab, '.', 'MOL', 'A', 1, '.', cart[0].toFixed(3), cart[1].toFixed(3), cart[2].toFixed(3),
+                        coreToNumber(get(row, '_atom_site_occupancy') === '?' ? 1 : get(row, '_atom_site_occupancy')), '0.00', 1, 'A', 1].join(' '));
+                }
+            }
+            out.push('#');
+            return out.join('\n') + '\n';
+        }
         function parse(data) {
+            if (isCoreCif(data)) {
+                var converted = convertCoreCif(data);
+                if (converted) data = converted;
+            }
+            else {
+                // "_cell_angle_alpha" -> "_cell.angle_alpha"
+                data = data.replace(/^(\s*_cell)_(?=\w)/gm, '$1.');
+            }
             return parseInternal(data);
         }
         Text.parse = parse;
@@ -59374,6 +59514,16 @@ class ClickMenu {
            thisClass.setLogCmd('set axis off', true);
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn6_showucYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
+           ic.setOptionCls.setOption('unitcell', 'yes');
+           thisClass.setLogCmd('set unitcell on', true);
+        });
+
+        me.myEventCls.onIds("#" + me.pre + "mn6_showucNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
+           ic.setOptionCls.setOption('unitcell', 'no');
+           thisClass.setLogCmd('set unitcell off', true);
+        });
+
         me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
            ic.bAxisOnly = false;
            await ic.symdCls.retrieveSymmetry(Object.keys(ic.structures)[0]);
@@ -60693,6 +60843,15 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
+        // if(me.cfg.mmcifid !== undefined) {
+            html += this.getMenuText('mn2_unitcell', 'Unit Cell', undefined, undefined, 1);
+            html += "<ul>";
+            html += this.getRadio('mn6_showuc', 'mn6_showucYes', 'Show', undefined, undefined, 2);
+            html += this.getRadio('mn6_showuc', 'mn6_showucNo', 'Hide', true, undefined, 2);
+            html += "</ul>";
+            html += "</li>";
+        // }
+
         html += this.getMenuSep();
 
         html += this.getMenuText('mn2_resetwrap', 'Reset', undefined, 1, 1);
@@ -81656,6 +81815,57 @@ class Axes {
 
        return axisPos;
     }
+
+    buildUnitcell() { let ic = this.icn3d, me = ic.icn3dui;
+        if(!ic.cell) {
+            var aaa = 1; //alert("Unit cell information is available for structures from mmCIF files. Please load a structure with 'mmcifid=', 'bcifid=', or from a mmCIF file.");
+            return;
+        }
+
+        let a = ic.cell.length_a;
+        let b = ic.cell.length_b;
+        let c = ic.cell.length_c;
+        let alpha = ic.cell.angle_alpha;
+        let beta = ic.cell.angle_beta;
+        let gamma = ic.cell.angle_gamma;
+        
+        const rad = d => d * Math.PI / 180;
+        const ca = Math.cos(rad(alpha));
+        const cb = Math.cos(rad(beta));
+        const cg = Math.cos(rad(gamma));
+        const sg = Math.sin(rad(gamma));
+
+        // Lattice vectors
+        const va = [a, 0, 0];
+        const vb = [b * cg, b * sg, 0];
+        const cx = c * cb;
+        const cy = c * (ca - cb * cg) / sg;
+        const cz = Math.sqrt(c * c - cx * cx - cy * cy);
+        const vc = [cx, cy, cz];
+
+        // 8 corners, indexed by bits (i, j, k) -> i*va + j*vb + k*vc
+        const corner = (i, j, k) => [0, 1, 2].map(n => i * va[n] + j * vb[n] + k * vc[n]);
+
+        let color = me.htmlCls.ORANGE, radius = 0.1;
+        let atomColor = me.parasCls.thr(color);
+
+        for (let i = 0; i < 2; i++) {
+            for (let j = 0; j < 2; j++) {
+                ic.analysisCls.addLine(corner(0, i, j)[0], corner(0, i, j)[1], corner(0, i, j)[2], corner(1, i, j)[0], corner(1, i, j)[1], corner(1, i, j)[2], color, false, 'unitcell', radius); // edges along a
+                ic.analysisCls.addLine(corner(i, 0, j)[0], corner(i, 0, j)[1], corner(i, 0, j)[2], corner(i, 1, j)[0], corner(i, 1, j)[1], corner(i, 1, j)[2], color, false, 'unitcell', radius); // edges along b
+                ic.analysisCls.addLine(corner(i, j, 0)[0], corner(i, j, 0)[1], corner(i, j, 0)[2], corner(i, j, 1)[0], corner(i, j, 1)[1], corner(i, j, 1)[2], color, false, 'unitcell', radius); // edges along c
+            }
+        }
+
+        // add sphere at each corner
+        for (let i = 0; i < 2; i++) {
+            for (let j = 0; j < 2; j++) {
+                for (let k = 0; k < 2; k++) {
+                    ic.sphereCls.createSphereBase(new Vector3$1(corner(i, j, k)[0], corner(i, j, k)[1], corner(i, j, k)[2]), atomColor, radius, 1, false, false, 1);
+                }   
+            }
+        }
+    }
 }
 
 /**
@@ -85652,7 +85862,7 @@ class ApplyOther {
         ic.applyCenterCls.applyCenterOptions(options);
 
         ic.axesCls.buildAllAxes(undefined, true);
-
+        
         switch (options.axis.toLowerCase()) {
             case 'yes':
                 ic.axis = true;
@@ -85663,6 +85873,19 @@ class ApplyOther {
                 ic.axis = false;
                 break;
         }
+
+        ic.lines['unitcell'] = []; // reset
+
+        switch (options.unitcell.toLowerCase()) {
+            case 'yes':
+                ic.unitcell = true;
+                ic.axesCls.buildUnitcell();
+
+                break;
+            case 'no':
+                ic.unitcell = false;
+                break;
+        }
         switch (options.pk.toLowerCase()) {
             case 'atom':
                 ic.pk = 1;
@@ -115545,7 +115768,8 @@ class ShowAnno {
         }
 
         let nucleotide_chainid = {}, chemical_chainid = {}, chemical_set = {};
-        //ic.protein_chainid = {};
+        // ic.protein_chainid = {};
+
 
         if(ic.bAnnoShown === undefined || !ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
             ic.protein_chainid = {};
@@ -115572,7 +115796,7 @@ class ShowAnno {
                 dialogWidth =(me.cfg.notebook) ? me.htmlCls.WIDTH / 2 : $("#" + ic.pre + "dl_selectannotations").dialog( "option", "width" );
             }
             ic.seqAnnWidth = dialogWidth - 120 - 30*2 - 50; // title: 120px, start and end resi: 30px, extra space on the left and right: 50px
-            
+ 
             for(let i = 0, il = chainArray.length; i < il; ++i) {
                 if(!ic.chainsSeq[chainArray[i]]) continue; // skip empty chain
 
@@ -115682,8 +115906,8 @@ class ShowAnno {
 
                         await ic.mmcifParserCls.downloadMmcifSymmetry(id, 'mmtfid');
                     }
-                    
-                    await this.showAnnoSeqData(nucleotide_chainid, chemical_chainid, chemical_set);
+                  
+                    await this.showAnnoSeqData(nucleotide_chainid, chemical_chainid, chemical_set);               
                }
             }
             else if(me.cfg.blast_rep_id !== undefined && !ic.bSmithwm && !ic.bLocalSmithwm) { // align sequence to structure
@@ -126183,7 +126407,10 @@ class PdbParser {
 
         ic.saveFileCls.showTitle();
 
-        if(me.cfg.rotate !== undefined) ic.resizeCanvasCls.rotStruc(me.cfg.rotate, true);
+        // if(me.cfg.rotate !== undefined) {
+        if(me.cfg.rotate !== undefined && !(me.cfg.url && me.cfg.url.indexOf('membranome') != -1)) {
+            ic.resizeCanvasCls.rotStruc(me.cfg.rotate, true);
+        }
 
         if(bAppend && Object.keys(ic.structures).length == 1 && !me.bNode) {
             // show all
@@ -130436,6 +130663,7 @@ class ParserUtils {
               let angle = -0.5 * Math.PI;
               ic.transformCls.setRotation(axis, angle);
           }
+
           //if(Object.keys(ic.structures).length > 1) {
           //    $("#" + ic.pre + "alternate").show();
           //}
@@ -134398,6 +134626,16 @@ class LoadCIF {
                 = m24Array = m31Array = m32Array = m33Array = m34Array = [];
             }
 
+            if(block.getCategory("_cell")) {
+                ic.cell = {};
+                ic.cell.length_a = parseFloat(block.getCategory("_cell").getColumn("length_a").getString(0));
+                ic.cell.length_b = parseFloat(block.getCategory("_cell").getColumn("length_b").getString(0));
+                ic.cell.length_c = parseFloat(block.getCategory("_cell").getColumn("length_c").getString(0));
+                ic.cell.angle_alpha = parseFloat(block.getCategory("_cell").getColumn("angle_alpha").getString(0));
+                ic.cell.angle_beta = parseFloat(block.getCategory("_cell").getColumn("angle_beta").getString(0));
+                ic.cell.angle_gamma = parseFloat(block.getCategory("_cell").getColumn("angle_gamma").getString(0));
+            }
+
             // if (record === 'ENDMDL') {
             //     ++moleculeNum;
             //     id = ic.defaultPdbId;
@@ -134510,6 +134748,7 @@ 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) {
@@ -134740,7 +134979,7 @@ class LoadCIF {
                 // if(oriResidueNum !== prevOriResidueNum) {
                 if(oriResidueNum !== prevOriResidueNum || chain + "_" + resn != prevResn || prevAutochain != autochain) {
                     let residue = me.utilsCls.residueName2Abbr(resn);
-                    
+                   
                     ic.residueId2Name[residueNum] = residue;
 
                     if(serial !== 1 && prevResidueNum !== '') {
@@ -134865,7 +135104,7 @@ class LoadCIF {
 
                 resiArray = oriResiArray = resnArray = chainArray = [];
             }
-            
+  
             this.setSeq(structure, sChain, mChainSeq, ligSeqHash);
         }
 
@@ -135067,17 +135306,22 @@ class LoadCIF {
     }
 
     setSeq(structure, sChain, mChainSeq, ligSeqHash) { let ic = this.icn3d; ic.icn3dui;
+        // sometimes a chain appears in both ligSeqHash and mChainSeq, e.g., mmcif data for 1TOP
+/*
         for(let chain in sChain) {
             let chainNum = structure + '_' + chain;
 
-            if(ligSeqHash.hasOwnProperty(chain)) {
+            if(mChainSeq.hasOwnProperty(chain)) {
+                ic.chainsSeq[chainNum] = mChainSeq[chain];
+            }
+            else if(ligSeqHash.hasOwnProperty(chain)) {
                 ic.chainsSeq[chainNum] = ligSeqHash[chain];
             }
             else {
                 ic.chainsSeq[chainNum] = mChainSeq[chain];
             }
         }
-
+*/
         ic.loadPDBCls.setResidMapping();
     }
 }
@@ -136016,6 +136260,14 @@ class ApplyCommand {
         ic.opts['axis'] = 'no';
         ic.pc1 = false;
       }
+      else if(command == 'set unitcell on') {
+        ic.opts['unitcell'] = 'yes';
+        ic.drawCls.draw();
+      }
+      else if(command == 'set unitcell off') {
+        ic.opts['unitcell'] = 'no';
+        ic.drawCls.draw();
+      }
       else if(command == 'set fog on') {
         ic.opts['fog'] = 'yes';
         ic.fogCls.setFog(true);
@@ -146498,9 +146750,10 @@ class Diagram2d {
             // get the residues in the selection
             let ncbiresid = data;
             let resid = ic.ncbi2resid[ncbiresid];
-            let resi = resid.substr(resid.lastIndexOf('_') + 1);
 
-            if(ic.ig2ddgm_chainid && ic.resid2refnum && ic.resid2refnum[resid]) {
+            if(resid && ic.ig2ddgm_chainid && ic.resid2refnum && ic.resid2refnum[resid]) {
+                let resi = resid.substr(resid.lastIndexOf('_') + 1);
+
                 let refnumLabel = ic.resid2refnum[resid];
                 let refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
 
@@ -150273,7 +150526,8 @@ class SaveFile {
                 idName = "PDB ID";
             }
             else if(bAlphaFold) {
-                idName = "AlphaFold ID";
+                // idName = "AlphaFold ID";
+                idName = "ID";
             }
 
             if(structureidArray.length > 1) {
@@ -153194,6 +153448,7 @@ class iCn3D {
     this.radiusArraySphere = new Array();
 
     this.axis = false;  // used to turn on and off xyz axes
+    this.unitcell = false;  // used to turn on and off unit cell
 
     // pk
     //If its value is 1, selecting an atom will select the atom. If its value is 2, selecting an atom
@@ -153315,6 +153570,7 @@ class iCn3D {
     this.optsOri['clbonds']            = 'yes';                 //yes, no
     this.optsOri['rotationcenter']     = 'molecule center';    //molecule center, pick center, display center
     this.optsOri['axis']               = 'no';                 //yes, no
+    this.optsOri['unitcell']           = 'no';                 //yes, no
     this.optsOri['fog']                = 'no';                 //yes, no
     this.optsOri['slab']               = 'no';                 //yes, no
     this.optsOri['pk']                 = 'residue';            //no, atom, residue, strand, chain
@@ -153732,7 +153988,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.54.1';
+    this.REVISION = '3.54.2';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;