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biojs-vis-pdbviewer

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A BioJS 2.0 component to view protein structures

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Clazz.declarePackage ("JS"); Clazz.load (null, "JS.SpaceGroup", ["java.lang.Character", "$.Float", "java.util.Arrays", "$.Hashtable", "JU.AU", "$.Lst", "$.M4", "$.P3", "$.PT", "$.SB", "JS.HallInfo", "$.HallTranslation", "$.SymmetryOperation", "JU.Logger"], function () { c$ = Clazz.decorateAsClass (function () { this.index = 0; this.isSSG = false; this.name = "unknown!"; this.hallSymbol = null; this.hmSymbol = null; this.hmSymbolFull = null; this.hmSymbolExt = null; this.hmSymbolAbbr = null; this.hmSymbolAlternative = null; this.hmSymbolAbbrShort = null; this.ambiguityType = '\0'; this.uniqueAxis = '\0'; this.axisChoice = '\0'; this.intlTableNumber = null; this.intlTableNumberFull = null; this.intlTableNumberExt = null; this.hallInfo = null; this.latticeParameter = 0; this.latticeCode = '\0'; this.operations = null; this.finalOperations = null; this.operationCount = 0; this.latticeOp = -1; this.xyzList = null; this.modDim = 0; this.doNormalize = true; this.isBio = false; this.isBilbao = false; this.latticeOps = null; Clazz.instantialize (this, arguments); }, JS, "SpaceGroup"); c$.getNull = Clazz.defineMethod (c$, "getNull", function (doInit) { JS.SpaceGroup.getSpaceGroups (); return new JS.SpaceGroup (null, doInit); }, "~B"); Clazz.makeConstructor (c$, function (cifLine, doInit) { this.index = ++JS.SpaceGroup.sgIndex; this.init (doInit && cifLine == null); if (!doInit) return; if (cifLine != null) this.buildSpaceGroup (cifLine); }, "~S,~B"); Clazz.defineMethod (c$, "set", function (doNormalize) { this.doNormalize = doNormalize; return this; }, "~B"); Clazz.defineMethod (c$, "init", function (addXYZ) { this.xyzList = new java.util.Hashtable (); this.operationCount = 0; if (addXYZ) this.addSymmetry ("x,y,z", 0, false); }, "~B"); c$.createSpaceGroup = Clazz.defineMethod (c$, "createSpaceGroup", function (desiredSpaceGroupIndex, name, data) { var sg = null; if (desiredSpaceGroupIndex >= 0) { sg = JS.SpaceGroup.getSpaceGroups ()[desiredSpaceGroupIndex]; } else { if (Clazz.instanceOf (data, JU.Lst)) sg = JS.SpaceGroup.createSGFromList (name, data); else sg = JS.SpaceGroup.determineSpaceGroupNA (name, data); if (sg == null) sg = JS.SpaceGroup.createSpaceGroupN (name); }if (sg != null) sg.generateAllOperators (null); return sg; }, "~N,~S,~O"); c$.createSGFromList = Clazz.defineMethod (c$, "createSGFromList", function (name, data) { var sg = new JS.SpaceGroup ("0;--;--;--", true); sg.doNormalize = false; sg.name = name; var n = data.size (); for (var i = 0; i < n; i++) { var operation = data.get (i); if (Clazz.instanceOf (operation, JS.SymmetryOperation)) { var op = operation; var iop = sg.addOp (op, op.xyz, false); sg.operations[iop].timeReversal = op.timeReversal; } else { sg.addSymmetrySM ("xyz matrix:" + operation, operation); }} var sgn = sg.getDerivedSpaceGroup (); if (sgn != null) sg = sgn; return sg; }, "~S,JU.Lst"); Clazz.defineMethod (c$, "addSymmetry", function (xyz, opId, allowScaling) { xyz = xyz.toLowerCase (); return (xyz.indexOf ("[[") < 0 && xyz.indexOf ("x4") < 0 && xyz.indexOf (";") < 0 && (xyz.indexOf ("x") < 0 || xyz.indexOf ("y") < 0 || xyz.indexOf ("z") < 0) ? -1 : this.addOperation (xyz, opId, allowScaling)); }, "~S,~N,~B"); Clazz.defineMethod (c$, "setFinalOperations", function (atoms, atomIndex, count, doNormalize) { if (this.hallInfo == null && this.latticeParameter != 0) { var h = new JS.HallInfo (JS.HallTranslation.getHallLatticeEquivalent (this.latticeParameter)); this.generateAllOperators (h); }this.finalOperations = null; this.isBio = (this.name.indexOf ("bio") >= 0); if (this.index >= JS.SpaceGroup.getSpaceGroups ().length && !this.isBio && this.name.indexOf ("SSG:") < 0 && this.name.indexOf ("[subsystem") < 0) { var sg = this.getDerivedSpaceGroup (); if (sg != null) this.name = sg.getName (); }this.finalOperations = new Array (this.operationCount); if (doNormalize && count > 0 && atoms != null) { this.finalOperations[0] = new JS.SymmetryOperation (this.operations[0], atoms, atomIndex, count, true); var atom = atoms[atomIndex]; var c = JU.P3.newP (atom); this.finalOperations[0].rotTrans (c); if (c.distance (atom) > 0.0001) for (var i = 0; i < count; i++) { atom = atoms[atomIndex + i]; c.setT (atom); this.finalOperations[0].rotTrans (c); atom.setT (c); } }var centering = null; for (var i = 0; i < this.operationCount; i++) { this.finalOperations[i] = new JS.SymmetryOperation (this.operations[i], atoms, atomIndex, count, doNormalize); centering = this.finalOperations[i].setCentering (centering, true); } }, "~A,~N,~N,~B"); Clazz.defineMethod (c$, "getOperationCount", function () { return this.finalOperations.length; }); Clazz.defineMethod (c$, "getOperation", function (i) { return this.finalOperations[i]; }, "~N"); Clazz.defineMethod (c$, "getXyz", function (i, doNormalize) { return (this.finalOperations == null ? this.operations[i].getXyz (doNormalize) : this.finalOperations[i].getXyz (doNormalize)); }, "~N,~B"); Clazz.defineMethod (c$, "newPoint", function (i, atom1, atom2, transX, transY, transZ) { this.finalOperations[i].newPoint (atom1, atom2, transX, transY, transZ); }, "~N,JU.P3,JU.P3,~N,~N,~N"); c$.getInfo = Clazz.defineMethod (c$, "getInfo", function (spaceGroup, cellInfo) { var sg; if (cellInfo != null) { if (spaceGroup.indexOf ("[") >= 0) spaceGroup = spaceGroup.substring (0, spaceGroup.indexOf ("[")).trim (); if (spaceGroup.equals ("unspecified!")) return "no space group identified in file"; sg = JS.SpaceGroup.determineSpaceGroupNA (spaceGroup, cellInfo.getNotionalUnitCell ()); } else if (spaceGroup.equalsIgnoreCase ("ALL")) { return JS.SpaceGroup.dumpAll (); } else if (spaceGroup.equalsIgnoreCase ("ALLSEITZ")) { return JS.SpaceGroup.dumpAllSeitz (); } else { sg = JS.SpaceGroup.determineSpaceGroupN (spaceGroup); if (sg == null) { sg = JS.SpaceGroup.createSpaceGroupN (spaceGroup); } else { var sb = new JU.SB (); while (sg != null) { sb.append (sg.dumpInfo (null)); sg = JS.SpaceGroup.determineSpaceGroupNS (spaceGroup, sg); } return sb.toString (); }}return sg == null ? "?" : sg.dumpInfo (cellInfo); }, "~S,J.api.SymmetryInterface"); Clazz.defineMethod (c$, "dumpInfo", function (cellInfo) { var info = this.dumpCanonicalSeitzList (); if (Clazz.instanceOf (info, JS.SpaceGroup)) return (info).dumpInfo (null); var sb = new JU.SB ().append ("\nHermann-Mauguin symbol: "); sb.append (this.hmSymbol).append (this.hmSymbolExt.length > 0 ? ":" + this.hmSymbolExt : "").append ("\ninternational table number: ").append (this.intlTableNumber).append (this.intlTableNumberExt.length > 0 ? ":" + this.intlTableNumberExt : "").append ("\n\n").appendI (this.operationCount).append (" operators").append (!this.hallInfo.hallSymbol.equals ("--") ? " from Hall symbol " + this.hallInfo.hallSymbol : "").append (": "); for (var i = 0; i < this.operationCount; i++) { sb.append ("\n").append (this.operations[i].xyz); } sb.append ("\n\n").append (this.hallInfo == null ? "invalid Hall symbol" : this.hallInfo.dumpInfo ()); sb.append ("\n\ncanonical Seitz: ").append (info).append ("\n----------------------------------------------------\n"); return sb.toString (); }, "J.api.SymmetryInterface"); Clazz.defineMethod (c$, "getName", function () { return this.name; }); Clazz.defineMethod (c$, "getLatticeDesignation", function () { return this.latticeCode + ": " + JS.HallTranslation.getLatticeDesignation (this.latticeParameter); }); Clazz.defineMethod (c$, "setLatticeParam", function (latticeParameter) { this.latticeParameter = latticeParameter; this.latticeCode = JS.HallTranslation.getLatticeCode (latticeParameter); if (latticeParameter > 10) { this.latticeParameter = -JS.HallTranslation.getLatticeIndex (this.latticeCode); }}, "~N"); Clazz.defineMethod (c$, "dumpCanonicalSeitzList", function () { if (this.hallInfo == null) this.hallInfo = new JS.HallInfo (this.hallSymbol); this.generateAllOperators (null); var s = this.getCanonicalSeitzList (); if (this.index >= JS.SpaceGroup.SG.length) { var sgDerived = JS.SpaceGroup.findSpaceGroup (s); if (sgDerived != null) return sgDerived; }return (this.index >= 0 && this.index < JS.SpaceGroup.SG.length ? this.hallSymbol + " = " : "") + s; }); Clazz.defineMethod (c$, "getDerivedSpaceGroup", function () { if (this.index >= 0 && this.index < JS.SpaceGroup.SG.length || this.modDim > 0 || this.operations == null || this.operations.length == 0 || this.operations[0].timeReversal != 0) return this; if (this.finalOperations != null) this.setFinalOperations (null, 0, 0, false); var s = this.getCanonicalSeitzList (); return (s == null ? null : JS.SpaceGroup.findSpaceGroup (s)); }); Clazz.defineMethod (c$, "getCanonicalSeitzList", function () { var list = new Array (this.operationCount); for (var i = 0; i < this.operationCount; i++) list[i] = JS.SymmetryOperation.dumpSeitz (this.operations[i], true); java.util.Arrays.sort (list, 0, this.operationCount); var sb = new JU.SB ().append ("\n["); for (var i = 0; i < this.operationCount; i++) sb.append (list[i].$replace ('\t', ' ').$replace ('\n', ' ')).append ("; "); sb.append ("]"); return sb.toString (); }); c$.findSpaceGroup = Clazz.defineMethod (c$, "findSpaceGroup", function (s) { JS.SpaceGroup.getSpaceGroups (); if (JS.SpaceGroup.canonicalSeitzList == null) JS.SpaceGroup.canonicalSeitzList = new Array (JS.SpaceGroup.SG.length); for (var i = 0; i < JS.SpaceGroup.SG.length; i++) { if (JS.SpaceGroup.canonicalSeitzList[i] == null) JS.SpaceGroup.canonicalSeitzList[i] = JS.SpaceGroup.SG[i].dumpCanonicalSeitzList (); if (JS.SpaceGroup.canonicalSeitzList[i].indexOf (s) >= 0) return JS.SpaceGroup.SG[i]; } return null; }, "~S"); c$.dumpAll = Clazz.defineMethod (c$, "dumpAll", function () { var sb = new JU.SB (); JS.SpaceGroup.getSpaceGroups (); for (var i = 0; i < JS.SpaceGroup.SG.length; i++) sb.append ("\n----------------------\n" + JS.SpaceGroup.SG[i].dumpInfo (null)); return sb.toString (); }); c$.dumpAllSeitz = Clazz.defineMethod (c$, "dumpAllSeitz", function () { JS.SpaceGroup.getSpaceGroups (); var sb = new JU.SB (); for (var i = 0; i < JS.SpaceGroup.SG.length; i++) sb.append ("\n").appendO (JS.SpaceGroup.SG[i].dumpCanonicalSeitzList ()); return sb.toString (); }); Clazz.defineMethod (c$, "setLattice", function (latticeCode, isCentrosymmetric) { this.latticeCode = latticeCode; this.latticeParameter = JS.HallTranslation.getLatticeIndex (latticeCode); if (!isCentrosymmetric) this.latticeParameter = -this.latticeParameter; }, "~S,~B"); c$.createSpaceGroupN = Clazz.defineMethod (c$, "createSpaceGroupN", function (name) { JS.SpaceGroup.getSpaceGroups (); name = name.trim (); var sg = JS.SpaceGroup.determineSpaceGroupN (name); var hallInfo; if (sg == null) { hallInfo = new JS.HallInfo (name); if (hallInfo.nRotations > 0) { sg = new JS.SpaceGroup ("0;--;--;" + name, true); sg.hallInfo = hallInfo; } else if (name.indexOf (",") >= 0) { sg = new JS.SpaceGroup ("0;--;--;--", true); sg.doNormalize = false; sg.generateOperatorsFromXyzInfo (name); }}if (sg != null) sg.generateAllOperators (null); return sg; }, "~S"); Clazz.defineMethod (c$, "addOperation", function (xyz0, opId, allowScaling) { if (xyz0 == null || xyz0.length < 3) { this.init (false); return -1; }var isSpecial = (xyz0.charAt (0) == '='); if (isSpecial) xyz0 = xyz0.substring (1); if (this.xyzList.containsKey (xyz0)) return this.xyzList.get (xyz0).intValue (); if (xyz0.startsWith ("x1,x2,x3,x4") && this.modDim == 0) { this.xyzList.clear (); this.operationCount = 0; this.modDim = JU.PT.parseInt (xyz0.substring (xyz0.lastIndexOf ("x") + 1)) - 3; } else if (xyz0.equals ("x,y,z,m+1")) { this.xyzList.clear (); this.operationCount = 0; }var op = new JS.SymmetryOperation (null, null, 0, opId, this.doNormalize); if (!op.setMatrixFromXYZ (xyz0, this.modDim, allowScaling)) { JU.Logger.error ("couldn't interpret symmetry operation: " + xyz0); return -1; }return this.addOp (op, xyz0, isSpecial); }, "~S,~N,~B"); Clazz.defineMethod (c$, "addOp", function (op, xyz0, isSpecial) { var ext = ""; var xyz = op.xyz + ext; var xxx = JU.PT.replaceAllCharacters (xyz, "+123/", ""); if (!isSpecial) { if (this.xyzList.containsKey (xyz)) return this.xyzList.get (xyz).intValue (); if (this.latticeOp < 0) { if (this.xyzList.containsKey (xxx)) this.latticeOp = this.operationCount; else this.xyzList.put (xxx, Integer.$valueOf (this.operationCount)); }this.xyzList.put (xyz, Integer.$valueOf (this.operationCount)); }if (!xyz.equals (xyz0 + ext)) this.xyzList.put (xyz0 + ext, Integer.$valueOf (this.operationCount)); if (this.operations == null) this.operations = new Array (4); if (this.operationCount == this.operations.length) this.operations = JU.AU.arrayCopyObject (this.operations, this.operationCount * 2); this.operations[this.operationCount++] = op; op.index = this.operationCount; if (JU.Logger.debugging) JU.Logger.debug ("\naddOperation " + this.operationCount + op.dumpInfo ()); return this.operationCount - 1; }, "JS.SymmetryOperation,~S,~B"); Clazz.defineMethod (c$, "generateOperatorsFromXyzInfo", function (xyzInfo) { this.init (true); var terms = JU.PT.split (xyzInfo.toLowerCase (), ";"); for (var i = 0; i < terms.length; i++) this.addSymmetry (terms[i], 0, false); }, "~S"); Clazz.defineMethod (c$, "generateAllOperators", function (h) { if (h == null) { h = this.hallInfo; if (this.operationCount > 0) return; this.operations = new Array (4); if (this.hallInfo == null || this.hallInfo.nRotations == 0) h = this.hallInfo = new JS.HallInfo (this.hallSymbol); this.setLattice (this.hallInfo.latticeCode, this.hallInfo.isCentrosymmetric); this.init (true); }var mat1 = new JU.M4 (); var operation = new JU.M4 (); var newOps = new Array (7); for (var i = 0; i < 7; i++) newOps[i] = new JU.M4 (); for (var i = 0; i < h.nRotations; i++) { mat1.setM4 (h.rotationTerms[i].seitzMatrix12ths); var nRot = h.rotationTerms[i].order; newOps[0].setIdentity (); var nOps = this.operationCount; for (var j = 1; j <= nRot; j++) { newOps[j].mul2 (mat1, newOps[0]); newOps[0].setM4 (newOps[j]); for (var k = 0; k < nOps; k++) { operation.mul2 (newOps[j], this.operations[k]); JS.SymmetryOperation.normalizeTranslation (operation); var xyz = JS.SymmetryOperation.getXYZFromMatrix (operation, true, true, true); this.addSymmetrySM (xyz, operation); } } } }, "JS.HallInfo"); Clazz.defineMethod (c$, "addSymmetrySM", function (xyz, operation) { var iop = this.addOperation (xyz, 0, false); if (iop >= 0) { var symmetryOperation = this.operations[iop]; symmetryOperation.setM4 (operation); }return iop; }, "~S,JU.M4"); c$.determineSpaceGroupN = Clazz.defineMethod (c$, "determineSpaceGroupN", function (name) { return JS.SpaceGroup.determineSpaceGroup (name, 0, 0, 0, 0, 0, 0, -1); }, "~S"); c$.determineSpaceGroupNS = Clazz.defineMethod (c$, "determineSpaceGroupNS", function (name, sg) { return JS.SpaceGroup.determineSpaceGroup (name, 0, 0, 0, 0, 0, 0, sg.index); }, "~S,JS.SpaceGroup"); c$.determineSpaceGroupNA = Clazz.defineMethod (c$, "determineSpaceGroupNA", function (name, notionalUnitcell) { return (notionalUnitcell == null ? JS.SpaceGroup.determineSpaceGroup (name, 0, 0, 0, 0, 0, 0, -1) : JS.SpaceGroup.determineSpaceGroup (name, notionalUnitcell[0], notionalUnitcell[1], notionalUnitcell[2], notionalUnitcell[3], notionalUnitcell[4], notionalUnitcell[5], -1)); }, "~S,~A"); c$.determineSpaceGroup = Clazz.defineMethod (c$, "determineSpaceGroup", function (name, a, b, c, alpha, beta, gamma, lastIndex) { var i = JS.SpaceGroup.determineSpaceGroupIndex (name, a, b, c, alpha, beta, gamma, lastIndex); return (i >= 0 ? JS.SpaceGroup.SG[i] : null); }, "~S,~N,~N,~N,~N,~N,~N,~N"); c$.determineSpaceGroupIndex = Clazz.defineMethod (c$, "determineSpaceGroupIndex", function (name, a, b, c, alpha, beta, gamma, lastIndex) { JS.SpaceGroup.getSpaceGroups (); if (lastIndex < 0) lastIndex = JS.SpaceGroup.SG.length; name = name.trim ().toLowerCase (); var checkBilbao = false; if (name.startsWith ("bilbao:")) { checkBilbao = true; name = name.substring (7); }var nameType = (name.startsWith ("hall:") ? 5 : name.startsWith ("hm:") ? 3 : 0); if (nameType > 0) name = name.substring (nameType); else if (name.contains ("[")) { nameType = 5; name = name.substring (0, name.indexOf ("[")).trim (); }var nameExt = name; var i; var haveExtension = false; name = name.$replace ('_', ' '); if (name.length >= 2) { i = (name.indexOf ("-") == 0 ? 2 : 1); if (i < name.length && name.charAt (i) != ' ') name = name.substring (0, i) + " " + name.substring (i); name = name.substring (0, 2).toUpperCase () + name.substring (2); }var ext = ""; if ((i = name.indexOf (":")) > 0) { ext = name.substring (i + 1); name = name.substring (0, i).trim (); haveExtension = true; }if (nameType != 5 && !haveExtension && JU.PT.isOneOf (name, JS.SpaceGroup.ambiguousNames)) { ext = "?"; haveExtension = true; }var abbr = JU.PT.replaceAllCharacters (name, " ()", ""); var s; if (nameType != 3 && !haveExtension) for (i = lastIndex; --i >= 0; ) { s = JS.SpaceGroup.SG[i]; if (s.hallSymbol.equals (name)) return i; } if (nameType != 5) { if (nameType != 3) for (i = lastIndex; --i >= 0; ) { s = JS.SpaceGroup.SG[i]; if (s.intlTableNumberFull.equals (nameExt)) return i; } for (i = lastIndex; --i >= 0; ) { s = JS.SpaceGroup.SG[i]; if (s.hmSymbolFull.equals (nameExt)) return i; } for (i = lastIndex; --i >= 0; ) { s = JS.SpaceGroup.SG[i]; if (s.hmSymbolAlternative != null && s.hmSymbolAlternative.equals (nameExt)) return i; } if (haveExtension) for (i = lastIndex; --i >= 0; ) { s = JS.SpaceGroup.SG[i]; if (s.hmSymbolAbbr.equals (abbr) && s.intlTableNumberExt.equals (ext)) return i; } if (haveExtension) for (i = lastIndex; --i >= 0; ) { s = JS.SpaceGroup.SG[i]; if (s.hmSymbolAbbrShort.equals (abbr) && s.intlTableNumberExt.equals (ext)) return i; } var uniqueAxis = JS.SpaceGroup.determineUniqueAxis (a, b, c, alpha, beta, gamma); if (!haveExtension || ext.charAt (0) == '?') for (i = lastIndex; --i >= 0; ) { s = JS.SpaceGroup.SG[i]; if (s.hmSymbolAbbr.equals (abbr) || s.hmSymbolAbbrShort.equals (abbr)) { switch (s.ambiguityType) { case '\0': return i; case 'a': if (s.uniqueAxis == uniqueAxis || uniqueAxis == '\0') return i; break; case 'o': if (ext.length == 0) { if (s.hmSymbolExt.equals ("2")) return i; } else if (s.hmSymbolExt.equals (ext)) return i; break; case 't': if (ext.length == 0) { if (s.axisChoice == 'h') return i; } else if ((s.axisChoice + "").equals (ext)) return i; break; } }} }if (ext.length == 0) for (i = 0; i < lastIndex; i++) { s = JS.SpaceGroup.SG[i]; if (s.intlTableNumber.equals (nameExt) && (!checkBilbao || s.isBilbao)) return i; } return -1; }, "~S,~N,~N,~N,~N,~N,~N,~N"); c$.determineUniqueAxis = Clazz.defineMethod (c$, "determineUniqueAxis", function (a, b, c, alpha, beta, gamma) { if (a == b) return (b == c ? '\0' : 'c'); if (b == c) return 'a'; if (c == a) return 'b'; if (alpha == beta) return (beta == gamma ? '\0' : 'c'); if (beta == gamma) return 'a'; if (gamma == alpha) return 'b'; return '\0'; }, "~N,~N,~N,~N,~N,~N"); Clazz.defineMethod (c$, "buildSpaceGroup", function (cifLine) { var terms = JU.PT.split (cifLine.toLowerCase (), ";"); this.intlTableNumberFull = terms[0].trim (); this.isBilbao = (terms.length < 5 && !this.intlTableNumberFull.equals ("0")); var parts = JU.PT.split (this.intlTableNumberFull, ":"); this.intlTableNumber = parts[0]; this.intlTableNumberExt = (parts.length == 1 ? "" : parts[1]); this.ambiguityType = '\0'; if (this.intlTableNumberExt.length > 0) { var term = this.intlTableNumberExt; if (term.startsWith ("-")) term = term.substring (1); if (term.equals ("h") || term.equals ("r")) { this.ambiguityType = 't'; this.axisChoice = this.intlTableNumberExt.charAt (0); } else if (this.intlTableNumberExt.startsWith ("1") || this.intlTableNumberExt.startsWith ("2")) { this.ambiguityType = 'o'; } else if (this.intlTableNumberExt.length <= 2) { this.ambiguityType = 'a'; this.uniqueAxis = this.intlTableNumberExt.charAt (0); }}this.hmSymbolFull = Character.toUpperCase (terms[2].charAt (0)) + terms[2].substring (1); parts = JU.PT.split (this.hmSymbolFull, ":"); this.hmSymbol = parts[0]; this.hmSymbolExt = (parts.length == 1 ? "" : parts[1]); var pt = this.hmSymbol.indexOf (" -3"); if (pt >= 1) if ("admn".indexOf (this.hmSymbol.charAt (pt - 1)) >= 0) { this.hmSymbolAlternative = (this.hmSymbol.substring (0, pt) + " 3" + this.hmSymbol.substring (pt + 3)).toLowerCase (); }this.hmSymbolAbbr = JU.PT.rep (this.hmSymbol, " ", ""); this.hmSymbolAbbrShort = JU.PT.rep (this.hmSymbol, " 1", ""); this.hmSymbolAbbrShort = JU.PT.rep (this.hmSymbolAbbrShort, " ", ""); this.hallSymbol = terms[3]; if (this.hallSymbol.length > 1) this.hallSymbol = this.hallSymbol.substring (0, 2).toUpperCase () + this.hallSymbol.substring (2); var info = this.intlTableNumber + this.hallSymbol; if (this.intlTableNumber.charAt (0) != '0' && JS.SpaceGroup.lastInfo.equals (info)) JS.SpaceGroup.ambiguousNames += this.hmSymbol + ";"; JS.SpaceGroup.lastInfo = info; this.name = this.hallSymbol + " [" + this.hmSymbolFull + "] #" + this.intlTableNumber; }, "~S"); c$.getSpaceGroups = Clazz.defineMethod (c$, "getSpaceGroups", function () { return (JS.SpaceGroup.SG == null ? (JS.SpaceGroup.SG = JS.SpaceGroup.createSpaceGroups ()) : JS.SpaceGroup.SG); }); c$.createSpaceGroups = Clazz.defineMethod (c$, "createSpaceGroups", function () { var n = JS.SpaceGroup.STR_SG.length; var defs = new Array (n); for (var i = 0; i < n; i++) defs[i] = new JS.SpaceGroup (JS.SpaceGroup.STR_SG[i], true); JS.SpaceGroup.STR_SG = null; return defs; }); Clazz.defineMethod (c$, "addLatticeVectors", function (lattvecs) { if (this.latticeOp >= 0) return false; var nOps = this.latticeOp = this.operationCount; for (var j = 0; j < lattvecs.size (); j++) { var data = lattvecs.get (j); var magRev = Clazz.floatToInt (data.length == 5 && Float.isNaN (data[4]) ? data[3] : -2); if (magRev != -2) data = [data[0], data[1], data[2]]; if (data.length > this.modDim + 3) return false; for (var i = 0; i < nOps; i++) { var newOp = new JS.SymmetryOperation (null, null, 0, 0, this.doNormalize); newOp.modDim = this.modDim; var op = this.operations[i]; newOp.linearRotTrans = JU.AU.arrayCopyF (op.linearRotTrans, -1); newOp.setFromMatrix (data, false); newOp.xyzOriginal = newOp.xyz; if (magRev != -2) newOp.setTimeReversal (op.timeReversal * magRev); this.addOp (newOp, newOp.xyz, true); } } return true; }, "JU.Lst"); Clazz.defineMethod (c$, "getSiteMultiplicity", function (pt, unitCell) { var n = this.finalOperations.length; var pts = new JU.Lst (); for (var i = n; --i >= 0; ) { var pt1 = JU.P3.newP (pt); this.finalOperations[i].rotTrans (pt1); unitCell.unitize (pt1); for (var j = pts.size (); --j >= 0; ) { var pt0 = pts.get (j); if (pt1.distanceSquared (pt0) < 0.000001) { pt1 = null; break; }} if (pt1 != null) pts.addLast (pt1); } return Clazz.doubleToInt (n / pts.size ()); }, "JU.P3,JS.UnitCell"); Clazz.defineMethod (c$, "getAllLatticeOps", function () { if (this.latticeOp < 0 || this.modDim > 0) return null; if (this.latticeOps == null) { this.latticeOps = Clazz.newIntArray (3, 0); var nOps = 0; for (var i = this.latticeOp; i < this.operationCount; i++) { var o = this.finalOperations[i]; if (o.m00 + o.m01 + o.m02 == 3) { System.out.println ("spacegroup " + o); this.latticeOps[nOps++] = i; }} }return this.latticeOps; }); Clazz.defineStatics (c$, "canonicalSeitzList", null, "NAME_HALL", 5, "NAME_HM", 3, "sgIndex", -1, "ambiguousNames", "", "lastInfo", "", "SG", null, "STR_SG", ["1;c1^1;p 1;p 1", "2;ci^1;p -1;-p 1", "3:b;c2^1;p 1 2 1;p 2y", "3:b;c2^1;p 2;p 2y", "3:c;c2^1;p 1 1 2;p 2", "3:a;c2^1;p 2 1 1;p 2x", "4:b;c2^2;p 1 21 1;p 2yb", "4:b;c2^2;p 21;p 2yb", "4:b*;c2^2;p 1 21 1*;p 2y1", "4:c;c2^2;p 1 1 21;p 2c", "4:c*;c2^2;p 1 1 21*;p 21", "4:a;c2^2;p 21 1 1;p 2xa", "4:a*;c2^2;p 21 1 1*;p 2x1", "5:b1;c2^3;c 1 2 1;c 2y", "5:b1;c2^3;c 2;c 2y", "5:b2;c2^3;a 1 2 1;a 2y", "5:b3;c2^3;i 1 2 1;i 2y", "5:c1;c2^3;a 1 1 2;a 2", "5:c2;c2^3;b 1 1 2;b 2", "5:c3;c2^3;i 1 1 2;i 2", "5:a1;c2^3;b 2 1 1;b 2x", "5:a2;c2^3;c 2 1 1;c 2x", "5:a3;c2^3;i 2 1 1;i 2x", "6:b;cs^1;p 1 m 1;p -2y", "6:b;cs^1;p m;p -2y", "6:c;cs^1;p 1 1 m;p -2", "6:a;cs^1;p m 1 1;p -2x", "7:b1;cs^2;p 1 c 1;p -2yc", "7:b1;cs^2;p c;p -2yc", "7:b2;cs^2;p 1 n 1;p -2yac", "7:b2;cs^2;p n;p -2yac", "7:b3;cs^2;p 1 a 1;p -2ya", "7:b3;cs^2;p a;p -2ya", "7:c1;cs^2;p 1 1 a;p -2a", "7:c2;cs^2;p 1 1 n;p -2ab", "7:c3;cs^2;p 1 1 b;p -2b", "7:a1;cs^2;p b 1 1;p -2xb", "7:a2;cs^2;p n 1 1;p -2xbc", "7:a3;cs^2;p c 1 1;p -2xc", "8:b1;cs^3;c 1 m 1;c -2y", "8:b1;cs^3;c m;c -2y", "8:b2;cs^3;a 1 m 1;a -2y", "8:b3;cs^3;i 1 m 1;i -2y", "8:b3;cs^3;i m;i -2y", "8:c1;cs^3;a 1 1 m;a -2", "8:c2;cs^3;b 1 1 m;b -2", "8:c3;cs^3;i 1 1 m;i -2", "8:a1;cs^3;b m 1 1;b -2x", "8:a2;cs^3;c m 1 1;c -2x", "8:a3;cs^3;i m 1 1;i -2x", "9:b1;cs^4;c 1 c 1;c -2yc", "9:b1;cs^4;c c;c -2yc", "9:b2;cs^4;a 1 n 1;a -2yab", "9:b3;cs^4;i 1 a 1;i -2ya", "9:-b1;cs^4;a 1 a 1;a -2ya", "9:-b2;cs^4;c 1 n 1;c -2yac", "9:-b3;cs^4;i 1 c 1;i -2yc", "9:c1;cs^4;a 1 1 a;a -2a", "9:c2;cs^4;b 1 1 n;b -2ab", "9:c3;cs^4;i 1 1 b;i -2b", "9:-c1;cs^4;b 1 1 b;b -2b", "9:-c2;cs^4;a 1 1 n;a -2ab", "9:-c3;cs^4;i 1 1 a;i -2a", "9:a1;cs^4;b b 1 1;b -2xb", "9:a2;cs^4;c n 1 1;c -2xac", "9:a3;cs^4;i c 1 1;i -2xc", "9:-a1;cs^4;c c 1 1;c -2xc", "9:-a2;cs^4;b n 1 1;b -2xab", "9:-a3;cs^4;i b 1 1;i -2xb", "10:b;c2h^1;p 1 2/m 1;-p 2y", "10:b;c2h^1;p 2/m;-p 2y", "10:c;c2h^1;p 1 1 2/m;-p 2", "10:a;c2h^1;p 2/m 1 1;-p 2x", "11:b;c2h^2;p 1 21/m 1;-p 2yb", "11:b;c2h^2;p 21/m;-p 2yb", "11:b*;c2h^2;p 1 21/m 1*;-p 2y1", "11:c;c2h^2;p 1 1 21/m;-p 2c", "11:c*;c2h^2;p 1 1 21/m*;-p 21", "11:a;c2h^2;p 21/m 1 1;-p 2xa", "11:a*;c2h^2;p 21/m 1 1*;-p 2x1", "12:b1;c2h^3;c 1 2/m 1;-c 2y", "12:b1;c2h^3;c 2/m;-c 2y", "12:b2;c2h^3;a 1 2/m 1;-a 2y", "12:b3;c2h^3;i 1 2/m 1;-i 2y", "12:b3;c2h^3;i 2/m;-i 2y", "12:c1;c2h^3;a 1 1 2/m;-a 2", "12:c2;c2h^3;b 1 1 2/m;-b 2", "12:c3;c2h^3;i 1 1 2/m;-i 2", "12:a1;c2h^3;b 2/m 1 1;-b 2x", "12:a2;c2h^3;c 2/m 1 1;-c 2x", "12:a3;c2h^3;i 2/m 1 1;-i 2x", "13:b1;c2h^4;p 1 2/c 1;-p 2yc", "13:b1;c2h^4;p 2/c;-p 2yc", "13:b2;c2h^4;p 1 2/n 1;-p 2yac", "13:b2;c2h^4;p 2/n;-p 2yac", "13:b3;c2h^4;p 1 2/a 1;-p 2ya", "13:b3;c2h^4;p 2/a;-p 2ya", "13:c1;c2h^4;p 1 1 2/a;-p 2a", "13:c2;c2h^4;p 1 1 2/n;-p 2ab", "13:c3;c2h^4;p 1 1 2/b;-p 2b", "13:a1;c2h^4;p 2/b 1 1;-p 2xb", "13:a2;c2h^4;p 2/n 1 1;-p 2xbc", "13:a3;c2h^4;p 2/c 1 1;-p 2xc", "14:b1;c2h^5;p 1 21/c 1;-p 2ybc", "14:b1;c2h^5;p 21/c;-p 2ybc", "14:b2;c2h^5;p 1 21/n 1;-p 2yn", "14:b2;c2h^5;p 21/n;-p 2yn", "14:b3;c2h^5;p 1 21/a 1;-p 2yab", "14:b3;c2h^5;p 21/a;-p 2yab", "14:c1;c2h^5;p 1 1 21/a;-p 2ac", "14:c2;c2h^5;p 1 1 21/n;-p 2n", "14:c3;c2h^5;p 1 1 21/b;-p 2bc", "14:a1;c2h^5;p 21/b 1 1;-p 2xab", "14:a2;c2h^5;p 21/n 1 1;-p 2xn", "14:a3;c2h^5;p 21/c 1 1;-p 2xac", "15:b1;c2h^6;c 1 2/c 1;-c 2yc", "15:b1;c2h^6;c 2/c;-c 2yc", "15:b2;c2h^6;a 1 2/n 1;-a 2yab", "15:b3;c2h^6;i 1 2/a 1;-i 2ya", "15:b3;c2h^6;i 2/a;-i 2ya", "15:-b1;c2h^6;a 1 2/a 1;-a 2ya", "15:-b2;c2h^6;c 1 2/n 1;-c 2yac", "15:-b2;c2h^6;c 2/n;-c 2yac", "15:-b3;c2h^6;i 1 2/c 1;-i 2yc", "15:-b3;c2h^6;i 2/c;-i 2yc", "15:c1;c2h^6;a 1 1 2/a;-a 2a", "15:c2;c2h^6;b 1 1 2/n;-b 2ab", "15:c3;c2h^6;i 1 1 2/b;-i 2b", "15:-c1;c2h^6;b 1 1 2/b;-b 2b", "15:-c2;c2h^6;a 1 1 2/n;-a 2ab", "15:-c3;c2h^6;i 1 1 2/a;-i 2a", "15:a1;c2h^6;b 2/b 1 1;-b 2xb", "15:a2;c2h^6;c 2/n 1 1;-c 2xac", "15:a3;c2h^6;i 2/c 1 1;-i 2xc", "15:-a1;c2h^6;c 2/c 1 1;-c 2xc", "15:-a2;c2h^6;b 2/n 1 1;-b 2xab", "15:-a3;c2h^6;i 2/b 1 1;-i 2xb", "16;d2^1;p 2 2 2;p 2 2", "17;d2^2;p 2 2 21;p 2c 2", "17*;d2^2;p 2 2 21*;p 21 2", "17:cab;d2^2;p 21 2 2;p 2a 2a", "17:bca;d2^2;p 2 21 2;p 2 2b", "18;d2^3;p 21 21 2;p 2 2ab", "18:cab;d2^3;p 2 21 21;p 2bc 2", "18:bca;d2^3;p 21 2 21;p 2ac 2ac", "19;d2^4;p 21 21 21;p 2ac 2ab", "20;d2^5;c 2 2 21;c 2c 2", "20*;d2^5;c 2 2 21*;c 21 2", "20:cab;d2^5;a 21 2 2;a 2a 2a", "20:cab*;d2^5;a 21 2 2*;a 2a 21", "20:bca;d2^5;b 2 21 2;b 2 2b", "21;d2^6;c 2 2 2;c 2 2", "21:cab;d2^6;a 2 2 2;a 2 2", "21:bca;d2^6;b 2 2 2;b 2 2", "22;d2^7;f 2 2 2;f 2 2", "23;d2^8;i 2 2 2;i 2 2", "24;d2^9;i 21 21 21;i 2b 2c", "25;c2v^1;p m m 2;p 2 -2", "25:cab;c2v^1;p 2 m m;p -2 2", "25:bca;c2v^1;p m 2 m;p -2 -2", "26;c2v^2;p m c 21;p 2c -2", "26*;c2v^2;p m c 21*;p 21 -2", "26:ba-c;c2v^2;p c m 21;p 2c -2c", "26:ba-c*;c2v^2;p c m 21*;p 21 -2c", "26:cab;c2v^2;p 21 m a;p -2a 2a", "26:-cba;c2v^2;p 21 a m;p -2 2a", "26:bca;c2v^2;p b 21 m;p -2 -2b", "26:a-cb;c2v^2;p m 21 b;p -2b -2", "27;c2v^3;p c c 2;p 2 -2c", "27:cab;c2v^3;p 2 a a;p -2a 2", "27:bca;c2v^3;p b 2 b;p -2b -2b", "28;c2v^4;p m a 2;p 2 -2a", "28*;c2v^4;p m a 2*;p 2 -21", "28:ba-c;c2v^4;p b m 2;p 2 -2b", "28:cab;c2v^4;p 2 m b;p -2b 2", "28:-cba;c2v^4;p 2 c m;p -2c 2", "28:-cba*;c2v^4;p 2 c m*;p -21 2", "28:bca;c2v^4;p c 2 m;p -2c -2c", "28:a-cb;c2v^4;p m 2 a;p -2a -2a", "29;c2v^5;p c a 21;p 2c -2ac", "29:ba-c;c2v^5;p b c 21;p 2c -2b", "29:cab;c2v^5;p 21 a b;p -2b 2a", "29:-cba;c2v^5;p 21 c a;p -2ac 2a", "29:bca;c2v^5;p c 21 b;p -2bc -2c", "29:a-cb;c2v^5;p b 21 a;p -2a -2ab", "30;c2v^6;p n c 2;p 2 -2bc", "30:ba-c;c2v^6;p c n 2;p 2 -2ac", "30:cab;c2v^6;p 2 n a;p -2ac 2", "30:-cba;c2v^6;p 2 a n;p -2ab 2", "30:bca;c2v^6;p b 2 n;p -2ab -2ab", "30:a-cb;c2v^6;p n 2 b;p -2bc -2bc", "31;c2v^7;p m n 21;p 2ac -2", "31:ba-c;c2v^7;p n m 21;p 2bc -2bc", "31:cab;c2v^7;p 21 m n;p -2ab 2ab", "31:-cba;c2v^7;p 21 n m;p -2 2ac", "31:bca;c2v^7;p n 21 m;p -2 -2bc", "31:a-cb;c2v^7;p m 21 n;p -2ab -2", "32;c2v^8;p b a 2;p 2 -2ab", "32:cab;c2v^8;p 2 c b;p -2bc 2", "32:bca;c2v^8;p c 2 a;p -2ac -2ac", "33;c2v^9;p n a 21;p 2c -2n", "33*;c2v^9;p n a 21*;p 21 -2n", "33:ba-c;c2v^9;p b n 21;p 2c -2ab", "33:ba-c*;c2v^9;p b n 21*;p 21 -2ab", "33:cab;c2v^9;p 21 n b;p -2bc 2a", "33:cab*;c2v^9;p 21 n b*;p -2bc 21", "33:-cba;c2v^9;p 21 c n;p -2n 2a", "33:-cba*;c2v^9;p 21 c n*;p -2n 21", "33:bca;c2v^9;p c 21 n;p -2n -2ac", "33:a-cb;c2v^9;p n 21 a;p -2ac -2n", "34;c2v^10;p n n 2;p 2 -2n", "34:cab;c2v^10;p 2 n n;p -2n 2", "34:bca;c2v^10;p n 2 n;p -2n -2n", "35;c2v^11;c m m 2;c 2 -2", "35:cab;c2v^11;a 2 m m;a -2 2", "35:bca;c2v^11;b m 2 m;b -2 -2", "36;c2v^12;c m c 21;c 2c -2", "36*;c2v^12;c m c 21*;c 21 -2", "36:ba-c;c2v^12;c c m 21;c 2c -2c", "36:ba-c*;c2v^12;c c m 21*;c 21 -2c", "36:cab;c2v^12;a 21 m a;a -2a 2a", "36:cab*;c2v^12;a 21 m a*;a -2a 21", "36:-cba;c2v^12;a 21 a m;a -2 2a", "36:-cba*;c2v^12;a 21 a m*;a -2 21", "36:bca;c2v^12;b b 21 m;b -2 -2b", "36:a-cb;c2v^12;b m 21 b;b -2b -2", "37;c2v^13;c c c 2;c 2 -2c", "37:cab;c2v^13;a 2 a a;a -2a 2", "37:bca;c2v^13;b b 2 b;b -2b -2b", "38;c2v^14;a m m 2;a 2 -2", "38:ba-c;c2v^14;b m m 2;b 2 -2", "38:cab;c2v^14;b 2 m m;b -2 2", "38:-cba;c2v^14;c 2 m m;c -2 2", "38:bca;c2v^14;c m 2 m;c -2 -2", "38:a-cb;c2v^14;a m 2 m;a -2 -2", "39;c2v^15;a e m 2;a 2 -2b", "39;c2v^15;a b m 2;a 2 -2b", "39:ba-c;c2v^15;b m a 2;b 2 -2a", "39:cab;c2v^15;b 2 c m;b -2a 2", "39:-cba;c2v^15;c 2 m b;c -2a 2", "39:bca;c2v^15;c m 2 a;c -2a -2a", "39:a-cb;c2v^15;a c 2 m;a -2b -2b", "40;c2v^16;a m a 2;a 2 -2a", "40:ba-c;c2v^16;b b m 2;b 2 -2b", "40:cab;c2v^16;b 2 m b;b -2b 2", "40:-cba;c2v^16;c 2 c m;c -2c 2", "40:bca;c2v^16;c c 2 m;c -2c -2c", "40:a-cb;c2v^16;a m 2 a;a -2a -2a", "41;c2v^17;a e a 2;a 2 -2ab", "41;c2v^17;a b a 2;a 2 -2ab;-b", "41:ba-c;c2v^17;b b a 2;b 2 -2ab", "41:cab;c2v^17;b 2 c b;b -2ab 2", "41:-cba;c2v^17;c 2 c b;c -2ac 2", "41:bca;c2v^17;c c 2 a;c -2ac -2ac", "41:a-cb;c2v^17;a c 2 a;a -2ab -2ab", "42;c2v^18;f m m 2;f 2 -2", "42:cab;c2v^18;f 2 m m;f -2 2", "42:bca;c2v^18;f m 2 m;f -2 -2", "43;c2v^19;f d d 2;f 2 -2d", "43:cab;c2v^19;f 2 d d;f -2d 2", "43:bca;c2v^19;f d 2 d;f -2d -2d", "44;c2v^20;i m m 2;i 2 -2", "44:cab;c2v^20;i 2 m m;i -2 2", "44:bca;c2v^20;i m 2 m;i -2 -2", "45;c2v^21;i b a 2;i 2 -2c", "45:cab;c2v^21;i 2 c b;i -2a 2", "45:bca;c2v^21;i c 2 a;i -2b -2b", "46;c2v^22;i m a 2;i 2 -2a", "46:ba-c;c2v^22;i b m 2;i 2 -2b", "46:cab;c2v^22;i 2 m b;i -2b 2", "46:-cba;c2v^22;i 2 c m;i -2c 2", "46:bca;c2v^22;i c 2 m;i -2c -2c", "46:a-cb;c2v^22;i m 2 a;i -2a -2a", "47;d2h^1;p m m m;-p 2 2", "48:1;d2h^2;p n n n:1;p 2 2 -1n;-b", "48:2;d2h^2;p n n n:2;-p 2ab 2bc", "49;d2h^3;p c c m;-p 2 2c", "49:cab;d2h^3;p m a a;-p 2a 2", "49:bca;d2h^3;p b m b;-p 2b 2b", "50:1;d2h^4;p b a n:1;p 2 2 -1ab;-b", "50:2;d2h^4;p b a n:2;-p 2ab 2b", "50:1cab;d2h^4;p n c b:1;p 2 2 -1bc", "50:2cab;d2h^4;p n c b:2;-p 2b 2bc", "50:1bca;d2h^4;p c n a:1;p 2 2 -1ac", "50:2bca;d2h^4;p c n a:2;-p 2a 2c", "51;d2h^5;p m m a;-p 2a 2a", "51:ba-c;d2h^5;p m m b;-p 2b 2", "51:cab;d2h^5;p b m m;-p 2 2b", "51:-cba;d2h^5;p c m m;-p 2c 2c", "51:bca;d2h^5;p m c m;-p 2c 2", "51:a-cb;d2h^5;p m a m;-p 2 2a", "52;d2h^6;p n n a;-p 2a 2bc", "52:ba-c;d2h^6;p n n b;-p 2b 2n", "52:cab;d2h^6;p b n n;-p 2n 2b", "52:-cba;d2h^6;p c n n;-p 2ab 2c", "52:bca;d2h^6;p n c n;-p 2ab 2n", "52:a-cb;d2h^6;p n a n;-p 2n 2bc", "53;d2h^7;p m n a;-p 2ac 2", "53:ba-c;d2h^7;p n m b;-p 2bc 2bc", "53:cab;d2h^7;p b m n;-p 2ab 2ab", "53:-cba;d2h^7;p c n m;-p 2 2ac", "53:bca;d2h^7;p n c m;-p 2 2bc", "53:a-cb;d2h^7;p m a n;-p 2ab 2", "54;d2h^8;p c c a;-p 2a 2ac", "54:ba-c;d2h^8;p c c b;-p 2b 2c", "54:cab;d2h^8;p b a a;-p 2a 2b", "54:-cba;d2h^8;p c a a;-p 2ac 2c", "54:bca;d2h^8;p b c b;-p 2bc 2b", "54:a-cb;d2h^8;p b a b;-p 2b 2ab", "55;d2h^9;p b a m;-p 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m:2;-p 4bc 2bc 3", "225;oh^5;f m -3 m;-f 4 2 3", "226;oh^6;f m -3 c;-f 4a 2 3", "227:1;oh^7;f d -3 m:1;f 4d 2 3 -1d;-b", "227:2;oh^7;f d -3 m:2;-f 4vw 2vw 3", "228:1;oh^8;f d -3 c:1;f 4d 2 3 -1ad;-b", "228:2;oh^8;f d -3 c:2;-f 4ud 2vw 3", "229;oh^9;i m -3 m;-i 4 2 3", "230;oh^10;i a -3 d;-i 4bd 2c 3"]); });