| (function(Clazz
|
| ,Clazz_getClassName
|
| ,Clazz_newLongArray
|
| ,Clazz_doubleToByte
|
| ,Clazz_doubleToInt
|
| ,Clazz_doubleToLong
|
| ,Clazz_declarePackage
|
| ,Clazz_instanceOf
|
| ,Clazz_load
|
| ,Clazz_instantialize
|
| ,Clazz_decorateAsClass
|
| ,Clazz_floatToInt
|
| ,Clazz_floatToLong
|
| ,Clazz_makeConstructor
|
| ,Clazz_defineEnumConstant
|
| ,Clazz_exceptionOf
|
| ,Clazz_newIntArray
|
| ,Clazz_defineStatics
|
| ,Clazz_newFloatArray
|
| ,Clazz_declareType
|
| ,Clazz_prepareFields
|
| ,Clazz_superConstructor
|
| ,Clazz_newByteArray
|
| ,Clazz_declareInterface
|
| ,Clazz_p0p
|
| ,Clazz_pu$h
|
| ,Clazz_newShortArray
|
| ,Clazz_innerTypeInstance
|
| ,Clazz_isClassDefined
|
| ,Clazz_prepareCallback
|
| ,Clazz_newArray
|
| ,Clazz_castNullAs
|
| ,Clazz_floatToShort
|
| ,Clazz_superCall
|
| ,Clazz_decorateAsType
|
| ,Clazz_newBooleanArray
|
| ,Clazz_newCharArray
|
| ,Clazz_implementOf
|
| ,Clazz_newDoubleArray
|
| ,Clazz_overrideConstructor
|
| ,Clazz_clone
|
| ,Clazz_doubleToShort
|
| ,Clazz_getInheritedLevel
|
| ,Clazz_getParamsType
|
| ,Clazz_isAF
|
| ,Clazz_isAB
|
| ,Clazz_isAI
|
| ,Clazz_isAS
|
| ,Clazz_isASS
|
| ,Clazz_isAP
|
| ,Clazz_isAFloat
|
| ,Clazz_isAII
|
| ,Clazz_isAFF
|
| ,Clazz_isAFFF
|
| ,Clazz_tryToSearchAndExecute
|
| ,Clazz_getStackTrace
|
| ,Clazz_inheritArgs
|
| ,Clazz_alert
|
| ,Clazz_defineMethod
|
| ,Clazz_overrideMethod
|
| ,Clazz_declareAnonymous
|
|
|
| ,Clazz_cloneFinals
|
| ){
|
| var $t$;
|
|
|
| Clazz_declarePackage ("JS");
|
| Clazz_load (null, "JS.ScriptExt", ["JU.AU"], function () {
|
| c$ = Clazz_decorateAsClass (function () {
|
| this.vwr = null;
|
| this.e = null;
|
| this.chk = false;
|
| this.st = null;
|
| this.slen = 0;
|
| Clazz_instantialize (this, arguments);
|
| }, JS, "ScriptExt");
|
| Clazz_defineMethod (c$, "init",
|
| function (eval) {
|
| this.e = eval;
|
| this.vwr = this.e.vwr;
|
| return this;
|
| }, "~O");
|
| Clazz_defineMethod (c$, "atomExpressionAt",
|
| function (i) {
|
| return this.e.atomExpressionAt (i);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "checkLength",
|
| function (i) {
|
| this.e.checkLength (i);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "error",
|
| function (err) {
|
| this.e.error (err);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "invArg",
|
| function () {
|
| this.e.invArg ();
|
| });
|
| Clazz_defineMethod (c$, "invPO",
|
| function () {
|
| this.error (23);
|
| });
|
| Clazz_defineMethod (c$, "getShapeProperty",
|
| function (shapeType, propertyName) {
|
| return this.e.getShapeProperty (shapeType, propertyName);
|
| }, "~N,~S");
|
| Clazz_defineMethod (c$, "paramAsStr",
|
| function (i) {
|
| return this.e.paramAsStr (i);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "centerParameter",
|
| function (i) {
|
| return this.e.centerParameter (i, null);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "floatParameter",
|
| function (i) {
|
| return this.e.floatParameter (i);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "getPoint3f",
|
| function (i, allowFractional) {
|
| return this.e.getPoint3f (i, allowFractional, true);
|
| }, "~N,~B");
|
| Clazz_defineMethod (c$, "intParameter",
|
| function (index) {
|
| return this.e.intParameter (index);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "isFloatParameter",
|
| function (index) {
|
| switch (this.e.tokAt (index)) {
|
| case 2:
|
| case 3:
|
| return true;
|
| }
|
| return false;
|
| }, "~N");
|
| Clazz_defineMethod (c$, "setShapeProperty",
|
| function (shapeType, propertyName, propertyValue) {
|
| this.e.setShapeProperty (shapeType, propertyName, propertyValue);
|
| }, "~N,~S,~O");
|
| Clazz_defineMethod (c$, "showString",
|
| function (s) {
|
| this.e.showString (s);
|
| }, "~S");
|
| Clazz_defineMethod (c$, "stringParameter",
|
| function (index) {
|
| return this.e.stringParameter (index);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "getToken",
|
| function (i) {
|
| return this.e.getToken (i);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "tokAt",
|
| function (i) {
|
| return this.e.tokAt (i);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "setShapeId",
|
| function (iShape, i, idSeen) {
|
| if (idSeen) this.invArg ();
|
| var name = this.e.setShapeNameParameter (i).toLowerCase ();
|
| this.setShapeProperty (iShape, "thisID", name);
|
| return name;
|
| }, "~N,~N,~B");
|
| Clazz_defineMethod (c$, "getColorTrans",
|
| function (eval, i, allowNone, ret) {
|
| var translucentLevel = 3.4028235E38;
|
| if (eval.theTok != 1765808134) --i;
|
| switch (this.tokAt (i + 1)) {
|
| case 603979967:
|
| i++;
|
| translucentLevel = (this.isFloatParameter (i + 1) ? eval.getTranslucentLevel (++i) : this.vwr.getFloat (570425354));
|
| break;
|
| case 1073742074:
|
| i++;
|
| translucentLevel = 0;
|
| break;
|
| }
|
| if (eval.isColorParam (i + 1)) {
|
| ret[0] = eval.getArgbParam (++i);
|
| } else if (this.tokAt (i + 1) == 1073742333) {
|
| ret[0] = 0;
|
| eval.iToken = i + 1;
|
| } else if (translucentLevel == 3.4028235E38) {
|
| this.invArg ();
|
| } else {
|
| ret[0] = -2147483648;
|
| }i = eval.iToken;
|
| return translucentLevel;
|
| }, "JS.ScriptEval,~N,~B,~A");
|
| Clazz_defineMethod (c$, "finalizeObject",
|
| function (shapeID, colorArgb, translucentLevel, intScale, doSet, data, iptDisplayProperty, bs) {
|
| if (doSet) {
|
| this.setShapeProperty (shapeID, "set", data);
|
| }if (colorArgb != -2147483648) this.e.setShapePropertyBs (shapeID, "color", Integer.$valueOf (colorArgb), bs);
|
| if (translucentLevel != 3.4028235E38) this.e.setShapeTranslucency (shapeID, "", "translucent", translucentLevel, bs);
|
| if (intScale != 0) {
|
| this.setShapeProperty (shapeID, "scale", Integer.$valueOf (intScale));
|
| }if (iptDisplayProperty > 0) {
|
| if (!this.e.setMeshDisplayProperty (shapeID, iptDisplayProperty, 0)) this.invArg ();
|
| }}, "~N,~N,~N,~N,~B,~O,~N,JU.BS");
|
| Clazz_defineMethod (c$, "getIntArray2",
|
| function (i) {
|
| var list = (this.e.getToken (i)).getList ();
|
| var faces = JU.AU.newInt2 (list.size ());
|
| for (var vi = faces.length; --vi >= 0; ) {
|
| var face = list.get (vi).getList ();
|
| if (face == null) this.invArg ();
|
| faces[vi] = Clazz_newIntArray (face.size (), 0);
|
| for (var vii = faces[vi].length; --vii >= 0; ) faces[vi][vii] = face.get (vii).intValue;
|
|
|
| }
|
| return faces;
|
| }, "~N");
|
| Clazz_defineMethod (c$, "getAllPoints",
|
| function (index) {
|
| var points = null;
|
| var bs = null;
|
| try {
|
| switch (this.e.tokAt (index)) {
|
| case 7:
|
| points = this.e.getPointArray (index, -1, false);
|
| break;
|
| case 12290:
|
| case 10:
|
| case 1073742325:
|
| bs = this.atomExpressionAt (index);
|
| break;
|
| }
|
| if (points == null) {
|
| if (bs == null) bs = this.vwr.getAllAtoms ();
|
| points = new Array (bs.cardinality ());
|
| for (var i = bs.nextSetBit (0), pt = 0; i >= 0; i = bs.nextSetBit (i + 1)) points[pt++] = this.vwr.ms.at[i];
|
|
|
| }} catch (e) {
|
| if (Clazz_exceptionOf (e, Exception)) {
|
| } else {
|
| throw e;
|
| }
|
| }
|
| if (points.length < 3) this.invArg ();
|
| return points;
|
| }, "~N");
|
| });
|
| Clazz_declarePackage ("JS");
|
| Clazz_load (["JS.ScriptExt"], "JS.CmdExt", ["java.lang.Boolean", "$.Float", "$.Long", "java.util.Hashtable", "$.Map", "JU.AU", "$.BS", "$.Base64", "$.Lst", "$.M3", "$.M4", "$.Measure", "$.P3", "$.P4", "$.PT", "$.Quat", "$.SB", "$.V3", "J.api.Interface", "J.atomdata.RadiusData", "J.c.STER", "$.VDW", "J.i18n.GT", "JM.Atom", "$.AtomCollection", "$.BondSet", "$.LabelToken", "JS.SV", "$.ScriptCompiler", "$.ScriptError", "$.ScriptEval", "$.ScriptInterruption", "$.ScriptMathProcessor", "$.ScriptParam", "$.T", "JU.BSUtil", "$.BoxInfo", "$.C", "$.Edge", "$.Elements", "$.Escape", "$.Logger", "$.Parser", "$.Point3fi", "$.SimpleUnitCell", "JV.FileManager", "$.JC", "$.StateManager", "$.Viewer"], function () {
|
| c$ = Clazz_declareType (JS, "CmdExt", JS.ScriptExt);
|
| Clazz_makeConstructor (c$,
|
| function () {
|
| Clazz_superConstructor (this, JS.CmdExt, []);
|
| });
|
| Clazz_overrideMethod (c$, "dispatch",
|
| function (iTok, b, st) {
|
| this.chk = this.e.chk;
|
| this.slen = this.e.slen;
|
| this.st = st;
|
| switch (iTok) {
|
| case 1073741866:
|
| st[0].value = this.prepareBinaryOutput (st[0]);
|
| return null;
|
| case 4098:
|
| this.assign ();
|
| break;
|
| case 134221829:
|
| this.cache ();
|
| break;
|
| case 4102:
|
| this.calculate ();
|
| break;
|
| case 4103:
|
| this.capture ();
|
| break;
|
| case 4105:
|
| this.centerAt ();
|
| break;
|
| case 134221831:
|
| this.compare ();
|
| break;
|
| case 528395:
|
| this.console ();
|
| break;
|
| case 4106:
|
| this.connect (1);
|
| break;
|
| case 1094717448:
|
| this.configuration ();
|
| break;
|
| case 134221834:
|
| this.data ();
|
| break;
|
| case 1613238294:
|
| this.connect (0);
|
| break;
|
| case 4120:
|
| this.image ();
|
| break;
|
| case 4122:
|
| this.invertSelected ();
|
| break;
|
| case 4124:
|
| this.macro ();
|
| break;
|
| case 4125:
|
| this.mapProperty ();
|
| break;
|
| case 4126:
|
| this.minimize ();
|
| break;
|
| case 1275072532:
|
| this.modulation ();
|
| break;
|
| case 4130:
|
| this.mutate ();
|
| break;
|
| case 4131:
|
| this.navigate ();
|
| break;
|
| case 4133:
|
| case 134221850:
|
| case 4138:
|
| this.plot (st);
|
| break;
|
| case 134222350:
|
| this.show ();
|
| break;
|
| case 528443:
|
| this.stereo ();
|
| break;
|
| case 1814695966:
|
| this.unitcell (b ? 2 : 1);
|
| break;
|
| case 134221856:
|
| return this.write (b ? st : null);
|
| case 6:
|
| this.measure ();
|
| break;
|
| case 21:
|
| this.polyhedra ();
|
| break;
|
| case 20:
|
| this.ellipsoid ();
|
| break;
|
| case 4:
|
| this.struts ();
|
| break;
|
| }
|
| return null;
|
| }, "~N,~B,~A");
|
| Clazz_defineMethod (c$, "macro",
|
| function () {
|
| var key = this.e.optParameterAsString (1);
|
| if (key.length == 0) return;
|
| if (this.chk) return;
|
| var macro = JV.JC.getMacro (key);
|
| if (macro == null) {
|
| this.showString ("macro " + key + " could not be found. Current macros include:\n" + JV.JC.getMacroList ());
|
| return;
|
| }this.showString ("running " + macro);
|
| this.e.cmdScript (4124, macro, null);
|
| });
|
| Clazz_defineMethod (c$, "evalParallel",
|
| function (context, shapeManager) {
|
| this.chk = this.e.chk;
|
| this.slen = this.e.slen;
|
| var se = new JS.ScriptEval ().setViewer (this.vwr);
|
| se.historyDisabled = true;
|
| se.compiler = new JS.ScriptCompiler (this.vwr);
|
| se.sm = shapeManager;
|
| try {
|
| se.restoreScriptContext (context, true, false, false);
|
| se.allowJSThreads = false;
|
| se.dispatchCommands (false, false, false);
|
| } catch (ex) {
|
| if (Clazz_exceptionOf (ex, Exception)) {
|
| this.e.vwr.setStringProperty ("_errormessage", "" + ex);
|
| if (se.thisContext == null) {
|
| JU.Logger.error ("Error evaluating context " + ex);
|
| ex.printStackTrace ();
|
| }return false;
|
| } else {
|
| throw ex;
|
| }
|
| }
|
| return true;
|
| }, "JS.ScriptContext,JV.ShapeManager");
|
| Clazz_defineMethod (c$, "getBitsetIdent",
|
| function (bs, label, tokenValue, useAtomMap, index, isExplicitlyAll) {
|
| var isAtoms = !(Clazz_instanceOf (tokenValue, JM.BondSet));
|
| if (isAtoms) {
|
| if (label == null) label = this.vwr.getStandardLabelFormat (0);
|
| else if (label.length == 0) label = "%[label]";
|
| }var pt = (label == null ? -1 : label.indexOf ("%"));
|
| var haveIndex = (index != 2147483647);
|
| if (bs == null || this.chk || isAtoms && pt < 0) {
|
| if (label == null) label = "";
|
| return isExplicitlyAll ? Clazz_newArray (-1, [label]) : label;
|
| }var modelSet = this.vwr.ms;
|
| var n = 0;
|
| var labeler = modelSet.getLabeler ();
|
| var indices = (isAtoms || !useAtomMap ? null : (tokenValue).associatedAtoms);
|
| if (indices == null && label != null && label.indexOf ("%D") > 0) indices = this.vwr.ms.getAtomIndices (bs);
|
| var asIdentity = (label == null || label.length == 0);
|
| var htValues = (isAtoms || asIdentity ? null : JM.LabelToken.getBondLabelValues ());
|
| var tokens = (asIdentity ? null : isAtoms ? labeler.compile (this.vwr, label, '\0', null) : labeler.compile (this.vwr, label, '\1', htValues));
|
| var nmax = (haveIndex ? 1 : bs.cardinality ());
|
| var sout = new Array (nmax);
|
| var ptTemp = new JU.P3 ();
|
| for (var j = (haveIndex ? index : bs.nextSetBit (0)); j >= 0; j = bs.nextSetBit (j + 1)) {
|
| var str;
|
| if (isAtoms) {
|
| if (asIdentity) str = modelSet.at[j].getInfo ();
|
| else str = labeler.formatLabelAtomArray (this.vwr, modelSet.at[j], tokens, '\0', indices, ptTemp);
|
| } else {
|
| var bond = modelSet.bo[j];
|
| if (asIdentity) str = bond.getIdentity ();
|
| else str = labeler.formatLabelBond (this.vwr, bond, tokens, htValues, indices, ptTemp);
|
| }str = JU.PT.formatStringI (str, "#", (n + 1));
|
| sout[n++] = str;
|
| if (haveIndex) break;
|
| }
|
| return nmax == 1 && !isExplicitlyAll ? sout[0] : sout;
|
| }, "JU.BS,~S,~O,~B,~N,~B");
|
| Clazz_defineMethod (c$, "getLoadSymmetryParams",
|
| function (i, sOptions, htParams) {
|
| var eval = this.e;
|
| this.chk = eval.chk;
|
| this.slen = eval.slen;
|
| var lattice = null;
|
| var tok = this.tokAt (i);
|
| if (tok == 1073742332 || tok == 8) {
|
| lattice = eval.getPointOrPlane (i, false, true, false, true, 3, 3, true);
|
| tok = this.tokAt (i = eval.iToken + 1);
|
| }switch (tok) {
|
| case 1073741938:
|
| case 1073742080:
|
| case 1094713350:
|
| case 1073742163:
|
| case 1073742114:
|
| case 1073742152:
|
| case 1814695966:
|
| if (lattice == null) lattice = JU.P3.new3 (555, 555, -1);
|
| eval.iToken = i - 1;
|
| }
|
| var offset = null;
|
| if (lattice != null) {
|
| htParams.put ("lattice", lattice);
|
| i = eval.iToken + 1;
|
| sOptions.append (" " + JU.SimpleUnitCell.escapeMultiplier (lattice));
|
| i = this.checkPacked (i, htParams, sOptions);
|
| if (this.tokAt (i) == 1094713350) {
|
| htParams.put ("centroid", Boolean.TRUE);
|
| sOptions.append (" CENTROID");
|
| i = this.checkPacked (++i, htParams, sOptions);
|
| }if (this.tokAt (i) == 1073742163) {
|
| var supercell;
|
| sOptions.append (" SUPERCELL ");
|
| if (eval.isPoint3f (++i)) {
|
| var pt = this.getPoint3f (i, false);
|
| if (pt.x != Clazz_floatToInt (pt.x) || pt.y != Clazz_floatToInt (pt.y) || pt.z != Clazz_floatToInt (pt.z) || pt.x < 1 || pt.y < 1 || pt.z < 1) {
|
| eval.iToken = i;
|
| this.invArg ();
|
| }supercell = pt;
|
| i = eval.iToken;
|
| } else {
|
| supercell = this.stringParameter (i);
|
| }sOptions.append (JU.Escape.e (supercell));
|
| htParams.put ("supercell", supercell);
|
| i = this.checkPacked (++i, htParams, sOptions);
|
| }var distance = 0;
|
| if (this.tokAt (i) == 1073742114) {
|
| i++;
|
| distance = this.floatParameter (i++);
|
| sOptions.append (" range " + distance);
|
| }htParams.put ("symmetryRange", Float.$valueOf (distance));
|
| var spacegroup = null;
|
| var sg;
|
| var iGroup = -2147483648;
|
| if (this.tokAt (i) == 1073742152) {
|
| ++i;
|
| spacegroup = JU.PT.rep (this.paramAsStr (i++), "''", "\"");
|
| sOptions.append (" spacegroup " + JU.PT.esc (spacegroup));
|
| if (spacegroup.equalsIgnoreCase ("ignoreOperators")) {
|
| iGroup = -999;
|
| } else {
|
| if (spacegroup.length == 0) {
|
| sg = this.vwr.getCurrentUnitCell ();
|
| if (sg != null) spacegroup = sg.getSpaceGroupName ();
|
| } else {
|
| if (spacegroup.indexOf (",") >= 0) if ((lattice.x < 9 && lattice.y < 9 && lattice.z == 0)) spacegroup += "#doNormalize=0";
|
| }htParams.put ("spaceGroupName", spacegroup);
|
| iGroup = -2;
|
| }}var fparams = null;
|
| if (this.tokAt (i) == 1814695966) {
|
| ++i;
|
| var s = eval.optParameterAsString (i);
|
| if (s.length == 0) {
|
| sg = this.vwr.getCurrentUnitCell ();
|
| if (sg != null) {
|
| fparams = sg.getUnitCellAsArray (true);
|
| offset = sg.getCartesianOffset ();
|
| }} else {
|
| if (this.tokAt (i) == 4) {
|
| fparams = Clazz_newFloatArray (6, 0);
|
| JU.SimpleUnitCell.setOabc (s, fparams, null);
|
| } else {
|
| fparams = eval.floatParameterSet (i, 6, 9);
|
| }}if (fparams == null || fparams.length != 6 && fparams.length != 9) this.invArg ();
|
| sOptions.append (" unitcell [");
|
| for (var j = 0; j < fparams.length; j++) sOptions.append ((j == 0 ? "" : " ") + fparams[j]);
|
|
|
| sOptions.append ("]");
|
| htParams.put ("unitcell", fparams);
|
| if (iGroup == -2147483648) iGroup = -1;
|
| i = eval.iToken + 1;
|
| }if (iGroup != -2147483648) htParams.put ("spaceGroupIndex", Integer.$valueOf (iGroup));
|
| }if (offset != null) eval.coordinatesAreFractional = false;
|
| else if (this.tokAt (i) == 1073742066) offset = this.getPoint3f (++i, true);
|
| if (offset != null) {
|
| if (eval.coordinatesAreFractional) {
|
| offset.setT (eval.fractionalPoint);
|
| htParams.put ("unitCellOffsetFractional", (eval.coordinatesAreFractional ? Boolean.TRUE : Boolean.FALSE));
|
| sOptions.append (" offset {" + offset.x + " " + offset.y + " " + offset.z + "/1}");
|
| } else {
|
| sOptions.append (" offset " + JU.Escape.eP (offset));
|
| }htParams.put ("unitCellOffset", offset);
|
| i = eval.iToken + 1;
|
| }return i;
|
| }, "~N,JU.SB,java.util.Map");
|
| Clazz_defineMethod (c$, "checkPacked",
|
| function (i, htParams, sOptions) {
|
| switch (this.tokAt (i)) {
|
| case 1073741938:
|
| htParams.put ("packed", Boolean.TRUE);
|
| var oabc = null;
|
| var tok = this.tokAt (++i);
|
| switch (tok) {
|
| case 1814695966:
|
| case 1678381065:
|
| break;
|
| default:
|
| if (this.e.isArrayParameter (i)) {
|
| oabc = this.e.getPointArray (i, -1, false);
|
| i = this.e.iToken;
|
| } else if (this.isFloatParameter (i)) {
|
| var d = this.floatParameter (i);
|
| oabc = Clazz_newArray (-1, [ new JU.P3 (), JU.P3.new3 (d, d, d)]);
|
| } else {
|
| oabc = new Array (0);
|
| --i;
|
| }}
|
| i++;
|
| if (this.e.chk) return i;
|
| switch (tok) {
|
| case 1814695966:
|
| var type = this.e.optParameterAsString (i++).toLowerCase ();
|
| if (JU.PT.isOneOf (type, ";conventional;primitive;")) {
|
| htParams.put ("fillRange", type);
|
| sOptions.append (" FILL UNITCELL \"" + type + "\"");
|
| return i;
|
| }var unitCell = this.vwr.getCurrentUnitCell ();
|
| if (unitCell != null) {
|
| oabc = JU.BoxInfo.toOABC (unitCell.getUnitCellVerticesNoOffset (), unitCell.getCartesianOffset ());
|
| break;
|
| }case 1678381065:
|
| oabc = JU.BoxInfo.toOABC (this.vwr.ms.getBBoxVertices (), null);
|
| break;
|
| }
|
| switch (oabc.length) {
|
| case 2:
|
| var a = oabc[1];
|
| oabc = Clazz_newArray (-1, [oabc[0], JU.P3.newP (oabc[0]), new JU.P3 (), new JU.P3 ()]);
|
| oabc[1].x = a.x;
|
| oabc[2].y = a.y;
|
| oabc[3].z = a.z;
|
| break;
|
| case 3:
|
| oabc = Clazz_newArray (-1, [ new JU.P3 (), oabc[0], oabc[1], oabc[2]]);
|
| break;
|
| case 4:
|
| break;
|
| default:
|
| oabc = Clazz_newArray (-1, [ new JU.P3 (), JU.P3.new3 (10, 0, 0), JU.P3.new3 (0, 10, 0), JU.P3.new3 (0, 0, 10)]);
|
| }
|
| htParams.put ("fillRange", oabc);
|
| sOptions.append (" FILL [" + oabc[0] + oabc[1] + oabc[2] + oabc[3] + "]");
|
| break;
|
| case 1073742080:
|
| var f = NaN;
|
| if (this.isFloatParameter (++i)) f = this.floatParameter (i++);
|
| if (!this.e.chk) {
|
| htParams.put ("packed", Boolean.TRUE);
|
| sOptions.append (" PACKED");
|
| if (!Float.isNaN (f)) {
|
| htParams.put ("packingError", Float.$valueOf (f));
|
| sOptions.append (" " + f);
|
| }}break;
|
| }
|
| return i;
|
| }, "~N,java.util.Map,JU.SB");
|
| Clazz_defineMethod (c$, "cache",
|
| function () {
|
| var tok = this.tokAt (1);
|
| var fileName = null;
|
| var n = 2;
|
| switch (tok) {
|
| case 1275069441:
|
| case 1073742119:
|
| fileName = this.e.optParameterAsString (n++);
|
| case 1073741882:
|
| this.checkLength (n);
|
| if (!this.chk) {
|
| if ("all".equals (fileName)) fileName = null;
|
| var nBytes = this.vwr.cacheFileByName (fileName, tok == 1275069441);
|
| this.showString (nBytes < 0 ? "cache cleared" : nBytes + " bytes " + (tok == 1275069441 ? " cached" : " removed"));
|
| }break;
|
| default:
|
| this.invArg ();
|
| }
|
| });
|
| Clazz_defineMethod (c$, "calculate",
|
| function () {
|
| var isSurface = false;
|
| var asDSSP = false;
|
| var bs1 = null;
|
| var bs2 = null;
|
| var eval = this.e;
|
| var n = -2147483648;
|
| var version = 2;
|
| if ((eval.iToken = eval.slen) >= 2) {
|
| eval.clearDefinedVariableAtomSets ();
|
| switch (this.getToken (1).tok) {
|
| case 1073741824:
|
| this.checkLength (2);
|
| break;
|
| case 1086324752:
|
| eval.iToken = 1;
|
| bs1 = (this.slen == 2 ? null : this.atomExpressionAt (2));
|
| eval.checkLast (eval.iToken);
|
| if (!this.chk) eval.showString (this.vwr.calculateChirality (bs1));
|
| return;
|
| case 1631586315:
|
| this.checkLength (2);
|
| if (this.chk) return;
|
| n = this.vwr.calculateFormalCharges (null);
|
| this.showString (J.i18n.GT.i (J.i18n.GT.$ ("{0} charges modified"), n));
|
| return;
|
| case 1075838996:
|
| this.checkLength (2);
|
| if (!this.chk) this.vwr.ms.assignAromaticBondsBs (true, null);
|
| return;
|
| case 1613238294:
|
| if (eval.slen != 2) {
|
| asDSSP = (this.tokAt (++eval.iToken) == 1639976963);
|
| if (asDSSP) bs1 = this.vwr.bsA ();
|
| else bs1 = this.atomExpressionAt (eval.iToken);
|
| if (!asDSSP && !(asDSSP = (this.tokAt (++eval.iToken) == 1639976963))) bs2 = this.atomExpressionAt (eval.iToken);
|
| }if (this.chk) return;
|
| n = this.vwr.autoHbond (bs1, bs2, false);
|
| if (n != -2147483648) eval.report (J.i18n.GT.i (J.i18n.GT.$ ("{0} hydrogen bonds"), Math.abs (n)), false);
|
| return;
|
| case 1612709900:
|
| var andBond = (this.tokAt (2) == 1073742335);
|
| if (andBond) eval.iToken++;
|
| bs1 = (this.slen == (andBond ? 3 : 2) ? null : this.atomExpressionAt (andBond ? 3 : 2));
|
| eval.checkLast (eval.iToken);
|
| if (!this.chk) {
|
| this.vwr.addHydrogens (bs1, false, false);
|
| if (andBond) {
|
| if (bs1 == null) bs1 = this.vwr.bsA ();
|
| this.vwr.makeConnections (0.1, 1e8, 515, 1073742025, bs1, bs1, null, false, false, 0);
|
| this.vwr.ms.assignAromaticBondsBs (true, null);
|
| }}return;
|
| case 1111492619:
|
| eval.iToken = 1;
|
| bs1 = (this.slen == 2 ? null : this.atomExpressionAt (2));
|
| eval.checkLast (eval.iToken);
|
| if (!this.chk) eval.getPartialCharges (bs1);
|
| return;
|
| case 1088421903:
|
| case 134217762:
|
| if (!this.chk) {
|
| if (this.tokAt (2) == 1275203608) {
|
| var id = (this.tokAt (3) == 4 ? this.stringParameter (3) : null);
|
| bs1 = (id != null || this.slen == 3 ? null : this.atomExpressionAt (3));
|
| var data = Clazz_newArray (-1, [id, null, bs1]);
|
| this.showString (eval.getShapePropertyData (21, "symmetry", data) ? data[1] : "");
|
| } else {
|
| this.showString (this.vwr.ms.calculatePointGroup (this.vwr.bsA ()));
|
| }}return;
|
| case 1111490574:
|
| this.checkLength (2);
|
| if (!this.chk) {
|
| this.vwr.calculateStraightness ();
|
| this.vwr.addStateScript ("set quaternionFrame '" + this.vwr.getQuaternionFrame () + "'; calculate straightness", false, true);
|
| }return;
|
| case 1639976963:
|
| bs1 = (this.slen < 4 || this.isFloatParameter (3) ? null : this.atomExpressionAt (2));
|
| switch (this.tokAt (++eval.iToken)) {
|
| case 4138:
|
| break;
|
| case 1111490587:
|
| if (this.chk) return;
|
| eval.showString (this.vwr.getAnnotationParser (true).calculateDSSRStructure (this.vwr, bs1));
|
| return;
|
| case 1073741915:
|
| asDSSP = true;
|
| version = (this.slen == eval.iToken + 1 ? 2 : Clazz_floatToInt (this.floatParameter (++eval.iToken)));
|
| break;
|
| case 0:
|
| asDSSP = this.vwr.getBoolean (603979826);
|
| break;
|
| default:
|
| this.invArg ();
|
| }
|
| if (!this.chk) this.showString (this.vwr.calculateStructures (bs1, asDSSP, true, version));
|
| return;
|
| case 659482:
|
| bs1 = (eval.iToken + 1 < this.slen ? this.atomExpressionAt (++eval.iToken) : null);
|
| bs2 = (eval.iToken + 1 < this.slen ? this.atomExpressionAt (++eval.iToken) : null);
|
| this.checkLength (++eval.iToken);
|
| if (!this.chk) {
|
| n = this.vwr.calculateStruts (bs1, bs2);
|
| if (n > 0) {
|
| this.setShapeProperty (1, "type", Integer.$valueOf (32768));
|
| eval.setShapePropertyBs (1, "color", Integer.$valueOf (0x0FFFFFF), null);
|
| eval.setShapeTranslucency (1, "", "translucent", 0.5, null);
|
| this.setShapeProperty (1, "type", Integer.$valueOf (1023));
|
| }this.showString (J.i18n.GT.i (J.i18n.GT.$ ("{0} struts added"), n));
|
| }return;
|
| case 2097180:
|
| isSurface = true;
|
| case 1111490575:
|
| var isFrom = false;
|
| switch (this.tokAt (2)) {
|
| case 134217759:
|
| eval.iToken++;
|
| break;
|
| case 0:
|
| isFrom = !isSurface;
|
| break;
|
| case 1073741952:
|
| isFrom = true;
|
| eval.iToken++;
|
| break;
|
| default:
|
| isFrom = true;
|
| }
|
| bs1 = (eval.iToken + 1 < this.slen ? this.atomExpressionAt (++eval.iToken) : this.vwr.bsA ());
|
| this.checkLength (++eval.iToken);
|
| if (!this.chk) this.vwr.calculateSurface (bs1, (isFrom ? 3.4028235E38 : -1));
|
| return;
|
| }
|
| }eval.errorStr2 (53, "CALCULATE", "aromatic? hbonds? hydrogen? formalCharge? partialCharge? pointgroup? straightness? structure? struts? surfaceDistance FROM? surfaceDistance WITHIN?");
|
| });
|
| Clazz_defineMethod (c$, "capture",
|
| function () {
|
| if (!this.chk && !this.vwr.allowCapture ()) {
|
| this.showString ("Cannot capture on this platform");
|
| return;
|
| }var params = this.vwr.captureParams;
|
| var type = (params == null ? "GIF" : params.get ("type"));
|
| var endTime = 0;
|
| var mode = 0;
|
| var slen = this.e.slen;
|
| var fileName = "";
|
| var looping = (this.vwr.am.animationReplayMode != 1073742070);
|
| var i = 1;
|
| var tok = this.tokAt (i);
|
| var isTransparent = (tok == 603979967);
|
| if (isTransparent) tok = this.tokAt (++i);
|
| switch (tok == 0 ? (tok = 102409) : tok) {
|
| case 4:
|
| fileName = this.e.optParameterAsString (i++);
|
| if (fileName.length == 0) {
|
| mode = 102409;
|
| break;
|
| }var lc = fileName.toLowerCase ();
|
| if (lc.endsWith (".gift") || lc.endsWith (".pngt")) {
|
| isTransparent = true;
|
| fileName = fileName.substring (0, fileName.length - 1);
|
| lc = fileName.toLowerCase ();
|
| } else if (!lc.endsWith (".gif") && !lc.contains (".png")) {
|
| fileName += ".gif";
|
| }if (lc.endsWith (".png")) {
|
| if (!lc.endsWith ("0.png")) fileName = fileName.substring (0, fileName.length - 4) + "0000.png";
|
| type = "PNG";
|
| } else {
|
| type = "GIF";
|
| }if (isTransparent) type += "T";
|
| var pt = fileName.indexOf ("0000.");
|
| var streaming = (pt < 0 || pt != fileName.lastIndexOf (".") - 4);
|
| var isRock = false;
|
| if (this.tokAt (i) == 528411) {
|
| looping = true;
|
| tok = this.tokAt (++i);
|
| }switch (this.tokAt (i)) {
|
| case 1073742129:
|
| isRock = true;
|
| case 1611141175:
|
| var s = null;
|
| var axis = "y";
|
| looping = true;
|
| i++;
|
| if (isRock) {
|
| if (i < slen && this.tokAt (i) != 2) axis = this.e.optParameterAsString (i++).toLowerCase ();
|
| s = "rotate Y 10 10;rotate Y -10 -10;rotate Y -10 -10;rotate Y 10 10";
|
| var n = (i < slen ? this.intParameter (i++) : 5);
|
| if (n < 0) {
|
| s = JU.PT.rep (s, "10;", "" + (-n) + ";");
|
| } else {
|
| s = JU.PT.rep (s, "10", "" + n);
|
| }} else {
|
| if (i < slen) axis = this.e.optParameterAsString (i++).toLowerCase ();
|
| s = "rotate Y 360 30;";
|
| }if (this.chk) return;
|
| this.vwr.setNavigationMode (false);
|
| if (axis === "" || "xyz".indexOf (axis) < 0) axis = "y";
|
| var wf = this.vwr.g.waitForMoveTo;
|
| s = "set waitformoveto true;" + JU.PT.rep (s, "Y", axis) + ";set waitformoveto " + wf;
|
| s = "capture " + (isTransparent ? "transparent " : "") + JU.PT.esc (fileName) + " LOOP;" + s + ";capture end;";
|
| this.e.cmdScript (0, null, s);
|
| return;
|
| case 3:
|
| case 2:
|
| endTime = this.floatParameter (i++);
|
| break;
|
| }
|
| if (this.chk) return;
|
| mode = 1073742031;
|
| params = new java.util.Hashtable ();
|
| var fps = this.vwr.getInt (553648132);
|
| if (streaming) {
|
| params.put ("streaming", Boolean.TRUE);
|
| if (!looping) this.showString (J.i18n.GT.o (J.i18n.GT.$ ("Note: Enable looping using {0}"), Clazz_newArray (-1, ["ANIMATION MODE LOOP"])));
|
| this.showString (J.i18n.GT.o (J.i18n.GT.$ ("Animation delay based on: {0}"), Clazz_newArray (-1, ["ANIMATION FPS " + fps])));
|
| }params.put ("captureFps", Integer.$valueOf (fps));
|
| break;
|
| case 102409:
|
| case 1073741874:
|
| if (params != null) params.put ("captureSilent", Boolean.TRUE);
|
| case 1073742335:
|
| case 1073742334:
|
| this.checkLength (-2);
|
| mode = tok;
|
| break;
|
| default:
|
| this.invArg ();
|
| }
|
| if (this.chk || params == null) return;
|
| params.put ("type", type);
|
| var c = Integer.$valueOf (this.vwr.getBackgroundArgb ());
|
| params.put ("backgroundColor", c);
|
| params.put ("fileName", fileName);
|
| params.put ("quality", Integer.$valueOf (-1));
|
| params.put ("endTime", Long.$valueOf (endTime <= 0 ? -1 : System.currentTimeMillis () + Clazz_floatToLong (endTime * 1000)));
|
| params.put ("captureMode", JS.T.nameOf (mode).toLowerCase ());
|
| params.put ("captureLooping", looping ? Boolean.TRUE : Boolean.FALSE);
|
| var msg = this.vwr.processWriteOrCapture (params);
|
| if (msg == null) msg = "canceled";
|
| JU.Logger.info (msg);
|
| });
|
| Clazz_defineMethod (c$, "centerAt",
|
| function () {
|
| var tok = this.getToken (1).tok;
|
| switch (tok) {
|
| case 1073741826:
|
| case 96:
|
| case 1678381065:
|
| break;
|
| default:
|
| this.invArg ();
|
| }
|
| var pt = JU.P3.new3 (0, 0, 0);
|
| if (this.slen == 5) {
|
| pt.x = this.floatParameter (2);
|
| pt.y = this.floatParameter (3);
|
| pt.z = this.floatParameter (4);
|
| } else if (this.e.isCenterParameter (2)) {
|
| pt = this.centerParameter (2);
|
| this.e.checkLast (this.e.iToken);
|
| } else {
|
| this.checkLength (2);
|
| }if (!this.chk && !this.vwr.isJmolDataFrame ()) this.vwr.tm.setCenterAt (tok, pt);
|
| });
|
| Clazz_defineMethod (c$, "compare",
|
| function () {
|
| var eval = this.e;
|
| var isQuaternion = false;
|
| var doRotate = false;
|
| var doTranslate = false;
|
| var doAnimate = false;
|
| var isFlexFit = false;
|
| var data1 = null;
|
| var data2 = null;
|
| var bsAtoms1 = null;
|
| var bsAtoms2 = null;
|
| var vAtomSets = null;
|
| var vQuatSets = null;
|
| eval.iToken = 0;
|
| var nSeconds = (this.isFloatParameter (1) ? this.floatParameter (++eval.iToken) : NaN);
|
| var bsFrom = this.atomExpressionAt (++eval.iToken);
|
| var coordTo = null;
|
| var bsTo = null;
|
| if (eval.isArrayParameter (++eval.iToken)) {
|
| coordTo = eval.getPointArray (eval.iToken, -1, false);
|
| } else if (this.tokAt (eval.iToken) != 1140850689) {
|
| bsTo = this.atomExpressionAt (eval.iToken);
|
| }var bsSubset = null;
|
| var isSmiles = false;
|
| var strSmiles = null;
|
| var bs = JU.BSUtil.copy (bsFrom);
|
| if (bsTo != null) bs.or (bsTo);
|
| var isToSubsetOfFrom = (coordTo == null && bsTo != null && bs.equals (bsFrom));
|
| var isFrames = isToSubsetOfFrom;
|
| for (var i = eval.iToken + 1; i < this.slen; ++i) {
|
| switch (this.getToken (i).tok) {
|
| case 4115:
|
| isFrames = true;
|
| break;
|
| case 134218757:
|
| isSmiles = true;
|
| if (this.tokAt (i + 1) != 4) {
|
| strSmiles = "*";
|
| break;
|
| }case 134218756:
|
| strSmiles = this.stringParameter (++i);
|
| break;
|
| case 1677721602:
|
| isFlexFit = true;
|
| doRotate = true;
|
| strSmiles = this.paramAsStr (++i);
|
| if (strSmiles.equalsIgnoreCase ("SMILES")) {
|
| isSmiles = true;
|
| strSmiles = "*";
|
| }break;
|
| case 3:
|
| case 2:
|
| nSeconds = Math.abs (this.floatParameter (i));
|
| if (nSeconds > 0) doAnimate = true;
|
| break;
|
| case 268435504:
|
| break;
|
| case 2109448:
|
| bsSubset = this.atomExpressionAt (++i);
|
| i = eval.iToken;
|
| break;
|
| case 10:
|
| case 1073742325:
|
| if (vQuatSets != null) this.invArg ();
|
| bsAtoms1 = this.atomExpressionAt (eval.iToken);
|
| var tok = (isToSubsetOfFrom ? 0 : this.tokAt (eval.iToken + 1));
|
| bsAtoms2 = (coordTo == null && eval.isArrayParameter (eval.iToken + 1) ? null : (tok == 10 || tok == 1073742325 ? this.atomExpressionAt (++eval.iToken) : JU.BSUtil.copy (bsAtoms1)));
|
| if (bsSubset != null) {
|
| bsAtoms1.and (bsSubset);
|
| if (bsAtoms2 != null) bsAtoms2.and (bsSubset);
|
| }if (bsAtoms2 == null) coordTo = eval.getPointArray (++eval.iToken, -1, false);
|
| else if (bsTo != null) bsAtoms2.and (bsTo);
|
| if (vAtomSets == null) vAtomSets = new JU.Lst ();
|
| vAtomSets.addLast ( Clazz_newArray (-1, [bsAtoms1, bsAtoms2]));
|
| i = eval.iToken;
|
| break;
|
| case 7:
|
| if (vAtomSets != null) this.invArg ();
|
| isQuaternion = true;
|
| data1 = eval.getQuaternionArray ((eval.theToken).getList (), 1073742001);
|
| this.getToken (++i);
|
| data2 = eval.getQuaternionArray ((eval.theToken).getList (), 1073742001);
|
| if (vQuatSets == null) vQuatSets = new JU.Lst ();
|
| vQuatSets.addLast ( Clazz_newArray (-1, [data1, data2]));
|
| break;
|
| case 1073742077:
|
| isQuaternion = true;
|
| break;
|
| case 134217751:
|
| case 1140850689:
|
| isQuaternion = false;
|
| break;
|
| case 528432:
|
| doRotate = true;
|
| break;
|
| case 4160:
|
| doTranslate = true;
|
| break;
|
| default:
|
| this.invArg ();
|
| }
|
| }
|
| if (this.chk) return;
|
| if (isFrames) nSeconds = 0;
|
| if (Float.isNaN (nSeconds) || nSeconds < 0) nSeconds = 1;
|
| else if (!doRotate && !doTranslate) doRotate = doTranslate = true;
|
| doAnimate = (nSeconds != 0);
|
| var isAtoms = (!isQuaternion && strSmiles == null || coordTo != null);
|
| if (isAtoms) J.api.Interface.getInterface ("JU.Eigen", this.vwr, "script");
|
| if (vAtomSets == null && vQuatSets == null) {
|
| if (bsSubset == null) {
|
| bsAtoms1 = (isAtoms ? this.vwr.getAtomBitSet ("spine") : new JU.BS ());
|
| if (bsAtoms1.nextSetBit (0) < 0) {
|
| bsAtoms1 = bsFrom;
|
| bsAtoms2 = bsTo;
|
| } else {
|
| bsAtoms2 = JU.BSUtil.copy (bsAtoms1);
|
| bsAtoms1.and (bsFrom);
|
| bsAtoms2.and (bsTo);
|
| }} else {
|
| bsAtoms1 = JU.BSUtil.copy (bsFrom);
|
| bsAtoms2 = JU.BSUtil.copy (bsTo);
|
| bsAtoms1.and (bsSubset);
|
| bsAtoms1.and (bsFrom);
|
| if (bsAtoms2 != null) {
|
| bsAtoms2.and (bsSubset);
|
| bsAtoms2.and (bsTo);
|
| }}vAtomSets = new JU.Lst ();
|
| vAtomSets.addLast ( Clazz_newArray (-1, [bsAtoms1, bsAtoms2]));
|
| }var bsFrames;
|
| if (isFrames) {
|
| var bsModels = this.vwr.ms.getModelBS (bsFrom, false);
|
| bsFrames = new Array (bsModels.cardinality ());
|
| for (var i = 0, iModel = bsModels.nextSetBit (0); iModel >= 0; iModel = bsModels.nextSetBit (iModel + 1), i++) bsFrames[i] = this.vwr.getModelUndeletedAtomsBitSet (iModel);
|
|
|
| } else {
|
| bsFrames = Clazz_newArray (-1, [bsFrom]);
|
| }for (var iFrame = 0; iFrame < bsFrames.length; iFrame++) {
|
| bsFrom = bsFrames[iFrame];
|
| var retStddev = Clazz_newFloatArray (2, 0);
|
| var q = null;
|
| var vQ = new JU.Lst ();
|
| var centerAndPoints = null;
|
| var vAtomSets2 = (isFrames ? new JU.Lst () : vAtomSets);
|
| for (var i = 0; i < vAtomSets.size (); ++i) {
|
| var bss = vAtomSets.get (i);
|
| if (isFrames) vAtomSets2.addLast (bss = Clazz_newArray (-1, [JU.BSUtil.copy (bss[0]), bss[1]]));
|
| bss[0].and (bsFrom);
|
| }
|
| var center = null;
|
| var translation = null;
|
| if (isAtoms) {
|
| if (coordTo != null) {
|
| vAtomSets2.clear ();
|
| vAtomSets2.addLast ( Clazz_newArray (-1, [bsAtoms1, coordTo]));
|
| }try {
|
| centerAndPoints = this.vwr.getCenterAndPoints (vAtomSets2, true);
|
| } catch (ex) {
|
| if (Clazz_exceptionOf (ex, Exception)) {
|
| this.invArg ();
|
| } else {
|
| throw ex;
|
| }
|
| }
|
| var n = centerAndPoints[0].length - 1;
|
| for (var i = 1; i <= n; i++) {
|
| var aij = centerAndPoints[0][i];
|
| var bij = centerAndPoints[1][i];
|
| if (!(Clazz_instanceOf (aij, JM.Atom)) || !(Clazz_instanceOf (bij, JM.Atom))) break;
|
| JU.Logger.info (" atom 1 " + (aij).getInfo () + "\tatom 2 " + (bij).getInfo ());
|
| }
|
| q = JU.Measure.calculateQuaternionRotation (centerAndPoints, retStddev);
|
| var r0 = (Float.isNaN (retStddev[1]) ? NaN : Math.round (retStddev[0] * 100) / 100);
|
| var r1 = (Float.isNaN (retStddev[1]) ? NaN : Math.round (retStddev[1] * 100) / 100);
|
| this.showString ("RMSD " + r0 + " --> " + r1 + " Angstroms");
|
| } else if (isQuaternion) {
|
| if (vQuatSets == null) {
|
| for (var i = 0; i < vAtomSets2.size (); i++) {
|
| var bss = vAtomSets2.get (i);
|
| data1 = this.vwr.getAtomGroupQuaternions (bss[0], 2147483647);
|
| data2 = this.vwr.getAtomGroupQuaternions (bss[1], 2147483647);
|
| for (var j = 0; j < data1.length && j < data2.length; j++) {
|
| vQ.addLast (data2[j].div (data1[j]));
|
| }
|
| }
|
| } else {
|
| for (var j = 0; j < data1.length && j < data2.length; j++) {
|
| vQ.addLast (data2[j].div (data1[j]));
|
| }
|
| }retStddev[0] = 0;
|
| data1 = vQ.toArray ( new Array (vQ.size ()));
|
| q = JU.Quat.sphereMean (data1, retStddev, 0.0001);
|
| this.showString ("RMSD = " + retStddev[0] + " degrees");
|
| } else {
|
| var m4 = new JU.M4 ();
|
| center = new JU.P3 ();
|
| if (("*".equals (strSmiles) || "".equals (strSmiles)) && bsFrom != null) try {
|
| strSmiles = this.vwr.getSmiles (bsFrom);
|
| } catch (ex) {
|
| if (Clazz_exceptionOf (ex, Exception)) {
|
| eval.evalError (ex.getMessage (), null);
|
| } else {
|
| throw ex;
|
| }
|
| }
|
| if (isFlexFit) {
|
| var list;
|
| if (bsFrom == null || bsTo == null || (list = eval.getSmilesExt ().getFlexFitList (bsFrom, bsTo, strSmiles, !isSmiles)) == null) return;
|
| this.vwr.setDihedrals (list, null, 1);
|
| }var stddev = eval.getSmilesExt ().getSmilesCorrelation (bsFrom, bsTo, strSmiles, null, null, m4, null, false, null, center, false, 32 | (isSmiles ? 1 : 2));
|
| if (Float.isNaN (stddev)) {
|
| this.showString ("structures do not match");
|
| return;
|
| }if (doTranslate) {
|
| translation = new JU.V3 ();
|
| m4.getTranslation (translation);
|
| }if (doRotate) {
|
| var m3 = new JU.M3 ();
|
| m4.getRotationScale (m3);
|
| q = JU.Quat.newM (m3);
|
| }this.showString ("RMSD = " + stddev + " Angstroms");
|
| }if (centerAndPoints != null) center = centerAndPoints[0][0];
|
| if (center == null) {
|
| centerAndPoints = this.vwr.getCenterAndPoints (vAtomSets2, true);
|
| center = centerAndPoints[0][0];
|
| }var pt1 = new JU.P3 ();
|
| var endDegrees = NaN;
|
| if (doTranslate) {
|
| if (translation == null) translation = JU.V3.newVsub (centerAndPoints[1][0], center);
|
| endDegrees = 1e10;
|
| }if (doRotate) {
|
| if (q == null) eval.evalError ("option not implemented", null);
|
| pt1.add2 (center, q.getNormal ());
|
| endDegrees = q.getTheta ();
|
| if (endDegrees == 0 && doTranslate) {
|
| if (translation.length () > 0.01) endDegrees = 1e10;
|
| else doRotate = doTranslate = doAnimate = false;
|
| }}if (Float.isNaN (endDegrees) || Float.isNaN (pt1.x)) continue;
|
| var ptsB = null;
|
| if (doRotate && doTranslate && nSeconds != 0) {
|
| var ptsA = this.vwr.ms.getAtomPointVector (bsFrom);
|
| var m4 = JS.ScriptMathProcessor.getMatrix4f (q.getMatrix (), translation);
|
| ptsB = JU.Measure.transformPoints (ptsA, m4, center);
|
| }if (!eval.useThreads ()) doAnimate = false;
|
| if (this.vwr.rotateAboutPointsInternal (eval, center, pt1, endDegrees / nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB, null, null) && doAnimate && eval.isJS) throw new JS.ScriptInterruption (eval, "compare", 1);
|
| }
|
| });
|
| Clazz_defineMethod (c$, "configuration",
|
| function () {
|
| var bsAtoms = null;
|
| var bsSelected = this.vwr.bsA ();
|
| if (this.slen == 1) {
|
| if (this.chk) return;
|
| bsAtoms = this.vwr.ms.setConformation (bsSelected);
|
| this.vwr.ms.addStateScript ("select", null, bsSelected, null, "configuration", true, false);
|
| } else {
|
| var n;
|
| if (this.isFloatParameter (1)) {
|
| n = this.intParameter (this.e.checkLast (1));
|
| if (this.chk) return;
|
| bsAtoms = this.vwr.ms.getConformation (this.vwr.am.cmi, n - 1, true, null);
|
| this.vwr.addStateScript ("configuration " + n + ";", true, false);
|
| } else {
|
| bsAtoms = this.atomExpressionAt (1);
|
| if (this.chk) return;
|
| n = this.intParameter (this.e.checkLast (this.e.iToken + 1));
|
| this.vwr.addStateScript ("configuration " + JU.Escape.eBS (bsAtoms) + " " + n + ";", true, false);
|
| bsAtoms = this.vwr.ms.getConformation (this.vwr.am.cmi, n - 1, true, bsAtoms);
|
| }}this.setShapeProperty (1, "type", Integer.$valueOf (30720));
|
| this.e.setShapeSizeBs (1, 0, bsAtoms);
|
| this.vwr.autoHbond (bsAtoms, bsAtoms, true);
|
| this.vwr.select (bsAtoms, false, 0, this.e.tQuiet);
|
| });
|
| Clazz_defineMethod (c$, "measure",
|
| function () {
|
| var eval = this.e;
|
| var id = null;
|
| var pt = 1;
|
| var colix = 0;
|
| var offset = null;
|
| if (this.slen == 2) switch (this.tokAt (1)) {
|
| case 1073742334:
|
| this.setShapeProperty (6, "hideAll", Boolean.TRUE);
|
| return;
|
| case 12291:
|
| if (!this.chk) this.vwr.clearAllMeasurements ();
|
| return;
|
| }
|
| this.vwr.shm.loadShape (6);
|
| switch (this.tokAt (1)) {
|
| case 134218756:
|
| var smarts = this.stringParameter (this.slen == 3 ? 2 : 4);
|
| if (this.chk) return;
|
| var atoms = this.vwr.ms.at;
|
| var ac = this.vwr.ms.ac;
|
| var maps = null;
|
| try {
|
| maps = this.vwr.getSmilesMatcher ().getCorrelationMaps (smarts, atoms, ac, this.vwr.bsA (), 2);
|
| } catch (ex) {
|
| if (Clazz_exceptionOf (ex, Exception)) {
|
| eval.evalError (ex.getMessage (), null);
|
| } else {
|
| throw ex;
|
| }
|
| }
|
| if (maps == null) return;
|
| this.setShapeProperty (6, "maps", maps);
|
| return;
|
| }
|
| switch (this.slen) {
|
| case 2:
|
| switch (this.getToken (pt).tok) {
|
| case 0:
|
| case 1073742335:
|
| this.vwr.shm.loadShape (6);
|
| this.setShapeProperty (6, "hideAll", Boolean.FALSE);
|
| return;
|
| case 1073742001:
|
| if (!this.chk) eval.showStringPrint (this.vwr.getMeasurementInfoAsString (), false);
|
| return;
|
| case 4:
|
| this.setShapeProperty (6, "setFormats", this.stringParameter (1));
|
| return;
|
| }
|
| eval.errorStr (24, "ON, OFF, DELETE");
|
| break;
|
| case 3:
|
| switch (this.getToken (1).tok) {
|
| case 12291:
|
| if (this.getToken (2).tok == 1073742327) {
|
| if (!this.chk) this.vwr.clearAllMeasurements ();
|
| } else {
|
| var i = this.intParameter (2) - 1;
|
| if (!this.chk) this.vwr.deleteMeasurement (i);
|
| }return;
|
| }
|
| }
|
| var nAtoms = 0;
|
| var expressionCount = 0;
|
| var modelIndex = -1;
|
| var atomIndex = -1;
|
| var ptFloat = -1;
|
| var countPlusIndexes = Clazz_newIntArray (5, 0);
|
| var rangeMinMax = Clazz_newFloatArray (-1, [3.4028235E38, 3.4028235E38]);
|
| var isAll = false;
|
| var isAllConnected = false;
|
| var isNotConnected = false;
|
| var isRange = true;
|
| var rd = null;
|
| var intramolecular = null;
|
| var tokAction = 268435538;
|
| var strFormat = null;
|
| var font = null;
|
| var points = new JU.Lst ();
|
| var bs = new JU.BS ();
|
| var value = null;
|
| var tickInfo = null;
|
| var nBitSets = 0;
|
| var mad = 0;
|
| var alignment = null;
|
| for (var i = 1; i < this.slen; ++i) {
|
| switch (this.getToken (i).tok) {
|
| case 1073741974:
|
| if (i != 1) this.invArg ();
|
| id = eval.optParameterAsString (++i);
|
| continue;
|
| case 1073741824:
|
| eval.errorStr (24, "ALL, ALLCONNECTED, DELETE");
|
| break;
|
| default:
|
| this.error (15);
|
| break;
|
| case 268435568:
|
| if (this.tokAt (i + 1) != 134217736) this.invArg ();
|
| i++;
|
| isNotConnected = true;
|
| break;
|
| case 1073741832:
|
| alignment = this.paramAsStr (++i).toLowerCase ();
|
| break;
|
| case 134217736:
|
| case 1073741834:
|
| case 1073742327:
|
| isAllConnected = (eval.theTok == 1073741834);
|
| atomIndex = -1;
|
| isAll = true;
|
| if (isAllConnected && isNotConnected) this.invArg ();
|
| break;
|
| case 1765808134:
|
| colix = JU.C.getColix (eval.getArgbParam (++i));
|
| i = eval.iToken;
|
| break;
|
| case 1073742066:
|
| if (eval.isPoint3f (++i)) {
|
| var p = this.getPoint3f (i, false);
|
| offset = Clazz_newFloatArray (-1, [1, p.x, p.y, p.z, 0, 0, 0]);
|
| } else {
|
| offset = eval.floatParameterSet (i, 7, 7);
|
| }i = eval.iToken;
|
| break;
|
| case 1665140738:
|
| case 1073741917:
|
| mad = Clazz_floatToInt ((eval.theTok == 1665140738 ? 2000 : 1000) * this.floatParameter (++i));
|
| if (id != null && mad <= 0) mad = -1;
|
| break;
|
| case 3:
|
| if (rd != null) this.invArg ();
|
| isAll = true;
|
| isRange = true;
|
| ptFloat = (ptFloat + 1) % 2;
|
| rangeMinMax[ptFloat] = this.floatParameter (i);
|
| break;
|
| case 12291:
|
| if (tokAction != 268435538) this.invArg ();
|
| tokAction = 12291;
|
| break;
|
| case 4114:
|
| var fontsize = this.floatParameter (++i);
|
| var fontface = this.paramAsStr (++i);
|
| var fontstyle = this.paramAsStr (++i);
|
| if (!this.chk) font = this.vwr.getFont3D (fontface, fontstyle, fontsize);
|
| break;
|
| case 2:
|
| var iParam = this.intParameter (i);
|
| if (isAll) {
|
| isRange = true;
|
| ptFloat = (ptFloat + 1) % 2;
|
| rangeMinMax[ptFloat] = iParam;
|
| } else {
|
| atomIndex = this.vwr.ms.getFirstAtomIndexFromAtomNumber (iParam, this.vwr.getVisibleFramesBitSet ());
|
| if (!this.chk && atomIndex < 0) return;
|
| if (value != null) this.invArg ();
|
| if ((countPlusIndexes[0] = ++nAtoms) > 4) eval.bad ();
|
| countPlusIndexes[nAtoms] = atomIndex;
|
| }break;
|
| case 1094713359:
|
| modelIndex = this.intParameter (++i);
|
| break;
|
| case 1073742334:
|
| if (tokAction != 268435538) this.invArg ();
|
| tokAction = 1073742334;
|
| break;
|
| case 1073742335:
|
| if (tokAction != 268435538) this.invArg ();
|
| tokAction = 1073742335;
|
| break;
|
| case 1073742114:
|
| isAll = true;
|
| isRange = true;
|
| atomIndex = -1;
|
| break;
|
| case 1073741989:
|
| case 1073741990:
|
| intramolecular = Boolean.$valueOf (eval.theTok == 1073741989);
|
| isAll = true;
|
| isNotConnected = (eval.theTok == 1073741990);
|
| break;
|
| case 1648363544:
|
| if (ptFloat >= 0) this.invArg ();
|
| rd = eval.encodeRadiusParameter (i, false, true);
|
| if (rd == null) return;
|
| rd.values = rangeMinMax;
|
| i = eval.iToken;
|
| isNotConnected = true;
|
| isAll = true;
|
| intramolecular = Boolean.$valueOf (false);
|
| if (nBitSets == 1) {
|
| nBitSets++;
|
| nAtoms++;
|
| var bs2 = JU.BSUtil.copy (bs);
|
| JU.BSUtil.invertInPlace (bs2, this.vwr.ms.ac);
|
| bs2.and (this.vwr.ms.getAtomsWithinRadius (5, bs, false, null));
|
| points.addLast (bs2);
|
| }break;
|
| case 12290:
|
| case 10:
|
| case 1073742325:
|
| nBitSets++;
|
| case 1073742332:
|
| case 8:
|
| case 1073742330:
|
| if (atomIndex >= 0) this.invArg ();
|
| var ret = new Array (1);
|
| value = eval.centerParameter (i, ret);
|
| if (Clazz_instanceOf (ret[0], JU.BS)) {
|
| value = bs = ret[0];
|
| if (!this.chk && bs.length () == 0) return;
|
| }if (Clazz_instanceOf (value, JU.P3)) {
|
| var v = new JU.Point3fi ();
|
| v.setT (value);
|
| v.mi = modelIndex;
|
| value = v;
|
| }if ((nAtoms = ++expressionCount) > 4) eval.bad ();
|
| i = eval.iToken;
|
| points.addLast (value);
|
| break;
|
| case 4:
|
| strFormat = this.stringParameter (i);
|
| break;
|
| case 1073742164:
|
| tickInfo = eval.tickParamAsStr (i, false, true, true);
|
| i = eval.iToken;
|
| tokAction = 12290;
|
| break;
|
| }
|
| }
|
| if (rd != null && (ptFloat >= 0 || nAtoms != 2) || nAtoms < 2 && id == null && (tickInfo == null || nAtoms == 1)) eval.bad ();
|
| if (strFormat != null && strFormat.indexOf (nAtoms + ":") != 0) strFormat = nAtoms + ":" + strFormat;
|
| if (isRange) {
|
| if (rangeMinMax[1] < rangeMinMax[0]) {
|
| rangeMinMax[1] = rangeMinMax[0];
|
| rangeMinMax[0] = (rangeMinMax[1] == 3.4028235E38 ? 3.4028235E38 : -200);
|
| }}if (this.chk) return;
|
| if (value != null || tickInfo != null) {
|
| if (rd == null) rd = new J.atomdata.RadiusData (rangeMinMax, 0, null, null);
|
| if (value == null) tickInfo.id = "default";
|
| if (value != null && strFormat != null && tokAction == 268435538) tokAction = 12290;
|
| var text = null;
|
| if (font != null || alignment != null || strFormat != null && strFormat.indexOf ('\n') >= 0) text = (J.api.Interface.getInterface ("JM.Text", this.vwr, "script")).newLabel (this.vwr, font, "", colix, 0, 0, 0);
|
| if (text != null) {
|
| text.pymolOffset = offset;
|
| text.setAlignmentLCR (alignment);
|
| }this.setShapeProperty (6, "measure", this.vwr.newMeasurementData (id, points).set (tokAction, null, rd, strFormat, null, tickInfo, isAllConnected, isNotConnected, intramolecular, isAll, mad, colix, text));
|
| return;
|
| }var propertyValue = (id == null ? countPlusIndexes : id);
|
| switch (tokAction) {
|
| case 12291:
|
| this.setShapeProperty (6, "delete", propertyValue);
|
| break;
|
| case 1073742335:
|
| this.setShapeProperty (6, "show", propertyValue);
|
| break;
|
| case 1073742334:
|
| this.setShapeProperty (6, "hide", propertyValue);
|
| break;
|
| default:
|
| this.setShapeProperty (6, (strFormat == null ? "toggle" : "toggleOn"), propertyValue);
|
| if (strFormat != null) this.setShapeProperty (6, "setFormats", strFormat);
|
| }
|
| });
|
| Clazz_defineMethod (c$, "connect",
|
| function (index) {
|
| var eval = this.e;
|
| var distances = Clazz_newFloatArray (2, 0);
|
| var atomSets = new Array (2);
|
| atomSets[0] = atomSets[1] = this.vwr.bsA ();
|
| var radius = NaN;
|
| var colorArgb = Clazz_newIntArray (-1, [-2147483648]);
|
| var distanceCount = 0;
|
| var bondOrder = 131071;
|
| var bo;
|
| var operation = 1073742026;
|
| var isDelete = false;
|
| var haveType = false;
|
| var haveOperation = false;
|
| var translucentLevel = 3.4028235E38;
|
| var isColorOrRadius = false;
|
| var nAtomSets = 0;
|
| var nDistances = 0;
|
| var bsBonds = new JU.BS ();
|
| var isBonds = false;
|
| var expression2 = 0;
|
| var ptColor = 0;
|
| var energy = 0;
|
| var addGroup = false;
|
| if (this.slen == 1) {
|
| if (!this.chk) this.vwr.rebondState (eval.$isStateScript);
|
| return;
|
| }if (this.tokAt (1) == 1073877011) {
|
| if (!this.chk) this.vwr.connectNBO (this.e.optParameterAsString (2));
|
| return;
|
| }for (var i = index; i < this.slen; ++i) {
|
| switch (this.getToken (i).tok) {
|
| case 1073742335:
|
| case 1073742334:
|
| this.checkLength (2);
|
| if (!this.chk) this.vwr.rebondState (eval.$isStateScript);
|
| return;
|
| case 2:
|
| case 3:
|
| if (nAtomSets > 0) {
|
| if (haveType || isColorOrRadius) eval.error (23);
|
| bo = JU.Edge.getBondOrderFromFloat (this.floatParameter (i));
|
| if (bo == 131071) this.invArg ();
|
| bondOrder = bo;
|
| haveType = true;
|
| break;
|
| }if (++nDistances > 2) eval.bad ();
|
| var dist = this.floatParameter (i);
|
| if (this.tokAt (i + 1) == 268435634) {
|
| dist = -dist / 100;
|
| i++;
|
| }distances[distanceCount++] = dist;
|
| break;
|
| case 12290:
|
| case 10:
|
| case 1073742325:
|
| if (nAtomSets > 2 || isBonds && nAtomSets > 0) eval.bad ();
|
| if (haveType || isColorOrRadius) this.invArg ();
|
| atomSets[nAtomSets++] = this.atomExpressionAt (i);
|
| isBonds = eval.isBondSet;
|
| if (nAtomSets == 2) {
|
| var pt = eval.iToken;
|
| for (var j = i; j < pt; j++) if (this.tokAt (j) == 1073741824 && this.paramAsStr (j).equals ("_1")) {
|
| expression2 = i;
|
| break;
|
| }
|
| eval.iToken = pt;
|
| }i = eval.iToken;
|
| break;
|
| case 1086324742:
|
| addGroup = true;
|
| break;
|
| case 1765808134:
|
| case 603979967:
|
| case 1073742074:
|
| isColorOrRadius = true;
|
| translucentLevel = this.getColorTrans (eval, i, false, colorArgb);
|
| i = eval.iToken;
|
| break;
|
| case 1073742086:
|
| var isAuto = (this.tokAt (2) == 1073741852);
|
| this.checkLength (isAuto ? 3 : 2);
|
| if (this.chk) return;
|
| this.vwr.clearModelDependentObjects ();
|
| this.vwr.ms.deleteAllBonds ();
|
| var bsExclude = new JU.BS ();
|
| this.vwr.ms.setPdbConectBonding (0, 0, bsExclude);
|
| if (isAuto) {
|
| var isLegacy = eval.$isStateScript && this.vwr.getBoolean (603979873);
|
| this.vwr.ms.autoBondBs4 (null, null, bsExclude, null, this.vwr.getMadBond (), isLegacy);
|
| this.vwr.addStateScript ((isLegacy ? "set legacyAutoBonding TRUE;connect PDB AUTO;set legacyAutoBonding FALSE;" : "connect PDB auto;"), false, true);
|
| return;
|
| }this.vwr.addStateScript ("connect PDB;", false, true);
|
| return;
|
| case 1073741830:
|
| case 1073741852:
|
| case 1073741904:
|
| case 1073742025:
|
| case 1073742026:
|
| haveOperation = true;
|
| if (++i != this.slen) this.invArg ();
|
| operation = eval.theTok;
|
| if (operation == 1073741852 && !(bondOrder == 131071 || bondOrder == 2048 || bondOrder == 515)) this.invArg ();
|
| break;
|
| case 659482:
|
| if (!isColorOrRadius) {
|
| colorArgb[0] = 0xFFFFFF;
|
| translucentLevel = 0.5;
|
| radius = this.vwr.getFloat (570425406);
|
| isColorOrRadius = true;
|
| }if (!haveOperation) {
|
| operation = 1073742026;
|
| haveOperation = true;
|
| }case 1073741824:
|
| if (eval.isColorParam (i)) {
|
| ptColor = -i;
|
| break;
|
| }case 1075838996:
|
| case 1613238294:
|
| var cmd = this.paramAsStr (i);
|
| if ((bo = JS.ScriptParam.getBondOrderFromString (cmd)) == 131071) this.invArg ();
|
| if (haveType) eval.error (18);
|
| haveType = true;
|
| switch (bo) {
|
| case 33:
|
| switch (this.tokAt (i + 1)) {
|
| case 3:
|
| bo = JS.ScriptParam.getPartialBondOrderFromFloatEncodedInt (this.st[++i].intValue);
|
| break;
|
| case 2:
|
| bo = this.intParameter (++i);
|
| break;
|
| }
|
| break;
|
| case 2048:
|
| if (this.tokAt (i + 1) == 2) {
|
| bo = (this.intParameter (++i) << 11);
|
| energy = this.floatParameter (++i);
|
| }break;
|
| case 65537:
|
| if (!haveOperation) {
|
| operation = 1073742025;
|
| haveOperation = true;
|
| }break;
|
| }
|
| bondOrder = bo;
|
| break;
|
| case 1665140738:
|
| radius = this.floatParameter (++i);
|
| isColorOrRadius = true;
|
| break;
|
| case 1073742333:
|
| case 12291:
|
| if (++i != this.slen) this.invArg ();
|
| operation = 12291;
|
| isDelete = true;
|
| isColorOrRadius = false;
|
| break;
|
| default:
|
| ptColor = i;
|
| break;
|
| }
|
| if (i > 0) {
|
| if (ptColor == -i || ptColor == i && eval.isColorParam (i)) {
|
| isColorOrRadius = true;
|
| colorArgb[0] = eval.getArgbParam (i);
|
| i = eval.iToken;
|
| } else if (ptColor == i) {
|
| this.invArg ();
|
| }}}
|
| if (this.chk) return;
|
| if (distanceCount < 2) {
|
| if (distanceCount == 0) distances[0] = 1.0E8;
|
| distances[1] = distances[0];
|
| distances[0] = 0.1;
|
| }if (isColorOrRadius) {
|
| if (!haveType) bondOrder = 65535;
|
| if (!haveOperation) operation = 1073742025;
|
| }var nNew = 0;
|
| var nModified = 0;
|
| var result;
|
| if (expression2 > 0) {
|
| var bs = new JU.BS ();
|
| this.vwr.definedAtomSets.put ("_1", bs);
|
| var bs0 = atomSets[0];
|
| for (var atom1 = bs0.nextSetBit (0); atom1 >= 0; atom1 = bs0.nextSetBit (atom1 + 1)) {
|
| bs.set (atom1);
|
| result = this.vwr.makeConnections (distances[0], distances[1], bondOrder, operation, bs, this.atomExpressionAt (expression2), bsBonds, isBonds, false, 0);
|
| nNew += Math.abs (result[0]);
|
| nModified += result[1];
|
| bs.clear (atom1);
|
| }
|
| } else {
|
| result = this.vwr.makeConnections (distances[0], distances[1], bondOrder, operation, atomSets[0], atomSets[1], bsBonds, isBonds, addGroup, energy);
|
| nNew += Math.abs (result[0]);
|
| nModified += result[1];
|
| }var report = eval.doReport ();
|
| if (isDelete) {
|
| if (report) eval.report (J.i18n.GT.i (J.i18n.GT.$ ("{0} connections deleted"), nModified), false);
|
| return;
|
| }if (isColorOrRadius) {
|
| this.vwr.selectBonds (bsBonds);
|
| if (!Float.isNaN (radius)) eval.setShapeSizeBs (1, Math.round (radius * 2000), null);
|
| this.finalizeObject (1, colorArgb[0], translucentLevel, 0, false, null, 0, bsBonds);
|
| this.vwr.selectBonds (null);
|
| }if (report) eval.report (J.i18n.GT.o (J.i18n.GT.$ ("{0} new bonds; {1} modified"), Clazz_newArray (-1, [Integer.$valueOf (nNew), Integer.$valueOf (nModified)])), false);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "console",
|
| function () {
|
| switch (this.getToken (1).tok) {
|
| case 1073742334:
|
| if (!this.chk) this.vwr.showConsole (false);
|
| break;
|
| case 1073742335:
|
| if (!this.chk) this.vwr.showConsole (true);
|
| break;
|
| case 1073741882:
|
| if (!this.chk) this.vwr.sm.clearConsole ();
|
| break;
|
| case 134221856:
|
| this.showString (this.stringParameter (2));
|
| break;
|
| default:
|
| this.invArg ();
|
| }
|
| });
|
| Clazz_defineMethod (c$, "data",
|
| function () {
|
| var eval = this.e;
|
| var dataString = null;
|
| var dataLabel = null;
|
| var isOneValue = false;
|
| var i;
|
| switch (eval.iToken = this.slen) {
|
| case 5:
|
| dataString = this.paramAsStr (2);
|
| case 4:
|
| case 2:
|
| dataLabel = this.paramAsStr (1);
|
| if (dataLabel.equalsIgnoreCase ("clear")) {
|
| if (!this.chk) this.vwr.setData (null, null, 0, 0, 0, 0, 0);
|
| return;
|
| }if ((i = dataLabel.indexOf ("@")) >= 0) {
|
| dataString = "" + eval.getParameter (dataLabel.substring (i + 1), 4, true);
|
| dataLabel = dataLabel.substring (0, i).trim ();
|
| } else if (dataString == null && (i = dataLabel.indexOf (" ")) >= 0) {
|
| dataString = dataLabel.substring (i + 1).trim ();
|
| dataLabel = dataLabel.substring (0, i).trim ();
|
| isOneValue = true;
|
| }break;
|
| default:
|
| eval.bad ();
|
| }
|
| var dataType = dataLabel.substring (0, (dataLabel + " ").indexOf (" ")).toLowerCase ();
|
| if (dataType.equals ("model") || dataType.equals ("append")) {
|
| eval.cmdLoad ();
|
| return;
|
| }if (this.chk) return;
|
| var isDefault = (dataLabel.toLowerCase ().indexOf ("(default)") >= 0);
|
| if (dataType.equals ("connect_atoms")) {
|
| this.vwr.ms.connect (this.parseDataArray (dataString, false));
|
| return;
|
| }if (dataType.indexOf ("ligand_") == 0) {
|
| this.vwr.setLigandModel (dataLabel.substring (7).toUpperCase () + "_data", dataString.trim ());
|
| return;
|
| }if (dataType.indexOf ("file_") == 0) {
|
| this.vwr.setLigandModel (dataLabel.substring (5) + "_file", dataString.trim ());
|
| return;
|
| }var d = new Array (4);
|
| if (dataType.equals ("element_vdw")) {
|
| d[0] = dataType;
|
| d[1] = dataString.$replace (';', '\n');
|
| var n = JU.Elements.elementNumberMax;
|
| var eArray = Clazz_newIntArray (n + 1, 0);
|
| for (var ie = 1; ie <= n; ie++) eArray[ie] = ie;
|
|
|
| d[2] = eArray;
|
| d[3] = Integer.$valueOf (0);
|
| this.vwr.setData ("element_vdw", d, n, 0, 0, 0, 0);
|
| return;
|
| }if (dataType.indexOf ("data2d_") == 0) {
|
| d[0] = dataLabel;
|
| d[1] = this.parseDataArray (dataString, false);
|
| d[3] = Integer.$valueOf (2);
|
| this.vwr.setData (dataLabel, d, 0, 0, 0, 0, 0);
|
| return;
|
| }if (dataType.indexOf ("data3d_") == 0) {
|
| d[0] = dataLabel;
|
| d[1] = this.parseDataArray (dataString, true);
|
| d[3] = Integer.$valueOf (3);
|
| this.vwr.setData (dataLabel, d, 0, 0, 0, 0, 0);
|
| return;
|
| }var tokens = JU.PT.getTokens (dataLabel);
|
| if (dataType.indexOf ("property_") == 0 && !(tokens.length == 2 && tokens[1].equals ("set"))) {
|
| var bs = this.vwr.bsA ();
|
| d[0] = dataType;
|
| var atomNumberField = (isOneValue ? 0 : (this.vwr.getP ("propertyAtomNumberField")).intValue ());
|
| var atomNumberFieldColumnCount = (isOneValue ? 0 : (this.vwr.getP ("propertyAtomNumberColumnCount")).intValue ());
|
| var propertyField = (isOneValue ? -2147483648 : (this.vwr.getP ("propertyDataField")).intValue ());
|
| var propertyFieldColumnCount = (isOneValue ? 0 : (this.vwr.getP ("propertyDataColumnCount")).intValue ());
|
| if (!isOneValue && dataLabel.indexOf (" ") >= 0) {
|
| if (tokens.length == 3) {
|
| dataLabel = tokens[0];
|
| atomNumberField = JU.PT.parseInt (tokens[1]);
|
| propertyField = JU.PT.parseInt (tokens[2]);
|
| }if (tokens.length == 5) {
|
| dataLabel = tokens[0];
|
| atomNumberField = JU.PT.parseInt (tokens[1]);
|
| atomNumberFieldColumnCount = JU.PT.parseInt (tokens[2]);
|
| propertyField = JU.PT.parseInt (tokens[3]);
|
| propertyFieldColumnCount = JU.PT.parseInt (tokens[4]);
|
| }}if (atomNumberField < 0) atomNumberField = 0;
|
| if (propertyField < 0) propertyField = 0;
|
| var ac = this.vwr.ms.ac;
|
| var atomMap = null;
|
| var bsTemp = JU.BS.newN (ac);
|
| if (atomNumberField > 0) {
|
| atomMap = Clazz_newIntArray (ac + 2, 0);
|
| for (var j = 0; j <= ac; j++) atomMap[j] = -1;
|
|
|
| for (var j = bs.nextSetBit (0); j >= 0; j = bs.nextSetBit (j + 1)) {
|
| var atomNo = this.vwr.ms.at[j].getAtomNumber ();
|
| if (atomNo > ac + 1 || atomNo < 0 || bsTemp.get (atomNo)) continue;
|
| bsTemp.set (atomNo);
|
| atomMap[atomNo] = j;
|
| }
|
| d[2] = atomMap;
|
| } else {
|
| d[2] = JU.BSUtil.copy (bs);
|
| }d[1] = dataString;
|
| d[3] = Integer.$valueOf (0);
|
| this.vwr.setData (dataType, d, ac, atomNumberField, atomNumberFieldColumnCount, propertyField, propertyFieldColumnCount);
|
| return;
|
| }if ("occupany".equals (dataType)) dataType = "occupancy";
|
| var userType = JM.AtomCollection.getUserSettableType (dataType);
|
| if (userType > -1) {
|
| this.vwr.setAtomData (userType, dataType, dataString, isDefault);
|
| return;
|
| }d[0] = dataLabel;
|
| d[1] = dataString;
|
| d[3] = Integer.$valueOf (0);
|
| this.vwr.setData (dataType, d, 0, 0, 0, 0, 0);
|
| });
|
| Clazz_defineMethod (c$, "ellipsoid",
|
| function () {
|
| var eval = this.e;
|
| var mad = 0;
|
| var i = 1;
|
| var translucentLevel = 3.4028235E38;
|
| var checkMore = false;
|
| var isSet = false;
|
| this.setShapeProperty (20, "thisID", null);
|
| switch (this.getToken (1).tok) {
|
| case 1073742335:
|
| mad = 2147483647;
|
| break;
|
| case 1073742334:
|
| break;
|
| case 2:
|
| mad = this.intParameter (1);
|
| break;
|
| case 36867:
|
| this.e.sm.loadShape (20);
|
| this.setShapeProperty (20, "select", this.paramAsStr (2));
|
| i = eval.iToken;
|
| checkMore = true;
|
| isSet = true;
|
| break;
|
| case 1073741974:
|
| case 268435633:
|
| case 1073741824:
|
| this.e.sm.loadShape (20);
|
| if (eval.theTok == 1073741974) i++;
|
| this.setShapeId (20, i, false);
|
| i = eval.iToken;
|
| checkMore = true;
|
| break;
|
| default:
|
| this.invArg ();
|
| }
|
| if (!checkMore) {
|
| eval.setShapeSizeBs (20, mad, null);
|
| return;
|
| }var colorArgb = Clazz_newIntArray (-1, [-2147483648]);
|
| while (++i < this.slen) {
|
| var key = this.paramAsStr (i);
|
| var value = null;
|
| this.getToken (i);
|
| if (!isSet) switch (eval.theTok) {
|
| case 1073742330:
|
| key = "points";
|
| var data = new Array (3);
|
| data[0] = eval.objectNameParameter (++i);
|
| if (this.chk) continue;
|
| eval.getShapePropertyData (24, "getVertices", data);
|
| value = data;
|
| break;
|
| case 1611272194:
|
| var axes = new Array (3);
|
| for (var j = 0; j < 3; j++) {
|
| axes[j] = new JU.V3 ();
|
| axes[j].setT (this.centerParameter (++i));
|
| i = eval.iToken;
|
| }
|
| value = axes;
|
| break;
|
| case 12289:
|
| value = this.centerParameter (++i);
|
| i = eval.iToken;
|
| break;
|
| case 1094713359:
|
| value = Integer.$valueOf (this.intParameter (++i));
|
| break;
|
| case 12291:
|
| value = Boolean.TRUE;
|
| this.checkLength (i + 1);
|
| break;
|
| }
|
| if (value == null) switch (eval.theTok) {
|
| case 1073742335:
|
| key = "on";
|
| value = Boolean.TRUE;
|
| break;
|
| case 1073742334:
|
| key = "on";
|
| value = Boolean.FALSE;
|
| break;
|
| case 1073742138:
|
| value = Float.$valueOf (this.floatParameter (++i));
|
| break;
|
| case 12290:
|
| case 10:
|
| case 1073742325:
|
| key = "atoms";
|
| value = this.atomExpressionAt (i);
|
| i = eval.iToken;
|
| break;
|
| case 1765808134:
|
| case 603979967:
|
| case 1073742074:
|
| translucentLevel = this.getColorTrans (eval, i, true, colorArgb);
|
| i = eval.iToken;
|
| continue;
|
| case 1073742075:
|
| value = this.paramAsStr (++i);
|
| break;
|
| }
|
| if (value == null) this.invArg ();
|
| this.setShapeProperty (20, key.toLowerCase (), value);
|
| }
|
| this.finalizeObject (20, colorArgb[0], translucentLevel, 0, false, null, 0, null);
|
| this.setShapeProperty (20, "thisID", null);
|
| });
|
| Clazz_defineMethod (c$, "image",
|
| function () {
|
| if (!this.chk) this.vwr.getConsole ();
|
| var pt = 1;
|
| var id = null;
|
| if (this.tokAt (1) == 1073741974) {
|
| id = this.e.optParameterAsString (++pt);
|
| pt++;
|
| }var fileName = this.e.optParameterAsString (pt);
|
| var isClose = this.e.optParameterAsString (this.slen - 1).equalsIgnoreCase ("close");
|
| if (!isClose && (this.slen == pt || this.slen == pt + 2)) {
|
| var width = (this.slen == pt + 2 ? this.intParameter (pt++) : -1);
|
| var height = (width < 0 ? -1 : this.intParameter (pt));
|
| var params = new java.util.Hashtable ();
|
| params.put ("fileName", "\1\1" + id);
|
| params.put ("backgroundColor", Integer.$valueOf (this.vwr.getBackgroundArgb ()));
|
| params.put ("type", "png");
|
| params.put ("quality", Integer.$valueOf (-1));
|
| params.put ("width", Integer.$valueOf (width));
|
| params.put ("height", Integer.$valueOf (height));
|
| if (!this.chk) this.vwr.processWriteOrCapture (params);
|
| return;
|
| }pt++;
|
| if (isClose) {
|
| switch (this.slen) {
|
| case 2:
|
| fileName = "closeall";
|
| break;
|
| case 3:
|
| case 4:
|
| break;
|
| default:
|
| this.checkLength (0);
|
| }
|
| }if (!this.chk) this.vwr.fm.loadImage (isClose ? "\1close" : fileName, "\1" + fileName + "\1" + ("".equals (id) || id == null ? null : id), false);
|
| });
|
| Clazz_defineMethod (c$, "invertSelected",
|
| function () {
|
| var eval = this.e;
|
| var pt = null;
|
| var plane = null;
|
| var bs = null;
|
| var iAtom = -2147483648;
|
| var ipt = 1;
|
| switch (this.tokAt (1)) {
|
| case 0:
|
| if (this.chk) return;
|
| bs = this.vwr.bsA ();
|
| pt = this.vwr.ms.getAtomSetCenter (bs);
|
| this.vwr.invertAtomCoordPt (pt, bs);
|
| return;
|
| case 528443:
|
| case 1140850689:
|
| ipt++;
|
| case 10:
|
| case 1073742325:
|
| case 12290:
|
| bs = this.atomExpressionAt (ipt);
|
| if (!eval.isAtomExpression (eval.iToken + 1)) {
|
| eval.checkLengthErrorPt (eval.iToken + 1, eval.iToken + 1);
|
| if (!this.chk) {
|
| for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) {
|
| this.vwr.invertRingAt (i, false);
|
| }
|
| }return;
|
| }iAtom = bs.nextSetBit (0);
|
| bs = this.atomExpressionAt (eval.iToken + 1);
|
| break;
|
| case 134217751:
|
| pt = eval.centerParameter (2, null);
|
| break;
|
| case 134217750:
|
| plane = eval.planeParameter (1);
|
| break;
|
| case 134219265:
|
| plane = eval.hklParameter (2);
|
| break;
|
| }
|
| eval.checkLengthErrorPt (eval.iToken + 1, 1);
|
| if (plane == null && pt == null && iAtom == -2147483648) this.invArg ();
|
| if (this.chk) return;
|
| if (iAtom == -1) return;
|
| this.vwr.invertSelected (pt, plane, iAtom, bs);
|
| });
|
| Clazz_defineMethod (c$, "mapProperty",
|
| function () {
|
| var bsFrom;
|
| var bsTo;
|
| var property1;
|
| var property2;
|
| var mapKey;
|
| var tokProp1 = 0;
|
| var tokProp2 = 0;
|
| var tokKey = 0;
|
| var eval = this.e;
|
| while (true) {
|
| if (this.tokAt (1) == 1113589787) {
|
| bsFrom = this.vwr.bsA ();
|
| bsTo = this.atomExpressionAt (2);
|
| property1 = property2 = "selected";
|
| } else {
|
| bsFrom = this.atomExpressionAt (1);
|
| if (this.tokAt (++eval.iToken) != 1073742336 || !JS.T.tokAttr (tokProp1 = this.tokAt (++eval.iToken), 1077936128)) break;
|
| property1 = this.paramAsStr (eval.iToken);
|
| bsTo = this.atomExpressionAt (++eval.iToken);
|
| if (this.tokAt (++eval.iToken) != 1073742336 || !JS.T.tokAttr (tokProp2 = this.tokAt (++eval.iToken), 2048)) break;
|
| property2 = this.paramAsStr (eval.iToken);
|
| }if (JS.T.tokAttr (tokKey = this.tokAt (eval.iToken + 1), 1077936128)) mapKey = this.paramAsStr (++eval.iToken);
|
| else mapKey = JS.T.nameOf (tokKey = 1094715393);
|
| eval.checkLast (eval.iToken);
|
| if (this.chk) return;
|
| var bsOut = null;
|
| this.showString ("mapping " + property1.toUpperCase () + " for " + bsFrom.cardinality () + " atoms to " + property2.toUpperCase () + " for " + bsTo.cardinality () + " atoms using " + mapKey.toUpperCase ());
|
| if (JS.T.tokAttrOr (tokProp1, 1094713344, 1111490560) && JS.T.tokAttrOr (tokProp2, 1094713344, 1111490560) && JS.T.tokAttrOr (tokKey, 1094713344, 1111490560)) {
|
| var data1 = this.getBitsetPropertyFloat (bsFrom, tokProp1 | 224, null, NaN, NaN);
|
| var data2 = this.getBitsetPropertyFloat (bsFrom, tokKey | 224, null, NaN, NaN);
|
| var data3 = this.getBitsetPropertyFloat (bsTo, tokKey | 224, null, NaN, NaN);
|
| var isProperty = (tokProp2 == 1715472409);
|
| var dataOut = Clazz_newFloatArray (isProperty ? this.vwr.ms.ac : data3.length, 0);
|
| bsOut = new JU.BS ();
|
| if (data1.length == data2.length) {
|
| var ht = new java.util.Hashtable ();
|
| for (var i = 0; i < data1.length; i++) {
|
| ht.put (Float.$valueOf (data2[i]), Float.$valueOf (data1[i]));
|
| }
|
| var pt = -1;
|
| var nOut = 0;
|
| for (var i = 0; i < data3.length; i++) {
|
| pt = bsTo.nextSetBit (pt + 1);
|
| var F = ht.get (Float.$valueOf (data3[i]));
|
| if (F == null) continue;
|
| bsOut.set (pt);
|
| dataOut[(isProperty ? pt : nOut)] = F.floatValue ();
|
| nOut++;
|
| }
|
| if (isProperty) this.vwr.setData (property2, Clazz_newArray (-1, [property2, dataOut, bsOut, Integer.$valueOf (1), Boolean.TRUE]), this.vwr.ms.ac, 0, 0, 2147483647, 0);
|
| else if (!JS.T.tokAttr (tokProp2, 2048)) this.error (56);
|
| else this.vwr.setAtomProperty (bsOut, tokProp2, 0, 0, null, dataOut, null);
|
| }}if (bsOut == null) {
|
| var format = "{" + mapKey + "=%[" + mapKey + "]}." + property2 + " = %[" + property1 + "]";
|
| var data = this.getBitsetIdent (bsFrom, format, null, false, 2147483647, false);
|
| var sb = new JU.SB ();
|
| for (var i = 0; i < data.length; i++) if (data[i].indexOf ("null") < 0) sb.append (data[i]).appendC ('\n');
|
|
|
| if (JU.Logger.debugging) JU.Logger.debug (sb.toString ());
|
| var bsSubset = JU.BSUtil.copy (this.vwr.slm.bsSubset);
|
| this.vwr.slm.setSelectionSubset (bsTo);
|
| try {
|
| eval.runScript (sb.toString ());
|
| } catch (e$$) {
|
| if (Clazz_exceptionOf (e$$, Exception)) {
|
| var ex = e$$;
|
| {
|
| this.vwr.slm.setSelectionSubset (bsSubset);
|
| eval.errorStr (-1, "Error: " + ex.getMessage ());
|
| }
|
| } else if (Clazz_exceptionOf (e$$, Error)) {
|
| var er = e$$;
|
| {
|
| this.vwr.slm.setSelectionSubset (bsSubset);
|
| eval.errorStr (-1, "Error: " + er.toString ());
|
| }
|
| } else {
|
| throw e$$;
|
| }
|
| }
|
| this.vwr.slm.setSelectionSubset (bsSubset);
|
| }this.showString ("DONE");
|
| return;
|
| }
|
| this.invArg ();
|
| });
|
| Clazz_defineMethod (c$, "minimize",
|
| function () {
|
| var bsSelected = null;
|
| var steps = 2147483647;
|
| var crit = 0;
|
| var addHydrogen = false;
|
| var isSilent = false;
|
| var bsFixed = null;
|
| var isOnly = false;
|
| var minimizer = this.vwr.getMinimizer (false);
|
| for (var i = 1; i < this.slen; i++) switch (this.getToken (i).tok) {
|
| case 1073741828:
|
| addHydrogen = true;
|
| continue;
|
| case 1073741874:
|
| case 1073742162:
|
| this.checkLength (2);
|
| if (this.chk || minimizer == null) return;
|
| minimizer.setProperty (this.paramAsStr (i), null);
|
| return;
|
| case 1073741882:
|
| this.checkLength (2);
|
| if (this.chk || minimizer == null) return;
|
| minimizer.setProperty ("clear", null);
|
| return;
|
| case 1073741894:
|
| if (i != 1) this.invArg ();
|
| var n = 0;
|
| var targetValue = 0;
|
| var aList = Clazz_newIntArray (5, 0);
|
| if (this.tokAt (++i) == 1073741882) {
|
| this.checkLength (3);
|
| } else {
|
| while (n < 4 && !this.isFloatParameter (i)) {
|
| aList[++n] = this.atomExpressionAt (i).nextSetBit (0);
|
| i = this.e.iToken + 1;
|
| }
|
| aList[0] = n;
|
| if (n == 1) this.invArg ();
|
| targetValue = this.floatParameter (this.e.checkLast (i));
|
| }if (!this.chk) this.vwr.getMinimizer (true).setProperty ("constraint", Clazz_newArray (-1, [aList, Clazz_newIntArray (n, 0), Float.$valueOf (targetValue)]));
|
| return;
|
| case 1073741905:
|
| crit = this.floatParameter (++i);
|
| continue;
|
| case 1073741935:
|
| steps = 0;
|
| continue;
|
| case 12293:
|
| if (i != 1) this.invArg ();
|
| bsFixed = this.atomExpressionAt (++i);
|
| if (bsFixed.nextSetBit (0) < 0) bsFixed = null;
|
| i = this.e.iToken;
|
| if (!this.chk) this.vwr.getMinimizer (true).setProperty ("fixed", bsFixed);
|
| if (i + 1 == this.slen) return;
|
| continue;
|
| case 10:
|
| case 1073742325:
|
| isOnly = true;
|
| case 1275082245:
|
| if (this.e.theTok == 1275082245) i++;
|
| bsSelected = this.atomExpressionAt (i);
|
| i = this.e.iToken;
|
| if (this.tokAt (i + 1) == 1073742072) {
|
| i++;
|
| isOnly = true;
|
| }continue;
|
| case 1073742148:
|
| isSilent = true;
|
| break;
|
| case 266298:
|
| steps = this.intParameter (++i);
|
| continue;
|
| default:
|
| this.invArg ();
|
| break;
|
| }
|
|
|
| if (!this.chk) try {
|
| this.vwr.minimize (this.e, steps, crit, bsSelected, bsFixed, 0, addHydrogen, isOnly, isSilent, false);
|
| } catch (e1) {
|
| if (Clazz_exceptionOf (e1, Exception)) {
|
| throw new JS.ScriptInterruption (this.e, "minimize", 1);
|
| } else {
|
| throw e1;
|
| }
|
| }
|
| });
|
| Clazz_defineMethod (c$, "modulation",
|
| function () {
|
| var qtOffset = null;
|
| var eval = this.e;
|
| var mod = true;
|
| var isQ = false;
|
| var bs = null;
|
| var i = 1;
|
| switch (this.getToken (i).tok) {
|
| case 1073742334:
|
| mod = false;
|
| case 0:
|
| case 1073742335:
|
| break;
|
| case 12290:
|
| case 10:
|
| case 1073742325:
|
| bs = this.atomExpressionAt (1);
|
| switch (this.tokAt (eval.iToken + 1)) {
|
| case 0:
|
| break;
|
| case 1073742334:
|
| mod = false;
|
| case 1073742335:
|
| eval.iToken++;
|
| break;
|
| }
|
| eval.checkLast (eval.iToken);
|
| break;
|
| case 1073742332:
|
| case 8:
|
| qtOffset = eval.getPoint3f (1, false, true);
|
| isQ = (this.tokAt (eval.iToken + 1) == 1073742335);
|
| break;
|
| default:
|
| var s = eval.theToken.value.toString ();
|
| i++;
|
| if (s.equalsIgnoreCase ("t")) {
|
| eval.theTok = 3;
|
| } else if (s.equalsIgnoreCase ("m") || s.equalsIgnoreCase ("q")) {
|
| eval.theTok = 2;
|
| } else {
|
| this.invArg ();
|
| }case 3:
|
| case 2:
|
| switch (eval.theTok) {
|
| case 3:
|
| if (this.isFloatParameter (i)) {
|
| var t1 = this.floatParameter (i);
|
| qtOffset = JU.P3.new3 (t1, t1, t1);
|
| } else {
|
| qtOffset = eval.getPoint3f (i, false, true);
|
| }break;
|
| case 2:
|
| if (this.tokAt (i) == 2) {
|
| var t = this.intParameter (i);
|
| qtOffset = JU.P3.new3 (t, t, t);
|
| } else {
|
| qtOffset = eval.getPoint3f (i, false, true);
|
| }isQ = true;
|
| break;
|
| }
|
| break;
|
| case 1073742138:
|
| var scale = this.floatParameter (2);
|
| if (!this.chk) this.vwr.setFloatProperty ("modulationScale", scale);
|
| return;
|
| }
|
| if (!this.chk) {
|
| this.vwr.tm.setVibrationPeriod (0);
|
| this.vwr.setModulation (bs, mod, qtOffset, isQ);
|
| }});
|
| Clazz_defineMethod (c$, "mutate",
|
| function () {
|
| var bs;
|
| var i;
|
| switch (this.tokAt (1)) {
|
| case 2:
|
| this.st[1] = JS.T.o (4, "" + this.st[1].value);
|
| default:
|
| bs = this.atomExpressionAt (1);
|
| i = ++this.e.iToken;
|
| break;
|
| case 268435633:
|
| bs = this.vwr.getAllAtoms ();
|
| i = 2;
|
| break;
|
| }
|
| bs.and (this.vwr.getModelUndeletedAtomsBitSet (this.vwr.ms.mc - 1));
|
| var iatom = bs.length () - 1;
|
| var imodel = 0;
|
| if (iatom < 0 || (imodel = this.vwr.ms.at[iatom].mi) != this.vwr.ms.mc - 1 || this.vwr.ms.isTrajectory (imodel)) return;
|
| var group = this.e.optParameterAsString (i);
|
| this.e.checkLast (i);
|
| if (this.chk || !this.vwr.ms.am[imodel].isBioModel) return;
|
| var isFile = (this.tokAt (i) == 4 && !group.startsWith ("~"));
|
| var list = null;
|
| if (isFile) {
|
| list = Clazz_newArray (-1, [group]);
|
| group = null;
|
| } else {
|
| group = JU.PT.replaceAllCharacters (group, ",; \t\n", " ").trim ().toUpperCase ();
|
| var isOneLetter = group.startsWith ("~");
|
| if (isOneLetter || group.length != 3 || !this.vwr.getJBR ().isKnownPDBGroup (group, 20)) group = this.vwr.getJBR ().toStdAmino3 (isOneLetter ? group.substring (1) : group);
|
| list = JU.PT.getTokens (group);
|
| }if (list.length > 0) this.vwr.ms.bioModelset.mutate (bs, group, list);
|
| });
|
| Clazz_defineMethod (c$, "navigate",
|
| function () {
|
| var eval = this.e;
|
| if (this.slen == 1) {
|
| eval.setBooleanProperty ("navigationMode", true);
|
| return;
|
| }var rotAxis = JU.V3.new3 (0, 1, 0);
|
| var list = new JU.Lst ();
|
| var pt;
|
| if (this.slen == 2) {
|
| switch (this.getToken (1).tok) {
|
| case 1073742335:
|
| case 1073742334:
|
| if (this.chk) return;
|
| eval.setObjectMad10 (34, "axes", 10);
|
| this.setShapeProperty (34, "position", JU.P3.new3 (50, 50, 3.4028235E38));
|
| eval.setBooleanProperty ("navigationMode", true);
|
| this.vwr.tm.setNavOn (eval.theTok == 1073742335);
|
| return;
|
| case 1073742162:
|
| if (!this.chk) this.vwr.tm.setNavXYZ (0, 0, 0);
|
| return;
|
| case 8:
|
| case 1112152078:
|
| break;
|
| default:
|
| this.invArg ();
|
| }
|
| }if (!this.chk && !this.vwr.getBoolean (603979889)) eval.setBooleanProperty ("navigationMode", true);
|
| for (var i = 1; i < this.slen; i++) {
|
| var timeSec = (this.isFloatParameter (i) ? this.floatParameter (i++) : 2);
|
| if (timeSec < 0) this.invArg ();
|
| if (!this.chk && timeSec > 0) eval.refresh (false);
|
| switch (this.getToken (i).tok) {
|
| case 8:
|
| case 1073742332:
|
| pt = this.getPoint3f (i, true);
|
| eval.iToken++;
|
| if (eval.iToken != this.slen) this.invArg ();
|
| if (!this.chk) this.vwr.tm.setNavXYZ (pt.x, pt.y, pt.z);
|
| return;
|
| case 554176526:
|
| var depth = this.floatParameter (++i);
|
| if (!this.chk) list.addLast ( Clazz_newArray (-1, [Integer.$valueOf (554176526), Float.$valueOf (timeSec), Float.$valueOf (depth)]));
|
| continue;
|
| case 12289:
|
| pt = this.centerParameter (++i);
|
| i = eval.iToken;
|
| if (!this.chk) list.addLast ( Clazz_newArray (-1, [Integer.$valueOf (134217751), Float.$valueOf (timeSec), pt]));
|
| continue;
|
| case 528432:
|
| switch (this.getToken (++i).tok) {
|
| case 1111492629:
|
| rotAxis.set (1, 0, 0);
|
| i++;
|
| break;
|
| case 1111492630:
|
| rotAxis.set (0, 1, 0);
|
| i++;
|
| break;
|
| case 1111492631:
|
| rotAxis.set (0, 0, 1);
|
| i++;
|
| break;
|
| case 8:
|
| case 1073742332:
|
| rotAxis.setT (this.getPoint3f (i, true));
|
| i = eval.iToken + 1;
|
| break;
|
| case 1073741824:
|
| this.invArg ();
|
| break;
|
| }
|
| var degrees = this.floatParameter (i);
|
| if (!this.chk) list.addLast ( Clazz_newArray (-1, [Integer.$valueOf (528432), Float.$valueOf (timeSec), rotAxis, Float.$valueOf (degrees)]));
|
| continue;
|
| case 4160:
|
| var x = NaN;
|
| var y = NaN;
|
| if (this.isFloatParameter (++i)) {
|
| x = this.floatParameter (i);
|
| y = this.floatParameter (++i);
|
| } else {
|
| switch (this.tokAt (i)) {
|
| case 1111492629:
|
| x = this.floatParameter (++i);
|
| break;
|
| case 1111492630:
|
| y = this.floatParameter (++i);
|
| break;
|
| default:
|
| pt = this.centerParameter (i);
|
| i = eval.iToken;
|
| if (!this.chk) list.addLast ( Clazz_newArray (-1, [Integer.$valueOf (4160), Float.$valueOf (timeSec), pt]));
|
| continue;
|
| }
|
| }if (!this.chk) list.addLast ( Clazz_newArray (-1, [Integer.$valueOf (268435634), Float.$valueOf (timeSec), Float.$valueOf (x), Float.$valueOf (y)]));
|
| continue;
|
| case 268435632:
|
| continue;
|
| case 1112152078:
|
| var pathGuide;
|
| var vp = new JU.Lst ();
|
| var bs;
|
| if (eval.isAtomExpression (i + 1)) {
|
| bs = this.atomExpressionAt (++i);
|
| i = eval.iToken;
|
| } else {
|
| bs = this.vwr.bsA ();
|
| }if (this.chk) return;
|
| this.vwr.getPolymerPointsAndVectors (bs, vp);
|
| var n;
|
| if ((n = vp.size ()) > 0) {
|
| pathGuide = new Array (n);
|
| for (var j = 0; j < n; j++) {
|
| pathGuide[j] = vp.get (j);
|
| }
|
| list.addLast ( Clazz_newArray (-1, [Integer.$valueOf (1112152078), Float.$valueOf (timeSec), pathGuide]));
|
| continue;
|
| }break;
|
| case 1073742084:
|
| var path;
|
| var theta = null;
|
| if (this.getToken (i + 1).tok == 1073742330) {
|
| i++;
|
| var pathID = eval.objectNameParameter (++i);
|
| if (this.chk) return;
|
| this.setShapeProperty (22, "thisID", pathID);
|
| path = this.getShapeProperty (22, "vertices");
|
| eval.refresh (false);
|
| if (path == null) this.invArg ();
|
| var indexStart = Clazz_floatToInt (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 0);
|
| var indexEnd = Clazz_floatToInt (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 2147483647);
|
| list.addLast ( Clazz_newArray (-1, [Integer.$valueOf (1073742084), Float.$valueOf (timeSec), path, theta, Clazz_newIntArray (-1, [indexStart, indexEnd])]));
|
| continue;
|
| }var v = new JU.Lst ();
|
| while (eval.isCenterParameter (i + 1)) {
|
| v.addLast (this.centerParameter (++i));
|
| i = eval.iToken;
|
| }
|
| if (v.size () > 0) {
|
| path = v.toArray ( new Array (v.size ()));
|
| if (!this.chk) list.addLast ( Clazz_newArray (-1, [Integer.$valueOf (1073742084), Float.$valueOf (timeSec), path, theta, Clazz_newIntArray (-1, [0, 2147483647])]));
|
| continue;
|
| }default:
|
| this.invArg ();
|
| }
|
| }
|
| if (!this.chk && !this.vwr.isJmolDataFrame ()) this.vwr.tm.navigateList (eval, list);
|
| });
|
| Clazz_defineMethod (c$, "plot",
|
| function (args) {
|
| var eval = this.e;
|
| var modelIndex = this.vwr.am.cmi;
|
| if (modelIndex < 0) eval.errorStr (30, "plot");
|
| modelIndex = this.vwr.ms.getJmolDataSourceFrame (modelIndex);
|
| var pt = args.length - 1;
|
| var isReturnOnly = (args !== this.st);
|
| var pdbFormat = true;
|
| var statementSave = this.st;
|
| if (isReturnOnly) eval.st = this.st = args;
|
| var tokCmd = (isReturnOnly ? 134222350 : args[0].tok);
|
| var pt0 = (isReturnOnly || tokCmd == 134221850 || tokCmd == 4138 ? 0 : 1);
|
| var filename = null;
|
| var makeNewFrame = true;
|
| var isDraw = false;
|
| switch (tokCmd) {
|
| case 4133:
|
| case 134221850:
|
| case 4138:
|
| break;
|
| case 135176:
|
| makeNewFrame = false;
|
| isDraw = true;
|
| break;
|
| case 134222350:
|
| makeNewFrame = false;
|
| pdbFormat = false;
|
| break;
|
| case 134221856:
|
| makeNewFrame = false;
|
| if (JS.CmdExt.tokAtArray (pt, args) == 4) {
|
| filename = this.stringParameter (pt--);
|
| } else if (JS.CmdExt.tokAtArray (pt - 1, args) == 1073742336) {
|
| filename = this.paramAsStr (pt - 2) + "." + this.paramAsStr (pt);
|
| pt -= 3;
|
| } else {
|
| eval.st = this.st = statementSave;
|
| eval.iToken = this.st.length;
|
| this.error (13);
|
| }eval.slen = this.slen = pt + 1;
|
| break;
|
| }
|
| var qFrame = "";
|
| var parameters = null;
|
| var stateScript = "";
|
| var isQuaternion = false;
|
| var isDerivative = false;
|
| var isSecondDerivative = false;
|
| var isRamachandranRelative = false;
|
| var props = new Array (3);
|
| var propToks = Clazz_newIntArray (3, 0);
|
| var bs = JU.BSUtil.copy (this.vwr.bsA ());
|
| var preSelected = "; select " + JU.Escape.eBS (bs) + ";\n ";
|
| var type = eval.optParameterAsString (pt).toLowerCase ();
|
| var minXYZ = null;
|
| var maxXYZ = null;
|
| var format = null;
|
| var tok = JS.CmdExt.tokAtArray (pt0, args);
|
| if (tok == 4) tok = JS.T.getTokFromName (args[pt0].value);
|
| switch (tok) {
|
| default:
|
| eval.iToken = 1;
|
| this.invArg ();
|
| break;
|
| case 134221834:
|
| eval.iToken = 1;
|
| type = "data";
|
| preSelected = "";
|
| break;
|
| case 1715472409:
|
| eval.iToken = pt0 + 1;
|
| for (var i = 0; i < 3; i++) {
|
| switch (this.tokAt (eval.iToken)) {
|
| case 4:
|
| propToks[i] = JS.T.getTokFromName (eval.getToken (eval.iToken).value);
|
| break;
|
| default:
|
| propToks[i] = this.tokAt (eval.iToken);
|
| break;
|
| case 0:
|
| if (i == 0) this.invArg ();
|
| case 1287653388:
|
| case 32:
|
| case 64:
|
| i = 2;
|
| continue;
|
| }
|
| if (propToks[i] != 1715472409 && !JS.T.tokAttr (propToks[i], 1077936128)) this.invArg ();
|
| props[i] = this.getToken (eval.iToken).value.toString ();
|
| eval.iToken++;
|
| }
|
| if (this.tokAt (eval.iToken) == 1287653388) {
|
| format = this.stringParameter (++eval.iToken);
|
| pdbFormat = false;
|
| eval.iToken++;
|
| }if (this.tokAt (eval.iToken) == 32) {
|
| minXYZ = this.getPoint3f (++eval.iToken, false);
|
| eval.iToken++;
|
| }if (this.tokAt (eval.iToken) == 64) {
|
| maxXYZ = this.getPoint3f (++eval.iToken, false);
|
| eval.iToken++;
|
| }type = "property " + props[0] + (props[1] == null ? "" : " " + props[1]) + (props[2] == null ? "" : " " + props[2]);
|
| if (bs.nextSetBit (0) < 0) bs = this.vwr.getModelUndeletedAtomsBitSet (modelIndex);
|
| stateScript = "select " + JU.Escape.eBS (bs) + ";\n ";
|
| break;
|
| case 4138:
|
| if (type.equalsIgnoreCase ("draw")) {
|
| isDraw = true;
|
| type = eval.optParameterAsString (--pt).toLowerCase ();
|
| }isRamachandranRelative = (pt > pt0 && type.startsWith ("r"));
|
| type = "ramachandran" + (isRamachandranRelative ? " r" : "") + (tokCmd == 135176 ? " draw" : "");
|
| break;
|
| case 134221850:
|
| case 136314895:
|
| qFrame = " \"" + this.vwr.getQuaternionFrame () + "\"";
|
| stateScript = "set quaternionFrame" + qFrame + ";\n ";
|
| isQuaternion = true;
|
| if (type.equalsIgnoreCase ("draw")) {
|
| isDraw = true;
|
| type = eval.optParameterAsString (--pt).toLowerCase ();
|
| }isDerivative = (type.startsWith ("deriv") || type.startsWith ("diff"));
|
| isSecondDerivative = (isDerivative && type.indexOf ("2") > 0);
|
| if (isDerivative) pt--;
|
| if (type.equalsIgnoreCase ("helix") || type.equalsIgnoreCase ("axis")) {
|
| isDraw = true;
|
| isDerivative = true;
|
| pt = -1;
|
| }type = ((pt <= pt0 ? "" : eval.optParameterAsString (pt)) + "w").substring (0, 1);
|
| if (type.equals ("a") || type.equals ("r")) isDerivative = true;
|
| if (!JU.PT.isOneOf (type, ";w;x;y;z;r;a;")) eval.evalError ("QUATERNION [w,x,y,z,a,r] [difference][2]", null);
|
| type = "quaternion " + type + (isDerivative ? " difference" : "") + (isSecondDerivative ? "2" : "") + (isDraw ? " draw" : "");
|
| break;
|
| }
|
| this.st = statementSave;
|
| if (this.chk) return "";
|
| if (makeNewFrame) {
|
| stateScript += "plot " + type;
|
| var ptDataFrame = this.vwr.ms.getJmolDataFrameIndex (modelIndex, stateScript);
|
| if (ptDataFrame > 0 && tokCmd != 134221856 && tokCmd != 134222350) {
|
| this.vwr.setCurrentModelIndexClear (ptDataFrame, true);
|
| return "";
|
| }}var dataX = null;
|
| var dataY = null;
|
| var dataZ = null;
|
| var propData = new Array (3);
|
| if (tok == 1715472409) {
|
| dataX = this.getBitsetPropertyFloat (bs, propToks[0] | 224, propToks[0] == 1715472409 ? props[0] : null, (minXYZ == null ? NaN : minXYZ.x), (maxXYZ == null ? NaN : maxXYZ.x));
|
| propData[0] = props[0] + " " + JU.Escape.eAF (dataX);
|
| if (props[1] != null) {
|
| dataY = this.getBitsetPropertyFloat (bs, propToks[1] | 224, propToks[1] == 1715472409 ? props[1] : null, (minXYZ == null ? NaN : minXYZ.y), (maxXYZ == null ? NaN : maxXYZ.y));
|
| propData[1] = props[1] + " " + JU.Escape.eAF (dataY);
|
| }if (props[2] != null) {
|
| dataZ = this.getBitsetPropertyFloat (bs, propToks[2] | 224, propToks[2] == 1715472409 ? props[2] : null, (minXYZ == null ? NaN : minXYZ.z), (maxXYZ == null ? NaN : maxXYZ.z));
|
| propData[2] = props[2] + " " + JU.Escape.eAF (dataZ);
|
| }if (minXYZ == null) minXYZ = JU.P3.new3 (this.getPlotMinMax (dataX, false, propToks[0]), this.getPlotMinMax (dataY, false, propToks[1]), this.getPlotMinMax (dataZ, false, propToks[2]));
|
| if (maxXYZ == null) maxXYZ = JU.P3.new3 (this.getPlotMinMax (dataX, true, propToks[0]), this.getPlotMinMax (dataY, true, propToks[1]), this.getPlotMinMax (dataZ, true, propToks[2]));
|
| JU.Logger.info ("plot min/max: " + minXYZ + " " + maxXYZ);
|
| var center = null;
|
| var factors = null;
|
| if (pdbFormat) {
|
| factors = JU.P3.new3 (1, 1, 1);
|
| center = new JU.P3 ();
|
| center.ave (maxXYZ, minXYZ);
|
| factors.sub2 (maxXYZ, minXYZ);
|
| factors.set (factors.x / 200, factors.y / 200, factors.z / 200);
|
| if (JS.T.tokAttr (propToks[0], 1094713344)) {
|
| factors.x = 1;
|
| center.x = 0;
|
| } else if (factors.x > 0.1 && factors.x <= 10) {
|
| factors.x = 1;
|
| }if (JS.T.tokAttr (propToks[1], 1094713344)) {
|
| factors.y = 1;
|
| center.y = 0;
|
| } else if (factors.y > 0.1 && factors.y <= 10) {
|
| factors.y = 1;
|
| }if (JS.T.tokAttr (propToks[2], 1094713344)) {
|
| factors.z = 1;
|
| center.z = 0;
|
| } else if (factors.z > 0.1 && factors.z <= 10) {
|
| factors.z = 1;
|
| }if (props[2] == null || props[1] == null) center.z = minXYZ.z = maxXYZ.z = factors.z = 0;
|
| for (var i = 0; i < dataX.length; i++) dataX[i] = (dataX[i] - center.x) / factors.x;
|
|
|
| if (props[1] != null) for (var i = 0; i < dataY.length; i++) dataY[i] = (dataY[i] - center.y) / factors.y;
|
|
|
| if (props[2] != null) for (var i = 0; i < dataZ.length; i++) dataZ[i] = (dataZ[i] - center.z) / factors.z;
|
|
|
| }parameters = Clazz_newArray (-1, [bs, dataX, dataY, dataZ, minXYZ, maxXYZ, factors, center, format, propData]);
|
| }if (tokCmd == 134221856) return this.vwr.writeFileData (filename, "PLOT_" + type, modelIndex, parameters);
|
| var data = (type.equals ("data") ? "1 0 H 0 0 0 # Jmol PDB-encoded data" : this.vwr.getPdbData (modelIndex, type, null, parameters, null, true));
|
| if (tokCmd == 134222350) return data;
|
| if (JU.Logger.debugging) JU.Logger.debug (data);
|
| if (tokCmd == 135176) {
|
| eval.runScript (data);
|
| return "";
|
| }var savedFileInfo = this.vwr.fm.getFileInfo ();
|
| var oldAppendNew = this.vwr.getBoolean (603979792);
|
| this.vwr.g.appendNew = true;
|
| var isOK = (data != null && this.vwr.openStringInlineParamsAppend (data, null, true) == null);
|
| this.vwr.g.appendNew = oldAppendNew;
|
| this.vwr.fm.setFileInfo (savedFileInfo);
|
| if (!isOK) return "";
|
| var modelCount = this.vwr.ms.mc;
|
| this.vwr.ms.setJmolDataFrame (stateScript, modelIndex, modelCount - 1);
|
| if (tok != 1715472409) stateScript += ";\n" + preSelected;
|
| var ss = this.vwr.addStateScript (stateScript, true, false);
|
| var radius = 150;
|
| var script;
|
| switch (tok) {
|
| default:
|
| script = "frame 0.0; frame last; reset;select visible;wireframe only;";
|
| radius = 10;
|
| break;
|
| case 1715472409:
|
| this.vwr.setFrameTitle (modelCount - 1, type + " plot for model " + this.vwr.getModelNumberDotted (modelIndex));
|
| script = "frame 0.0; frame last; reset;select visible; spacefill 3.0; wireframe 0;draw plotAxisX" + modelCount + " {100 -100 -100} {-100 -100 -100} \"" + props[0] + "\";" + "draw plotAxisY" + modelCount + " {-100 100 -100} {-100 -100 -100} \"" + props[1] + "\";";
|
| if (props[2] != null) script += "draw plotAxisZ" + modelCount + " {-100 -100 100} {-100 -100 -100} \"" + props[2] + "\";";
|
| break;
|
| case 4138:
|
| this.vwr.setFrameTitle (modelCount - 1, "ramachandran plot for model " + this.vwr.getModelNumberDotted (modelIndex));
|
| script = "frame 0.0; frame last; reset;select visible; color structure; spacefill 3.0; wireframe 0;draw ramaAxisX" + modelCount + " {100 0 0} {-100 0 0} \"phi\";" + "draw ramaAxisY" + modelCount + " {0 100 0} {0 -100 0} \"psi\";";
|
| break;
|
| case 134221850:
|
| case 136314895:
|
| this.vwr.setFrameTitle (modelCount - 1, type.$replace ('w', ' ') + qFrame + " for model " + this.vwr.getModelNumberDotted (modelIndex));
|
| var color = (JU.C.getHexCode (this.vwr.cm.colixBackgroundContrast));
|
| script = "frame 0.0; frame last; reset;select visible; wireframe 0; spacefill 3.0; isosurface quatSphere" + modelCount + " color " + color + " sphere 100.0 mesh nofill frontonly translucent 0.8;" + "draw quatAxis" + modelCount + "X {100 0 0} {-100 0 0} color red \"x\";" + "draw quatAxis" + modelCount + "Y {0 100 0} {0 -100 0} color green \"y\";" + "draw quatAxis" + modelCount + "Z {0 0 100} {0 0 -100} color blue \"z\";" + "color structure;" + "draw quatCenter" + modelCount + "{0 0 0} scale 0.02;";
|
| break;
|
| }
|
| eval.runScript (script + preSelected);
|
| ss.setModelIndex (this.vwr.am.cmi);
|
| this.vwr.setRotationRadius (radius, true);
|
| eval.sm.loadShape (31);
|
| this.showString ("frame " + this.vwr.getModelNumberDotted (modelCount - 1) + (type.length > 0 ? " created: " + type + (isQuaternion ? qFrame : "") : ""));
|
| return "";
|
| }, "~A");
|
| Clazz_defineMethod (c$, "polyhedra",
|
| function () {
|
| var eval = this.e;
|
| var haveBonds = (this.slen == 1);
|
| var haveCenter = false;
|
| var needsGenerating = haveBonds;
|
| var onOffDelete = false;
|
| var typeSeen = false;
|
| var edgeParameterSeen = false;
|
| var scale = NaN;
|
| var nAtomSets = 0;
|
| eval.sm.loadShape (21);
|
| this.setShapeProperty (21, "init", Boolean.TRUE);
|
| var translucentLevel = 3.4028235E38;
|
| var radius = -1;
|
| var colorArgb = Clazz_newIntArray (-1, [-2147483648]);
|
| var noToParam = -1;
|
| var offset = null;
|
| var id = null;
|
| var ok = false;
|
| var faces = null;
|
| var points = null;
|
| for (var i = 1; i < this.slen; ++i) {
|
| var propertyName = null;
|
| var propertyValue = null;
|
| switch (this.getToken (i).tok) {
|
| case 1073742197:
|
| scale = NaN;
|
| case 1073741872:
|
| var index = (this.e.theTok == 1073742197 ? -1 : (this.tokAt (i + 1) == 2 ? this.intParameter (++i) : 1));
|
| if (!this.chk) (J.api.Interface.getInterface ("JU.BZone", this.vwr, "script")).setViewer (this.vwr).createBZ (index, null, false, id, scale);
|
| this.setShapeProperty (21, "init", Boolean.FALSE);
|
| return;
|
| case 6:
|
| propertyName = "info";
|
| propertyValue = this.e.theToken.value;
|
| needsGenerating = true;
|
| break;
|
| case 134217751:
|
| propertyName = "points";
|
| propertyValue = Float.$valueOf (this.tokAt (++i) == 1073742334 ? 0 : this.e.floatParameter (i));
|
| ok = true;
|
| break;
|
| case 1073742138:
|
| scale = this.floatParameter (++i);
|
| ok = true;
|
| continue;
|
| case 1814695966:
|
| if (id != null) this.invArg ();
|
| propertyName = "unitCell";
|
| propertyValue = Boolean.TRUE;
|
| needsGenerating = true;
|
| break;
|
| case 1073742072:
|
| this.e.restrictSelected (false, false);
|
| eval.theTok = 1073742335;
|
| case 1073742335:
|
| case 12291:
|
| case 1073742334:
|
| if (i + 1 != this.slen || needsGenerating || nAtomSets > 1) this.error (18);
|
| propertyName = (eval.theTok == 1073742334 ? "off" : eval.theTok == 1073742335 ? "on" : "delete");
|
| onOffDelete = true;
|
| break;
|
| case 7:
|
| if (id == null || needsGenerating) this.invArg ();
|
| needsGenerating = true;
|
| faces = this.getIntArray2 (i);
|
| points = this.getAllPoints (eval.iToken + 1);
|
| i = eval.iToken;
|
| if (Clazz_instanceOf (points[0], JM.Atom)) this.setShapeProperty (21, "model", Integer.$valueOf ((points[0]).getModelIndex ()));
|
| propertyName = "definedFaces";
|
| propertyValue = Clazz_newArray (-1, [faces, points]);
|
| break;
|
| case 1073741961:
|
| propertyName = "full";
|
| break;
|
| case 2:
|
| if (id != null) this.invArg ();
|
| propertyName = "nVertices";
|
| propertyValue = Integer.$valueOf (this.intParameter (i));
|
| needsGenerating = true;
|
| if (this.tokAt (i + 1) == 268435504) i++;
|
| break;
|
| case 1677721602:
|
| if (id != null) this.invArg ();
|
| if (nAtomSets > 0) this.invPO ();
|
| needsGenerating = true;
|
| propertyName = "bonds";
|
| haveBonds = true;
|
| break;
|
| case 1073741852:
|
| if (radius != -1) this.invArg ();
|
| radius = 0;
|
| i--;
|
| case 1665140738:
|
| i++;
|
| case 3:
|
| if (id != null) this.invArg ();
|
| if (nAtomSets > 0) this.invPO ();
|
| propertyName = (radius <= 0 ? "radius" : "radius1");
|
| propertyValue = Float.$valueOf (radius = (radius == 0 ? 0 : this.floatParameter (i)));
|
| needsGenerating = true;
|
| break;
|
| case 1073742066:
|
| if (!this.isFloatParameter (i + 1)) {
|
| offset = this.e.centerParameter (++i, null);
|
| i = eval.iToken;
|
| ok = true;
|
| continue;
|
| }case 1073741937:
|
| this.setShapeProperty (21, "collapsed", null);
|
| case 1073742099:
|
| case 1073741924:
|
| propertyName = JS.T.nameOf (eval.theTok);
|
| switch (this.tokAt (i + 1)) {
|
| case 268435860:
|
| case 268435504:
|
| i++;
|
| break;
|
| }
|
| propertyValue = Float.$valueOf (this.floatParameter (++i));
|
| break;
|
| case 1094717454:
|
| if (id == null) this.invArg ();
|
| propertyName = "model";
|
| propertyValue = Integer.$valueOf (this.intParameter (++i));
|
| break;
|
| case 1073742170:
|
| if (nAtomSets > 1 || id != null && !haveCenter || noToParam == i) this.invPO ();
|
| nAtomSets = 3;
|
| if (eval.isAtomExpression (++i)) {
|
| propertyName = (needsGenerating || haveCenter ? "to" : "toBitSet");
|
| propertyValue = this.atomExpressionAt (i);
|
| } else if (eval.isArrayParameter (i)) {
|
| propertyName = "toVertices";
|
| propertyValue = eval.getPointArray (i, -1, false);
|
| } else {
|
| this.error (19);
|
| }i = eval.iToken;
|
| needsGenerating = true;
|
| break;
|
| case 12290:
|
| case 10:
|
| case 1073742325:
|
| if (typeSeen) this.invPO ();
|
| switch (++nAtomSets) {
|
| case 1:
|
| if (id != null) this.invArg ();
|
| propertyName = "centers";
|
| break;
|
| case 2:
|
| propertyName = "to";
|
| needsGenerating = true;
|
| break;
|
| default:
|
| eval.bad ();
|
| }
|
| propertyValue = this.atomExpressionAt (i);
|
| i = eval.iToken;
|
| needsGenerating = new Boolean (needsGenerating | (i + 1 == this.slen)).valueOf ();
|
| break;
|
| case 1765808134:
|
| case 603979967:
|
| case 1073742074:
|
| translucentLevel = this.getColorTrans (eval, i, true, colorArgb);
|
| i = eval.iToken;
|
| continue;
|
| case 1073741948:
|
| case 1073741886:
|
| if (typeSeen) this.error (18);
|
| typeSeen = true;
|
| if (this.isFloatParameter (i + 1)) this.setShapeProperty (21, "faceCenterOffset", Float.$valueOf (this.floatParameter (++i)));
|
| propertyName = (this.e.theTok == 1073741886 ? "collapsed" : null);
|
| break;
|
| case 1073742044:
|
| case 1073741933:
|
| case 1073741956:
|
| case 1073741934:
|
| if (edgeParameterSeen) this.error (18);
|
| edgeParameterSeen = true;
|
| ok = true;
|
| propertyName = JS.T.nameOf (eval.theTok);
|
| break;
|
| case 1073742182:
|
| case 1073742060:
|
| case 1073741861:
|
| case 1073741958:
|
| case 1073741964:
|
| continue;
|
| case 1073741974:
|
| case 268435633:
|
| case 1073741824:
|
| case 4:
|
| if (!eval.isColorParam (i)) {
|
| if (i != 1) this.invPO ();
|
| id = (eval.theTok == 1073741974 ? this.stringParameter (++i) : eval.optParameterAsString (i));
|
| this.setShapeProperty (21, "thisID", id);
|
| this.setShapeProperty (21, "model", Integer.$valueOf (this.vwr.am.cmi));
|
| if (!eval.isCenterParameter (i + 1)) continue;
|
| propertyName = "center";
|
| propertyValue = this.centerParameter (++i);
|
| i = eval.iToken;
|
| haveCenter = true;
|
| break;
|
| }default:
|
| if (eval.isColorParam (i)) {
|
| colorArgb[0] = eval.getArgbParam (i);
|
| if (eval.isCenterParameter (i)) noToParam = eval.iToken + 1;
|
| i = eval.iToken;
|
| continue;
|
| }this.invArg ();
|
| }
|
| if (propertyName != null) this.setShapeProperty (21, propertyName, propertyValue);
|
| if (onOffDelete) return;
|
| }
|
| if (needsGenerating) {
|
| if (!typeSeen && haveBonds) this.setShapeProperty (21, "bonds", null);
|
| this.setShapeProperty (21, "generate", null);
|
| } else if (!ok) {
|
| this.error (19);
|
| }if (offset != null) this.setShapeProperty (21, "offset", offset);
|
| if (!Float.isNaN (scale)) this.setShapeProperty (21, "scale", Float.$valueOf (scale));
|
| if (colorArgb[0] != -2147483648) this.setShapeProperty (21, "colorThis", Integer.$valueOf (colorArgb[0]));
|
| if (translucentLevel != 3.4028235E38) eval.setShapeTranslucency (21, "", "translucentThis", translucentLevel, null);
|
| this.setShapeProperty (21, "init", Boolean.FALSE);
|
| });
|
| Clazz_defineMethod (c$, "write",
|
| function (args) {
|
| var eval = this.e;
|
| var pt = 1;
|
| var pt0 = 1;
|
| var scripts = null;
|
| var msg = null;
|
| var localPath = null;
|
| var remotePath = null;
|
| var type = "SPT";
|
| var isCommand = true;
|
| var showOnly = false;
|
| var isContact = false;
|
| if (args == null) {
|
| args = this.st;
|
| showOnly = (this.vwr.isApplet && !this.vwr.isSignedApplet || !this.vwr.haveAccess (JV.Viewer.ACCESS.ALL) || this.vwr.fm.getPathForAllFiles ().length > 0);
|
| } else {
|
| pt = pt0 = 0;
|
| isCommand = false;
|
| showOnly = !isCommand;
|
| }var tok = JS.CmdExt.tokAtArray (pt, args);
|
| if (tok == 4 && !isCommand) {
|
| var t0 = JS.T.getTokenFromName (JS.SV.sValue (args[0]).toLowerCase ());
|
| if (t0 != null) tok = t0.tok;
|
| }switch (tok) {
|
| case 0:
|
| break;
|
| case 134221850:
|
| case 4138:
|
| case 1715472409:
|
| msg = this.plot (args);
|
| return (showOnly ? msg : this.writeMsg (msg));
|
| case 134222850:
|
| if (eval.isArrayParameter (pt + 1)) {
|
| scripts = eval.stringParameterSet (++pt);
|
| localPath = ".";
|
| remotePath = ".";
|
| pt0 = pt = eval.iToken + 1;
|
| tok = this.tokAt (pt);
|
| }break;
|
| default:
|
| type = JS.SV.sValue (this.tokenAt (pt, args)).toUpperCase ();
|
| }
|
| var driverList = this.vwr.getExportDriverList ();
|
| var data = null;
|
| var argCount = (isCommand ? this.slen : args.length);
|
| var type2 = "";
|
| var val = null;
|
| var tVar = null;
|
| var nVibes = 0;
|
| var sceneType = null;
|
| var isCoord = false;
|
| var bsFrames = null;
|
| var width = -1;
|
| var height = -1;
|
| var isExport = false;
|
| var fileName = null;
|
| var quality = -2147483648;
|
| if (tok != 0 && isCommand && this.slen > 1 && this.tokAt (this.slen - 2) == 1073741848) {
|
| type = this.paramAsStr (this.slen - 1).toUpperCase ();
|
| pt0 = argCount;
|
| argCount -= 2;
|
| tok = 0;
|
| }switch (tok) {
|
| case 0:
|
| break;
|
| case 15:
|
| case 6:
|
| type = "VAR";
|
| tVar = this.tokenAt (pt++, args);
|
| break;
|
| case 1073741984:
|
| type = "INLINE";
|
| data = JS.SV.sValue (this.tokenAt (++pt, args));
|
| pt++;
|
| break;
|
| case 134217762:
|
| type = "PGRP";
|
| pt++;
|
| type2 = JS.SV.sValue (this.tokenAt (pt, args)).toLowerCase ();
|
| if (type2.equals ("draw")) pt++;
|
| break;
|
| case 1073742329:
|
| pt++;
|
| isCoord = true;
|
| break;
|
| case 1073742158:
|
| case 134222850:
|
| val = JS.SV.sValue (this.tokenAt (++pt, args)).toLowerCase ();
|
| while (val.equals ("localpath") || val.equals ("remotepath")) {
|
| if (val.equals ("localpath")) localPath = JS.SV.sValue (this.tokenAt (++pt, args));
|
| else remotePath = JS.SV.sValue (this.tokenAt (++pt, args));
|
| val = JS.SV.sValue (this.tokenAt (++pt, args)).toLowerCase ();
|
| }
|
| type = "SPT";
|
| break;
|
| case 1228935687:
|
| case 134320141:
|
| case 1610616855:
|
| case 135180:
|
| case 1073742015:
|
| case 1073742018:
|
| case 1073877011:
|
| case 1073877010:
|
| case 135188:
|
| pt++;
|
| break;
|
| case 1073741991:
|
| type = "ZIPALL";
|
| pt++;
|
| break;
|
| case 36868:
|
| type = "VAR";
|
| pt += 2;
|
| break;
|
| case 4115:
|
| case 4120:
|
| case 1073742139:
|
| case 4166:
|
| case 1073741824:
|
| case 4:
|
| switch (tok) {
|
| case 4115:
|
| var bsAtoms;
|
| if (pt + 1 < argCount && args[++pt].tok == 1073742325 || args[pt].tok == 10) {
|
| bsAtoms = eval.atomExpression (args, pt, 0, true, false, null, true);
|
| pt = eval.iToken + 1;
|
| } else {
|
| bsAtoms = this.vwr.getAllAtoms ();
|
| }if (!this.chk) bsFrames = this.vwr.ms.getModelBS (bsAtoms, true);
|
| break;
|
| case 4120:
|
| type = "IMAGE";
|
| pt++;
|
| break;
|
| case 1073742139:
|
| val = JS.SV.sValue (this.tokenAt (++pt, args)).toUpperCase ();
|
| if (JU.PT.isOneOf (val, ";PNG;PNGJ;")) {
|
| sceneType = val;
|
| pt++;
|
| } else {
|
| sceneType = "PNG";
|
| }break;
|
| case 4166:
|
| nVibes = eval.intParameterRange (++pt, 1, 10);
|
| if (nVibes == 2147483647) return "";
|
| if (!this.chk) {
|
| this.vwr.tm.setVibrationPeriod (0);
|
| if (!eval.isJS) eval.delayScript (100);
|
| }pt++;
|
| break;
|
| default:
|
| tok = 4120;
|
| break;
|
| }
|
| if (tok == 4120 && pt < args.length) {
|
| var t = JS.T.getTokenFromName (JS.SV.sValue (args[pt]).toLowerCase ());
|
| if (t != null) type = JS.SV.sValue (t).toUpperCase ();
|
| if (JU.PT.isOneOf (type, driverList.toUpperCase ())) {
|
| pt++;
|
| type = type.substring (0, 1).toUpperCase () + type.substring (1).toLowerCase ();
|
| isExport = true;
|
| if (isCommand) fileName = "Jmol." + type.toLowerCase ();
|
| break;
|
| } else if (JU.PT.isOneOf (type, ";ZIP;ZIPALL;SPT;STATE;")) {
|
| pt++;
|
| break;
|
| } else {
|
| type = "IMAGE";
|
| }}if (JS.CmdExt.tokAtArray (pt, args) == 2) {
|
| width = JS.SV.iValue (this.tokenAt (pt++, args));
|
| if (width <= 0) this.invArg ();
|
| height = JS.SV.iValue (this.tokenAt (pt++, args));
|
| if (height <= 0) this.invArg ();
|
| }break;
|
| }
|
| if (pt0 < argCount) {
|
| val = JS.SV.sValue (this.tokenAt (pt, args));
|
| if (val.equalsIgnoreCase ("clipboard")) {
|
| if (this.chk) return "";
|
| } else if (JU.PT.isOneOf (val.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;")) {
|
| if (JS.CmdExt.tokAtArray (pt + 1, args) == 2 && JS.CmdExt.tokAtArray (pt + 2, args) == 2) {
|
| width = JS.SV.iValue (this.tokenAt (++pt, args));
|
| if (width <= 0) this.invArg ();
|
| height = JS.SV.iValue (this.tokenAt (++pt, args));
|
| if (height <= 0) this.invArg ();
|
| }if (JS.CmdExt.tokAtArray (pt + 1, args) == 2) quality = JS.SV.iValue (this.tokenAt (++pt, args));
|
| } else if (JU.PT.isOneOf (val.toLowerCase (), ";xyz;xyzrn;xyzvib;mol;mol67;sdf;v2000;v3000;json;pdb;pqr;cml;cif;qcjson;")) {
|
| type = val.toUpperCase ();
|
| if (pt + 1 == argCount) pt++;
|
| }if (type.equals ("IMAGE") && JU.PT.isOneOf (val.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;scene;")) {
|
| type = val.toUpperCase ();
|
| quality = -2147483648;
|
| pt++;
|
| }}if (pt + 2 == argCount) {
|
| var s = JS.SV.sValue (this.tokenAt (++pt, args));
|
| if (s.length > 0 && s.charAt (0) != '.') {
|
| if (val == null) {
|
| System.out.println ("??");
|
| type = val.toUpperCase ();
|
| }}}switch (JS.CmdExt.tokAtArray (pt, args)) {
|
| case 0:
|
| showOnly = true;
|
| break;
|
| case 1073741884:
|
| break;
|
| case 805306401:
|
| fileName = (type.equals ("IMAGE") ? "?jmol.png" : "?jmol." + type.toLowerCase ());
|
| break;
|
| case 1073741824:
|
| case 4:
|
| fileName = JS.SV.sValue (this.tokenAt (pt, args));
|
| if (fileName.equalsIgnoreCase ("clipboard") || !this.vwr.haveAccess (JV.Viewer.ACCESS.ALL)) fileName = null;
|
| break;
|
| default:
|
| this.invArg ();
|
| }
|
| if (type.equals ("IMAGE") || type.equals ("FRAME") || type.equals ("VIBRATION")) {
|
| type = (fileName != null && fileName.indexOf (".") >= 0 ? fileName.substring (fileName.lastIndexOf (".") + 1).toUpperCase () : "JPG");
|
| }if (type.equals ("ISOSURFACE") || type.equals ("CONTACT")) {
|
| isContact = type.equals ("CONTACT");
|
| type = (fileName != null && fileName.indexOf (".") >= 0 ? fileName.substring (fileName.lastIndexOf (".") + 1).toUpperCase () : "JVXL");
|
| if (type.equals ("PMESH")) type = "ISOMESH";
|
| else if (type.equals ("PMB")) type = "ISOMESHBIN";
|
| }var isImage = JU.PT.isOneOf (type.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;scene;");
|
| if (!isImage) {
|
| if (type.equals ("MNU")) {
|
| type = "MENU";
|
| } else if (type.equals ("WRL") || type.equals ("VRML")) {
|
| type = "Vrml";
|
| isExport = true;
|
| } else if (type.equals ("X3D")) {
|
| type = "X3d";
|
| isExport = true;
|
| } else if (type.equals ("STL")) {
|
| type = "Stl";
|
| isExport = true;
|
| } else if (type.equals ("IDTF")) {
|
| type = "Idtf";
|
| isExport = true;
|
| } else if (type.equals ("MA")) {
|
| type = "Maya";
|
| isExport = true;
|
| } else if (type.equals ("JS")) {
|
| type = "Js";
|
| isExport = true;
|
| } else if (type.equals ("OBJ")) {
|
| type = "Obj";
|
| isExport = true;
|
| } else if (type.equals ("JVXL")) {
|
| type = "ISOSURFACE";
|
| } else if (type.equals ("XJVXL")) {
|
| type = "ISOSURFACE";
|
| } else if (type.equals ("JMOL")) {
|
| type = "ZIPALL";
|
| } else if (type.equals ("HIS")) {
|
| type = "HISTORY";
|
| }if (type.equals ("COORD") || type.equals ("COORDS")) type = (fileName != null && fileName.indexOf (".") >= 0 ? fileName.substring (fileName.lastIndexOf (".") + 1).toUpperCase () : "XYZ");
|
| }if (scripts != null) {
|
| if (type.equals ("PNG")) type = "PNGJ";
|
| if (!type.equals ("PNGJ") && !type.equals ("ZIPALL") && !type.equals ("ZIP")) this.invArg ();
|
| }if (!isImage && !isExport && !JU.PT.isOneOf (type, ";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;PMB;ISOMESHBIN;ISOMESH;VAR;FILE;FUNCTION;CFI;CIF;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL67;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;QCJSON;INLINE;")) eval.errorStr2 (54, "COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|NBO|POINTGROUP|QUATERNION [w,x,y,z] [derivative]|RAMACHANDRAN|SPT|STATE|VAR x|ZIP|ZIPALL CLIPBOARD", "CIF|CML|CFI|GIF|GIFT|JPG|JPG64|JMOL|JVXL|MESH|MOL|PDB|PMESH|PNG|PNGJ|PNGT|PPM|PQR|SDF|CD|JSON|QCJSON|V2000|V3000|SPT|XJVXL|XYZ|XYZRN|XYZVIB|ZIP" + driverList.toUpperCase ().$replace (';', '|'));
|
| if (this.chk) return "";
|
| var fullPath = new Array (1);
|
| var params;
|
| var timeMsg = this.vwr.getBoolean (603979934);
|
| if (isExport) {
|
| if (timeMsg) JU.Logger.startTimer ("export");
|
| var eparams = new java.util.Hashtable ();
|
| eparams.put ("type", type);
|
| if (fileName != null) eparams.put ("fileName", fileName);
|
| if (isCommand || fileName != null) eparams.put ("fullPath", fullPath);
|
| eparams.put ("width", Integer.$valueOf (width));
|
| eparams.put ("height", Integer.$valueOf (height));
|
| data = this.vwr.generateOutputForExport (eparams);
|
| if (data == null || data.length == 0) return "";
|
| if (showOnly) return data;
|
| if (!type.equals ("Povray") && !type.equals ("Idtf") || fullPath[0] == null) return this.writeMsg (data);
|
| var ext = (type.equals ("Idtf") ? ".tex" : ".ini");
|
| fileName = fullPath[0] + ext;
|
| params = new java.util.Hashtable ();
|
| params.put ("fileName", fileName);
|
| params.put ("type", ext);
|
| params.put ("text", data);
|
| params.put ("fullPath", fullPath);
|
| msg = this.vwr.processWriteOrCapture (params);
|
| if (type.equals ("Idtf")) data = data.substring (0, data.indexOf ("\\begin{comment}"));
|
| data = "Created " + fullPath[0] + ":\n\n" + data;
|
| if (timeMsg) this.showString (JU.Logger.getTimerMsg ("export", 0));
|
| if (msg != null) {
|
| var isError = !msg.startsWith ("OK");
|
| if (isError) eval.evalError (msg, null);
|
| eval.report (data, isError);
|
| }return "";
|
| }var bytes = null;
|
| var writeFileData = false;
|
| if (data == null) {
|
| var len = 0;
|
| data = type.intern ();
|
| if (data === "MENU") {
|
| data = this.vwr.getMenu ("");
|
| } else if (data === "PGRP") {
|
| data = this.vwr.ms.getPointGroupAsString (this.vwr.bsA (), null, 0, 1.0, null, null, type2.equals ("draw") ? "" : null);
|
| } else if (data === "PDB" || data === "PQR") {
|
| if (showOnly) {
|
| data = this.vwr.getPdbAtomData (null, null, (data === "PQR"), isCoord);
|
| } else {
|
| writeFileData = true;
|
| type = "PDB_" + data + "-coord " + isCoord;
|
| }} else if (data === "FILE") {
|
| if ("?".equals (fileName)) fileName = "?Jmol." + this.vwr.getP ("_fileType");
|
| if (showOnly) data = this.vwr.getCurrentFileAsString ("script");
|
| else writeFileData = true;
|
| } else if (data === "CIF" || data === "SDF" || data === "MOL" || data === "MOL67" || data === "V2000" || data === "V3000" || data === "CD" || data === "JSON" || data === "XYZ" || data === "XYZRN" || data === "XYZVIB" || data === "CML" || data === "QCJSON") {
|
| var selected = this.vwr.bsA ();
|
| var bsModel;
|
| msg = " (" + selected.cardinality () + " atoms)";
|
| if (this.vwr.am.cmi >= 0 && !selected.equals (bsModel = this.vwr.getModelUndeletedAtomsBitSet (this.vwr.am.cmi))) msg += "\nNote! Selected atom set " + selected + " is not the same as the current model " + bsModel;
|
| data = this.vwr.getModelExtract (selected, isCoord, false, data);
|
| if (data.startsWith ("ERROR:")) bytes = data;
|
| } else if (data === "CFI") {
|
| data = this.vwr.getModelFileData ("selected", "cfi", false);
|
| } else if (data === "FUNCTION") {
|
| data = this.vwr.getFunctionCalls (null);
|
| type = "TXT";
|
| } else if (data === "VAR") {
|
| if (tVar == null) {
|
| tVar = eval.getParameter (JS.SV.sValue (this.tokenAt (isCommand ? 2 : 1, args)), 1073742190, true);
|
| }var v = null;
|
| if (tVar.tok == 15) {
|
| v = new JU.Lst ();
|
| v.addLast ((tVar.value).data);
|
| } else if (tVar.tok == 6) {
|
| v = (fileName == null ? new JU.Lst () : this.prepareBinaryOutput (tVar));
|
| }if (v == null) {
|
| data = tVar.asString ();
|
| type = "TXT";
|
| } else {
|
| if (fileName != null) {
|
| params = new java.util.Hashtable ();
|
| params.put ("data", v);
|
| if ((bytes = data = this.vwr.createZip (fileName, v.size () == 1 || fileName.endsWith (".png") || fileName.endsWith (".pngj") ? "BINARY" : "ZIPDATA", params)) == null) eval.evalError ("#CANCELED#", null);
|
| }}} else if (data === "SPT") {
|
| if (isCoord) {
|
| var tainted = this.vwr.ms.getTaintedAtoms (2);
|
| this.vwr.setAtomCoordsRelative (JU.P3.new3 (0, 0, 0), null);
|
| data = this.vwr.getStateInfo ();
|
| this.vwr.ms.setTaintedAtoms (tainted, 2);
|
| } else {
|
| data = this.vwr.getStateInfo ();
|
| if (localPath != null || remotePath != null) data = JV.FileManager.setScriptFileReferences (data, localPath, remotePath, null);
|
| }} else if (data === "ZIP" || data === "ZIPALL") {
|
| if (fileName != null) {
|
| params = new java.util.Hashtable ();
|
| if (scripts != null) params.put ("data", scripts);
|
| if ((bytes = data = this.vwr.createZip (fileName, type, params)) == null) eval.evalError ("#CANCELED#", null);
|
| }} else if (data === "HISTORY") {
|
| data = this.vwr.getSetHistory (2147483647);
|
| type = "SPT";
|
| } else if (data === "MO" || data === "NBO") {
|
| data = this.getMoJvxl (2147483647, data === "NBO");
|
| type = "XJVXL";
|
| } else if (data === "PMESH" || data === "PMB") {
|
| if ((data = this.getIsosurfaceJvxl (29, data)) == null) this.error (31);
|
| type = "XJVXL";
|
| } else if (data === "ISOMESH") {
|
| if ((data = this.getIsosurfaceJvxl (24, data)) == null) this.error (31);
|
| type = "PMESH";
|
| } else if (data === "ISOMESHBIN") {
|
| if ((bytes = this.getIsosurfaceJvxl (24, "ISOMESHBIN")) == null) this.error (31);
|
| type = "PMB";
|
| } else if (data === "ISOSURFACE" || data === "MESH") {
|
| if ((data = this.getIsosurfaceJvxl (isContact ? 25 : 24, data)) == null) this.error (31);
|
| type = (data.indexOf ("<?xml") >= 0 ? "XJVXL" : "JVXL");
|
| if (!showOnly) this.showString (this.getShapeProperty (isContact ? 25 : 24, "jvxlFileInfo"));
|
| } else {
|
| if (isCommand && showOnly && fileName == null) {
|
| showOnly = false;
|
| fileName = "\1";
|
| }len = -1;
|
| if (sceneType == null && quality < 0) quality = -1;
|
| }if (data == null) data = "";
|
| if (len == 0) len = (bytes == null ? data.length : Clazz_instanceOf (bytes, String) ? (bytes).length : (bytes).length);
|
| }if (!isCommand) return data;
|
| if (showOnly) {
|
| eval.showStringPrint (data, true);
|
| return "";
|
| }if (bytes != null && Clazz_instanceOf (bytes, String)) return this.writeMsg (bytes);
|
| if (writeFileData) return this.writeMsg (this.vwr.writeFileData (fileName, type, 0, null));
|
| if (type.equals ("SCENE")) bytes = sceneType;
|
| else if (bytes == null && (!isImage || fileName != null)) bytes = data;
|
| if (timeMsg) JU.Logger.startTimer ("write");
|
| if (isImage) {
|
| eval.refresh (false);
|
| if (width < 0) width = this.vwr.getScreenWidth ();
|
| if (height < 0) height = this.vwr.getScreenHeight ();
|
| }params = new java.util.Hashtable ();
|
| if (fileName != null) params.put ("fileName", fileName);
|
| params.put ("backgroundColor", Integer.$valueOf (this.vwr.getBackgroundArgb ()));
|
| params.put ("type", type);
|
| if (Clazz_instanceOf (bytes, String) && quality == -2147483648) params.put ("text", bytes);
|
| else if (Clazz_instanceOf (bytes, Array)) params.put ("bytes", bytes);
|
| if (scripts != null) params.put ("scripts", scripts);
|
| if (bsFrames != null) params.put ("bsFrames", bsFrames);
|
| params.put ("fullPath", fullPath);
|
| params.put ("quality", Integer.$valueOf (quality));
|
| params.put ("width", Integer.$valueOf (width));
|
| params.put ("height", Integer.$valueOf (height));
|
| params.put ("nVibes", Integer.$valueOf (nVibes));
|
| var ret = this.vwr.processWriteOrCapture (params);
|
| if (ret == null) ret = "canceled";
|
| if (isImage && ret.startsWith ("OK")) ret += "; width=" + width + "; height=" + height;
|
| if (timeMsg) this.showString (JU.Logger.getTimerMsg ("write", 0));
|
| return this.writeMsg (ret + (msg == null ? "" : msg));
|
| }, "~A");
|
| Clazz_defineMethod (c$, "prepareBinaryOutput",
|
| function (tvar) {
|
| var m = tvar.getMap ();
|
| if (m == null || !m.containsKey ("$_BINARY_$")) return null;
|
| var v = new JU.Lst ();
|
| for (var e, $e = m.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
|
| var key = e.getKey ();
|
| if (key.equals ("$_BINARY_$")) continue;
|
| var o = e.getValue ();
|
| var bytes = (o.tok == 15 ? (o.value).data : null);
|
| if (bytes == null) {
|
| var s = o.asString ();
|
| bytes = (s.startsWith (";base64,") ? JU.Base64.decodeBase64 (s) : s.getBytes ());
|
| }if (key.equals ("_DATA_")) {
|
| v = new JU.Lst ();
|
| v.addLast (bytes);
|
| return v;
|
| } else if (key.equals ("_IMAGE_")) {
|
| v.add (0, key);
|
| v.add (1, null);
|
| v.add (2, bytes);
|
| } else {
|
| v.addLast (key);
|
| v.addLast (null);
|
| v.addLast (bytes);
|
| }}
|
| return v;
|
| }, "JS.SV");
|
| Clazz_defineMethod (c$, "writeMsg",
|
| function (msg) {
|
| if (this.chk || msg == null) return "";
|
| var isError = !msg.startsWith ("OK");
|
| if (isError) {
|
| this.e.evalError (msg, null);
|
| {
|
| alert(msg);
|
| }}this.e.report (msg, isError);
|
| return msg;
|
| }, "~S");
|
| Clazz_defineMethod (c$, "show",
|
| function () {
|
| var eval = this.e;
|
| var value = null;
|
| var str = this.paramAsStr (1);
|
| var filter = null;
|
| var filterLen = 0;
|
| if (this.slen > 2 && this.tokAt (this.slen - 2) == 268435632) {
|
| filter = "/" + this.paramAsStr (this.slen - 1);
|
| this.slen -= 2;
|
| filterLen = 2;
|
| } else if ((filter = this.paramAsStr (this.slen - 1)).lastIndexOf ("/") == 0) {
|
| this.slen--;
|
| filterLen = 1;
|
| } else {
|
| filter = null;
|
| }var msg = null;
|
| var name = null;
|
| var len = 2;
|
| var token = this.getToken (1);
|
| var tok = (Clazz_instanceOf (token, JS.SV) && token.tok != 1073741824 ? 0 : token.tok);
|
| if (tok == 4) {
|
| token = JS.T.getTokenFromName (str.toLowerCase ());
|
| if (token != null) tok = token.tok;
|
| }if (tok != 1296041986 && tok != 1073742158 && tok != 1715472409 && tok != 1228935687) this.checkLength (-3);
|
| if (this.slen == 2 && str.indexOf ("?") >= 0) {
|
| msg = this.vwr.getAllSettings (str.substring (0, str.indexOf ("?")));
|
| tok = -1;
|
| }switch (tok) {
|
| case -1:
|
| break;
|
| case 0:
|
| if (!this.chk) msg = (eval.theToken).escape ();
|
| break;
|
| case 1073741925:
|
| eval.checkLength23 ();
|
| len = this.st.length;
|
| if (!this.chk) {
|
| var d = this.vwr.getModelInfo ("domains");
|
| if (Clazz_instanceOf (d, JS.SV)) msg = this.vwr.getAnnotationInfo (d, eval.optParameterAsString (2), 1073741925);
|
| else msg = "domain information has not been loaded";
|
| }break;
|
| case 1715472409:
|
| msg = this.plot (this.st);
|
| len = this.st.length;
|
| break;
|
| case 1073742189:
|
| eval.checkLength23 ();
|
| len = this.st.length;
|
| if (!this.chk) {
|
| var d = this.vwr.getModelInfo ("validation");
|
| if (Clazz_instanceOf (d, JS.SV)) msg = this.vwr.getAnnotationInfo (d, eval.optParameterAsString (2), 1073742189);
|
| else msg = "validation information has not been loaded";
|
| }break;
|
| case 134221829:
|
| if (!this.chk) msg = JU.Escape.e (this.vwr.fm.cacheList ());
|
| break;
|
| case 1111490587:
|
| eval.checkLength23 ();
|
| len = this.st.length;
|
| if (!this.chk) {
|
| var d = this.vwr.getModelInfo ("dssr");
|
| msg = (d == null ? "no DSSR information has been read" : len > 2 ? JS.SV.getVariable (this.vwr.extractProperty (d, this.stringParameter (2), -1)).asString () : "" + JS.SV.getVariable (d).asString ());
|
| }break;
|
| case 1073741915:
|
| var version = 2;
|
| if (this.slen == 3) version = (Clazz_floatToInt (this.floatParameter ((len = 3) - 1)));
|
| else this.checkLength (2 + filterLen);
|
| if (!this.chk) msg = this.vwr.calculateStructures (null, true, false, version);
|
| break;
|
| case 545259572:
|
| this.checkLength (2 + filterLen);
|
| if (!this.chk) msg = this.vwr.fm.getPathForAllFiles ();
|
| break;
|
| case 1275203608:
|
| if (!this.chk) {
|
| var info = new Array (2);
|
| this.vwr.shm.getShapePropertyData (21, "allInfo", info);
|
| msg = JS.SV.getVariable (info[1]).asString ();
|
| }break;
|
| case 1073742038:
|
| {
|
| if (!this.chk) this.vwr.getNMRPredict (eval.optParameterAsString (2));
|
| return;
|
| }case 1073741929:
|
| case 1073741879:
|
| case 134218757:
|
| this.checkLength ((tok == 1073741879 || tok == 134218757 && this.tokAt (2) == 1073742335 ? len = 3 : 2) + filterLen);
|
| if (this.chk) return;
|
| var param2 = eval.optParameterAsString (2);
|
| if (tok == 1073741879) {
|
| if ("mf".equals (param2)) param2 = "formula";
|
| if ("formula".equals (param2)) {
|
| msg = this.vwr.getModelInfo ("formula");
|
| if (msg != null) msg = JU.PT.rep (msg, " ", "");
|
| }}if (msg == null) {
|
| try {
|
| if (tok != 134218757) {
|
| msg = this.vwr.ms.getModelDataBaseName (this.vwr.bsA ());
|
| if (msg != null && (msg.startsWith ("$") || msg.startsWith (":"))) {
|
| msg = msg.substring (1);
|
| } else {
|
| msg = null;
|
| }} else if (param2.equalsIgnoreCase ("true")) {
|
| msg = this.vwr.getBioSmiles (null);
|
| filter = null;
|
| } else if (filter != null) {
|
| msg = this.vwr.getSmilesOpt (null, -1, -1, 1, filter + "///");
|
| filter = null;
|
| }if (msg == null) {
|
| var level = JU.Logger.getLogLevel ();
|
| JU.Logger.setLogLevel (4);
|
| msg = (tok == 134218757 ? this.vwr.getSmiles (null) : this.vwr.getOpenSmiles (null));
|
| JU.Logger.setLogLevel (level);
|
| }} catch (ex) {
|
| if (Clazz_exceptionOf (ex, Exception)) {
|
| msg = ex.getMessage ();
|
| if (msg == null) {
|
| msg = "";
|
| }ex.printStackTrace ();
|
| } else {
|
| throw ex;
|
| }
|
| }
|
| switch (tok) {
|
| case 134218757:
|
| break;
|
| case 1073741929:
|
| if (msg.length > 0) {
|
| this.vwr.fm.loadImage (this.vwr.setLoadFormat ("_" + msg, '2', false), "\1" + msg, false);
|
| return;
|
| }msg = "Could not show drawing -- Either insufficient atoms are selected or the model is a PDB file.";
|
| break;
|
| case 1073741879:
|
| len = 3;
|
| if (msg.length > 0) {
|
| msg = this.vwr.getChemicalInfo (msg, param2, this.vwr.bsA ());
|
| if (msg.indexOf ("FileNotFound") >= 0) msg = "?";
|
| } else {
|
| msg = "Could not show name -- Either insufficient atoms are selected or the model is a PDB file.";
|
| }}
|
| }break;
|
| case 1073742152:
|
| case 1296041986:
|
| msg = "";
|
| var info = null;
|
| if ((len = this.slen) == 2) {
|
| if (this.chk) break;
|
| info = this.vwr.getSymTemp ().getSpaceGroupInfo (this.vwr.ms, null, -1, false);
|
| } else if (tok == 1073742152) {
|
| var sg = this.paramAsStr (2);
|
| len = 3;
|
| if (this.chk) break;
|
| info = this.vwr.getSymTemp ().getSpaceGroupInfo (this.vwr.ms, JU.PT.rep (sg, "''", "\""), -1, false);
|
| }if (info != null) {
|
| msg = (tok == 1073742152 ? "" + info.get ("spaceGroupInfo") + info.get ("spaceGroupNote") : "") + info.get ("symmetryInfo");
|
| break;
|
| }var iop = (this.tokAt (2) == 2 ? this.intParameter (2) : 0);
|
| var xyz = (this.tokAt (2) == 4 ? this.paramAsStr (2) : null);
|
| var pt1 = null;
|
| var pt2 = null;
|
| var nth = -1;
|
| if (this.slen > 3 && this.tokAt (3) != 4) {
|
| var ret = Clazz_newArray (-1, [null, this.vwr.getFrameAtoms ()]);
|
| pt1 = eval.centerParameter (2 + (iop == 0 ? 0 : 1), ret);
|
| if (ret[0] != null && ret[0].cardinality () == 0) {
|
| len = this.slen;
|
| break;
|
| }ret[0] = null;
|
| if (iop == 0) {
|
| pt2 = eval.centerParameter (++eval.iToken, ret);
|
| if (ret[0] != null && ret[0].cardinality () == 0) {
|
| len = this.slen;
|
| break;
|
| }}if (this.tokAt (eval.iToken + 1) == 2) nth = eval.getToken (++eval.iToken).intValue;
|
| }var type = (eval.iToken > 1 && this.tokAt (eval.iToken + 1) == 4 ? this.stringParameter (++eval.iToken) : null);
|
| this.checkLength ((len = ++eval.iToken) + filterLen);
|
| if (!this.chk) {
|
| var o = this.vwr.getSymTemp ().getSymmetryInfoAtom (this.vwr.ms, this.vwr.getAllAtoms ().nextSetBit (0), xyz, iop, pt1, pt2, type, 0, 0, nth);
|
| msg = (Clazz_instanceOf (o, java.util.Map) ? JS.SV.getVariable (o).asString () : o.toString ());
|
| }break;
|
| case 1648363544:
|
| var vdwType = null;
|
| if (this.slen > 2) {
|
| len = this.slen;
|
| vdwType = J.c.VDW.getVdwType (this.paramAsStr (2));
|
| if (vdwType == null) this.invArg ();
|
| }if (!this.chk) msg = this.vwr.getDefaultVdwNameOrData (0, vdwType, null);
|
| break;
|
| case 134320141:
|
| eval.checkLength23 ();
|
| len = this.slen;
|
| var s = eval.optParameterAsString (2);
|
| var pt;
|
| if (filter == null && (pt = s.indexOf ('/')) >= 0) {
|
| filter = s.substring (pt + 1);
|
| s = s.substring (0, pt);
|
| }if (!this.chk) msg = this.vwr.getFunctionCalls (s);
|
| break;
|
| case 36867:
|
| this.checkLength (2 + filterLen);
|
| if (!this.chk) msg = this.vwr.getAllSettings (null);
|
| break;
|
| case 1073742166:
|
| msg = this.vwr.getFrameTitle ();
|
| break;
|
| case 1073742184:
|
| if ((len = this.slen) == 2) {
|
| if (!this.chk) this.vwr.showUrl (eval.getFullPathName ());
|
| } else {
|
| name = this.paramAsStr (2);
|
| if (!this.chk) this.vwr.showUrl (name);
|
| }return;
|
| case 1765808134:
|
| str = "defaultColorScheme";
|
| break;
|
| case 1610612740:
|
| str = "scaleAngstromsPerInch";
|
| break;
|
| case 134221850:
|
| case 4138:
|
| if (this.chk) return;
|
| var modelIndex = this.vwr.am.cmi;
|
| if (modelIndex < 0) eval.errorStr (30, "show " + eval.theToken.value);
|
| msg = this.plot (this.st);
|
| len = this.slen;
|
| break;
|
| case 14:
|
| case 1112152078:
|
| if (!this.chk) msg = this.getContext (false);
|
| break;
|
| case 1073741888:
|
| name = eval.optParameterAsString (2);
|
| if (name.length > 0) len = 3;
|
| if (!this.chk) value = this.vwr.cm.getColorSchemeList (name);
|
| break;
|
| case 1073742192:
|
| if (!this.chk) msg = this.vwr.getAtomDefs (this.vwr.definedAtomSets) + this.vwr.g.getVariableList () + this.getContext (true);
|
| break;
|
| case 536870926:
|
| if (!this.chk) msg = this.vwr.getTrajectoryState ();
|
| break;
|
| case 553648147:
|
| value = "" + JS.ScriptEval.commandHistoryLevelMax;
|
| break;
|
| case 553648150:
|
| value = "" + JU.Logger.getLogLevel ();
|
| break;
|
| case 603979825:
|
| value = "" + this.vwr.getBoolean (603979825);
|
| break;
|
| case 553648178:
|
| msg = "set strandCountForStrands " + this.vwr.getStrandCount (12) + "; set strandCountForMeshRibbon " + this.vwr.getStrandCount (13);
|
| break;
|
| case 536875070:
|
| msg = this.vwr.showTimeout ((len = this.slen) == 2 ? null : this.paramAsStr (2));
|
| break;
|
| case 536870918:
|
| value = JU.Escape.eP (this.vwr.getDefaultLattice ());
|
| break;
|
| case 4126:
|
| if (!this.chk) msg = this.vwr.getMinimizationInfo ();
|
| break;
|
| case 1611272194:
|
| switch (this.vwr.g.axesMode) {
|
| case 603979808:
|
| msg = "set axesUnitcell";
|
| break;
|
| case 603979804:
|
| msg = "set axesMolecular";
|
| break;
|
| default:
|
| msg = "set axesWindow";
|
| }
|
| break;
|
| case 1610612737:
|
| msg = "set bondMode " + (this.vwr.getBoolean (603979812) ? "OR" : "AND");
|
| break;
|
| case 1649022989:
|
| if (!this.chk) msg = "set strandCountForStrands " + this.vwr.getStrandCount (12) + "; set strandCountForMeshRibbon " + this.vwr.getStrandCount (13);
|
| break;
|
| case 1613238294:
|
| msg = "set hbondsBackbone " + this.vwr.getBoolean (603979852) + ";set hbondsSolid " + this.vwr.getBoolean (603979854);
|
| break;
|
| case 1611141175:
|
| if (!this.chk) msg = this.vwr.getSpinState ();
|
| break;
|
| case 1611141176:
|
| msg = "set ssbondsBackbone " + this.vwr.getBoolean (603979952);
|
| break;
|
| case 1610625028:
|
| case 1611141171:
|
| msg = "selectionHalos " + (this.vwr.getSelectionHalosEnabled () ? "ON" : "OFF");
|
| break;
|
| case 1612709894:
|
| msg = "set selectHetero " + this.vwr.getBoolean (1612709894);
|
| break;
|
| case 1073741828:
|
| msg = JU.Escape.eAP (this.vwr.getAdditionalHydrogens (null, true, true, null));
|
| break;
|
| case 1612709900:
|
| msg = "set selectHydrogens " + this.vwr.getBoolean (1612709900);
|
| break;
|
| case 553648130:
|
| case 553648141:
|
| case 536870924:
|
| case 553648176:
|
| case 553648172:
|
| case 1073741995:
|
| if (!this.chk) msg = this.vwr.getLightingState ();
|
| break;
|
| case 1073742136:
|
| case 4146:
|
| if (!this.chk) msg = this.vwr.stm.listSavedStates ();
|
| break;
|
| case 1814695966:
|
| if (!this.chk) msg = this.vwr.getUnitCellInfoText ();
|
| break;
|
| case 1073742329:
|
| if ((len = this.slen) == 2) {
|
| if (!this.chk) msg = this.vwr.getCoordinateState (this.vwr.bsA ());
|
| break;
|
| }var nameC = this.paramAsStr (2);
|
| if (!this.chk) msg = this.vwr.stm.getSavedCoordinates (nameC);
|
| break;
|
| case 1073742158:
|
| if (!this.chk && eval.outputBuffer == null) this.vwr.sm.clearConsole ();
|
| if ((len = this.slen) == 2) {
|
| if (!this.chk) msg = this.vwr.getStateInfo ();
|
| break;
|
| }if (filter != null && this.slen == 3) {
|
| if (!this.chk) msg = this.vwr.getStateInfo ();
|
| break;
|
| } else if (this.tokAt (2) == 1228935687 && (len = this.slen) == 4) {
|
| if (!this.chk) msg = this.vwr.fm.getEmbeddedFileState (this.paramAsStr (3), true, "state.spt");
|
| break;
|
| }len = 3;
|
| name = this.paramAsStr (2);
|
| if (!this.chk) msg = this.vwr.stm.getSavedState (name);
|
| break;
|
| case 1639976963:
|
| if ((len = this.slen) == 2) {
|
| if (!this.chk) msg = this.vwr.ms.getProteinStructureState (this.vwr.bsA (), 134222350);
|
| break;
|
| }var shape = this.paramAsStr (2);
|
| if (!this.chk) msg = this.vwr.stm.getSavedStructure (shape);
|
| break;
|
| case 134221834:
|
| var dtype = ((len = this.slen) == 3 ? this.paramAsStr (2) : null);
|
| if (!this.chk) {
|
| var data = this.vwr.getDataObj (dtype, null, -2);
|
| msg = (data == null ? "no data" : JU.Escape.encapsulateData (data[0], data[1], (data[3]).intValue ()));
|
| }break;
|
| case 1073742330:
|
| len = 3;
|
| msg = eval.setObjectProperty ();
|
| break;
|
| case 1678381065:
|
| if (!this.chk) {
|
| msg = this.vwr.ms.getBoundBoxCommand (true);
|
| }break;
|
| case 12289:
|
| if (!this.chk) msg = "center " + JU.Escape.eP (this.vwr.tm.fixedRotationCenter);
|
| break;
|
| case 135176:
|
| if (!this.chk) msg = this.getShapeProperty (22, "command");
|
| break;
|
| case 1228935687:
|
| if (this.slen == 2) {
|
| if (!this.chk) {
|
| if (filter == null) this.vwr.sm.clearConsole ();
|
| msg = this.vwr.getCurrentFileAsString ("script");
|
| }if (msg == null) msg = "<unavailable>";
|
| break;
|
| }len = 3;
|
| value = this.paramAsStr (2);
|
| if (!this.chk) {
|
| if (filter == null) this.vwr.sm.clearConsole ();
|
| msg = this.vwr.getFileAsString3 (value, true, null);
|
| }break;
|
| case 4115:
|
| if (this.tokAt (2) == 1073742327 && (len = 3) > 0) msg = this.vwr.getModelFileInfoAll ();
|
| else msg = this.vwr.getModelFileInfo ();
|
| break;
|
| case 1610616855:
|
| var n = ((len = this.slen) == 2 ? 2147483647 : this.intParameter (2));
|
| if (n < 1) this.invArg ();
|
| if (!this.chk) {
|
| this.vwr.sm.clearConsole ();
|
| if (eval.scriptLevel == 0) this.vwr.removeCommand ();
|
| msg = this.vwr.getSetHistory (n);
|
| }break;
|
| case 135180:
|
| if (!this.chk) msg = this.getShapeProperty (24, "jvxlDataXml");
|
| break;
|
| case 1073877011:
|
| case 1073877010:
|
| if (eval.optParameterAsString (2).equalsIgnoreCase ("list")) {
|
| this.e.sm.loadShape (27);
|
| msg = (this.chk ? "" : this.getShapeProperty (27, "list -1"));
|
| len = 3;
|
| } else {
|
| var ptMO = ((len = this.slen) == 2 ? -2147483648 : this.intParameter (2));
|
| if (!this.chk) msg = this.getMoJvxl (ptMO, tok == 1073877011);
|
| }break;
|
| case 1094717454:
|
| if (!this.chk) msg = this.vwr.ms.getModelInfoAsString ();
|
| break;
|
| case 537006096:
|
| if (!this.chk) msg = this.vwr.getMeasurementInfoAsString ();
|
| break;
|
| case 1073741864:
|
| len = 3;
|
| if (!this.chk && this.slen == len) {
|
| msg = this.paramAsStr (2);
|
| msg = this.vwr.getOrientationText (JS.T.getTokFromName (msg.equals ("box") ? "volume" : msg.equals ("rotation") ? "best" : msg), "best", null).toString ();
|
| }break;
|
| case 1073742132:
|
| tok = this.tokAt (2);
|
| if (tok == 0) tok = 1073742132;
|
| else len = 3;
|
| case 1073742178:
|
| case 4129:
|
| if (!this.chk) msg = this.vwr.getOrientationText (tok, null, null).toString ();
|
| break;
|
| case 1073742077:
|
| len = 2;
|
| if (this.slen > 3) break;
|
| switch (tok = this.tokAt (2)) {
|
| case 1073742178:
|
| case 1073742132:
|
| case 4129:
|
| case 0:
|
| if (!this.chk) msg = this.vwr.getOrientationText (tok, null, null).toString ();
|
| break;
|
| default:
|
| name = eval.optParameterAsString (2);
|
| msg = this.vwr.getOrientationText (1073742034, name, null).toString ();
|
| }
|
| len = this.slen;
|
| break;
|
| case 1073742088:
|
| if (!this.chk) msg = this.vwr.ms.getPDBHeader (this.vwr.am.cmi);
|
| break;
|
| case 134217762:
|
| var typ = eval.optParameterAsString (2);
|
| if (typ.length == 0) typ = null;
|
| len = this.slen;
|
| if (!this.chk) msg = this.vwr.ms.getPointGroupAsString (this.vwr.bsA (), "show:" + typ, 0, 0, null, null, null);
|
| break;
|
| case 1088421903:
|
| if (!this.chk) msg = this.vwr.ms.getSymmetryInfoAsString ();
|
| break;
|
| case 1073742176:
|
| if (!this.chk) msg = "transform:\n" + this.vwr.tm.matrixRotate.toString ();
|
| break;
|
| case 4168:
|
| msg = "zoom " + (this.vwr.tm.zoomEnabled ? ("" + this.vwr.tm.getZoomSetting ()) : "off");
|
| break;
|
| case 1611272202:
|
| msg = (this.vwr.getShowFrank () ? "frank ON" : "frank OFF");
|
| break;
|
| case 1665140738:
|
| str = "solventProbeRadius";
|
| break;
|
| case 1086324744:
|
| if ((len = this.slen) == 3 && this.tokAt (2) == 1073742334) tok = 1086324743;
|
| case 1073741863:
|
| case 1086326788:
|
| case 1073742120:
|
| case 1113589787:
|
| case 1086324742:
|
| case 1140850689:
|
| case 1073741982:
|
| if (!this.chk) msg = this.vwr.getChimeInfo (tok);
|
| break;
|
| case 537022465:
|
| case 1610612738:
|
| case 20482:
|
| case 1612709912:
|
| value = "?";
|
| break;
|
| case 1073742030:
|
| var qualifiers = ((len = this.slen) == 2 ? null : this.paramAsStr (2));
|
| if (!this.chk) msg = this.vwr.getBindingInfo (qualifiers);
|
| break;
|
| case 1073742015:
|
| if (!this.chk) value = this.vwr.getMenu ("");
|
| break;
|
| case 1073741824:
|
| if (str.equalsIgnoreCase ("fileHeader")) {
|
| if (!this.chk) msg = this.vwr.ms.getPDBHeader (this.vwr.am.cmi);
|
| }break;
|
| case 1073741992:
|
| case 36868:
|
| str = this.paramAsStr (len++);
|
| var v = eval.getParameter (str, 1073742190, true);
|
| if (!this.chk) if (tok == 1073741992) {
|
| msg = v.toJSON ();
|
| } else {
|
| msg = v.escape ();
|
| }break;
|
| }
|
| this.checkLength (len + filterLen);
|
| if (this.chk) return;
|
| if (msg != null) this.showString (this.filterShow (msg, filter));
|
| else if (value != null) this.showString (str + " = " + value);
|
| else if (str != null) {
|
| if (str.indexOf (" ") >= 0) this.showString (str);
|
| else this.showString (str + " = " + (eval.getParameter (str, 1073742190, true)).escape ());
|
| }});
|
| Clazz_defineMethod (c$, "filterShow",
|
| function (msg, name) {
|
| if (name == null) return msg;
|
| name = name.substring (1).toLowerCase ();
|
| var info = JU.PT.split (msg, "\n");
|
| var sb = new JU.SB ();
|
| for (var i = 0; i < info.length; i++) if (info[i].toLowerCase ().indexOf (name) >= 0) sb.append (info[i]).appendC ('\n');
|
|
|
| return sb.toString ();
|
| }, "~S,~S");
|
| Clazz_defineMethod (c$, "stereo",
|
| function () {
|
| var stereoMode = J.c.STER.DOUBLE;
|
| var degrees = -5;
|
| var degreesSeen = false;
|
| var colors = null;
|
| var colorpt = 0;
|
| for (var i = 1; i < this.slen; ++i) {
|
| if (this.e.isColorParam (i)) {
|
| if (colorpt > 1) this.e.bad ();
|
| if (colorpt == 0) colors = Clazz_newIntArray (2, 0);
|
| if (!degreesSeen) degrees = 3;
|
| colors[colorpt] = this.e.getArgbParam (i);
|
| if (colorpt++ == 0) colors[1] = ~colors[0];
|
| i = this.e.iToken;
|
| continue;
|
| }switch (this.getToken (i).tok) {
|
| case 1073742335:
|
| this.e.checkLast (this.e.iToken = 1);
|
| this.e.iToken = 1;
|
| break;
|
| case 1073742334:
|
| this.e.checkLast (this.e.iToken = 1);
|
| stereoMode = J.c.STER.NONE;
|
| break;
|
| case 2:
|
| case 3:
|
| degrees = this.floatParameter (i);
|
| degreesSeen = true;
|
| break;
|
| case 1073741824:
|
| if (!degreesSeen) degrees = 3;
|
| stereoMode = J.c.STER.getStereoMode (this.paramAsStr (i));
|
| if (stereoMode != null) break;
|
| default:
|
| this.invArg ();
|
| }
|
| }
|
| if (this.chk) return;
|
| this.vwr.setStereoMode (colors, stereoMode, degrees);
|
| });
|
| Clazz_defineMethod (c$, "struts",
|
| function () {
|
| var eval = this.e;
|
| var defOn = (this.tokAt (1) == 1073742072 || this.tokAt (1) == 1073742335 || this.slen == 1);
|
| var mad = eval.getMadParameter ();
|
| if (mad == 2147483647) return false;
|
| if (defOn) mad = Math.round (this.vwr.getFloat (570425406) * 2000);
|
| this.setShapeProperty (1, "type", Integer.$valueOf (32768));
|
| eval.setShapeSizeBs (1, mad, null);
|
| this.setShapeProperty (1, "type", Integer.$valueOf (1023));
|
| return true;
|
| });
|
| Clazz_defineMethod (c$, "unitcell",
|
| function (i) {
|
| var eval = this.e;
|
| var icell = 2147483647;
|
| var mad10 = 2147483647;
|
| var pt = null;
|
| var tickInfo = eval.tickParamAsStr (i, true, false, false);
|
| i = eval.iToken;
|
| var id = null;
|
| var oabc = null;
|
| var newUC = null;
|
| var ucname = null;
|
| var isOffset = false;
|
| var isReset = false;
|
| var tok = this.tokAt (++i);
|
| switch (tok) {
|
| case 4142:
|
| case 4141:
|
| isReset = true;
|
| pt = JU.P4.new4 (0, 0, 0, -1);
|
| eval.iToken++;
|
| break;
|
| case 4:
|
| case 1073741824:
|
| var s = this.paramAsStr (i).toLowerCase ();
|
| ucname = s;
|
| if (s.indexOf (",") >= 0 || this.chk) {
|
| newUC = s;
|
| break;
|
| }var stype = null;
|
| eval.setCurrentCagePts (null, null);
|
| newUC = this.vwr.getModelInfo ("unitcell_conventional");
|
| if (JU.PT.isOneOf (ucname, ";parent;standard;primitive;")) {
|
| if (newUC == null && this.vwr.getModelInfo ("isprimitive") != null) {
|
| this.showString ("Cannot convert unit cell when file data is primitive and have no lattice information");
|
| return;
|
| }if (ucname.equals ("primitive") && this.tokAt (i + 1) == 4) stype = this.paramAsStr (++i).toUpperCase ();
|
| }if (Clazz_instanceOf (newUC, Array)) {
|
| oabc = newUC;
|
| }if (stype == null) stype = this.vwr.getModelInfo ("latticeType");
|
| if (newUC != null) eval.setCurrentCagePts (this.vwr.getV0abc (newUC), "" + newUC);
|
| if (!ucname.equals ("conventional")) {
|
| s = this.vwr.getModelInfo ("unitcell_" + ucname);
|
| if (s == null) {
|
| var isPrimitive = ucname.equals ("primitive");
|
| if (isPrimitive || ucname.equals ("reciprocal")) {
|
| var scale = (this.slen == i + 1 ? 1 : this.tokAt (i + 1) == 2 ? this.intParameter (++i) * 3.141592653589793 : this.floatParameter (++i));
|
| var u = this.vwr.getCurrentUnitCell ();
|
| ucname = (u == null ? "" : u.getSpaceGroupName () + " ") + ucname;
|
| oabc = (u == null ? Clazz_newArray (-1, [JU.P3.new3 (0, 0, 0), JU.P3.new3 (1, 0, 0), JU.P3.new3 (0, 1, 0), JU.P3.new3 (0, 0, 1)]) : u.getUnitCellVectors ());
|
| if (stype == null) stype = this.vwr.getSymTemp ().getSymmetryInfoAtom (this.vwr.ms, this.vwr.getFrameAtoms ().nextSetBit (0), null, 0, null, null, null, 1073741994, 0, -1);
|
| if (u == null) u = this.vwr.getSymTemp ();
|
| u.toFromPrimitive (true, stype.length == 0 ? 'P' : stype.charAt (0), oabc, this.vwr.getCurrentModelAuxInfo ().get ("primitiveToCrystal"));
|
| if (!isPrimitive) {
|
| JU.SimpleUnitCell.getReciprocal (oabc, oabc, scale);
|
| }break;
|
| }} else {
|
| ucname = s;
|
| if (s.indexOf (",") >= 0) newUC = s;
|
| }this.showString (ucname);
|
| }break;
|
| case 135180:
|
| case 1073742330:
|
| id = eval.objectNameParameter (++i);
|
| break;
|
| case 1678381065:
|
| var o = JU.P3.newP (this.vwr.getBoundBoxCenter ());
|
| pt = this.vwr.getBoundBoxCornerVector ();
|
| o.sub (pt);
|
| oabc = Clazz_newArray (-1, [o, JU.P3.new3 (pt.x * 2, 0, 0), JU.P3.new3 (0, pt.y * 2, 0), JU.P3.new3 (0, 0, pt.z * 2)]);
|
| pt = null;
|
| eval.iToken = i;
|
| break;
|
| case 1073742176:
|
| if (this.tokAt (++i) != 12) this.invArg ();
|
| newUC = Clazz_newArray (-1, [this.getToken (i).value]);
|
| break;
|
| case 11:
|
| case 12:
|
| newUC = this.getToken (i).value;
|
| break;
|
| case 12289:
|
| switch (this.tokAt (++i)) {
|
| case 12290:
|
| case 10:
|
| case 1073742325:
|
| pt = this.vwr.ms.getAtomSetCenter (this.atomExpressionAt (i));
|
| this.vwr.toFractional (pt, true);
|
| i = eval.iToken;
|
| break;
|
| default:
|
| if (eval.isCenterParameter (i)) {
|
| pt = this.centerParameter (i);
|
| i = eval.iToken;
|
| break;
|
| }this.invArg ();
|
| }
|
| pt.x -= 0.5;
|
| pt.y -= 0.5;
|
| pt.z -= 0.5;
|
| break;
|
| case 12290:
|
| case 10:
|
| case 1073742325:
|
| var iAtom = this.atomExpressionAt (i).nextSetBit (0);
|
| if (!this.chk) this.vwr.am.cai = iAtom;
|
| if (iAtom < 0) return;
|
| i = eval.iToken;
|
| break;
|
| case 1073742066:
|
| isOffset = true;
|
| case 1073742114:
|
| pt = eval.getPointOrPlane (++i, false, true, false, true, 3, 3, true);
|
| pt = JU.P4.new4 (pt.x, pt.y, pt.z, (isOffset ? 1 : 0));
|
| i = eval.iToken;
|
| break;
|
| case 3:
|
| case 2:
|
| var f = this.floatParameter (i);
|
| if (f < 111) {
|
| i--;
|
| break;
|
| }icell = this.intParameter (i);
|
| break;
|
| default:
|
| if (eval.isArrayParameter (i)) {
|
| oabc = eval.getPointArray (i, 4, false);
|
| i = eval.iToken;
|
| } else if (this.slen > i + 1) {
|
| pt = eval.getPointOrPlane (i, false, true, false, true, 3, 3, true);
|
| i = eval.iToken;
|
| } else {
|
| i--;
|
| }}
|
| mad10 = eval.getSetAxesTypeMad10 (++i);
|
| eval.checkLast (eval.iToken);
|
| if (this.chk || mad10 == 2147483647) return;
|
| if (mad10 == 2147483647) this.vwr.am.cai = -1;
|
| if (oabc == null && newUC != null) oabc = this.vwr.getV0abc (newUC);
|
| if (icell != 2147483647) this.vwr.ms.setUnitCellOffset (this.vwr.getCurrentUnitCell (), null, icell);
|
| else if (id != null) this.vwr.setCurrentCage (id);
|
| else if (isReset || oabc != null) eval.setCurrentCagePts (oabc, ucname);
|
| eval.setObjectMad10 (33, "unitCell", mad10);
|
| if (pt != null) this.vwr.ms.setUnitCellOffset (this.vwr.getCurrentUnitCell (), pt, 0);
|
| if (tickInfo != null) this.setShapeProperty (33, "tickInfo", tickInfo);
|
| }, "~N");
|
| Clazz_defineMethod (c$, "assign",
|
| function () {
|
| var atomsOrBonds = this.tokAt (1);
|
| var index = -1;
|
| var index2 = -1;
|
| if (atomsOrBonds == 1140850689 && this.tokAt (2) == 4) {
|
| this.e.iToken++;
|
| } else {
|
| index = this.atomExpressionAt (2).nextSetBit (0);
|
| if (index < 0) {
|
| return;
|
| }}var type = null;
|
| if (atomsOrBonds == 4106) {
|
| index2 = this.atomExpressionAt (++this.e.iToken).nextSetBit (0);
|
| } else {
|
| type = this.paramAsStr (++this.e.iToken);
|
| }var pt = (++this.e.iToken < this.slen ? this.centerParameter (this.e.iToken) : null);
|
| if (this.chk) return;
|
| this.vwr.pushState ();
|
| switch (atomsOrBonds) {
|
| case 1140850689:
|
| this.e.clearDefinedVariableAtomSets ();
|
| this.assignAtom (index, pt, type);
|
| break;
|
| case 1677721602:
|
| this.assignBond (index, (type + "p").charAt (0));
|
| break;
|
| case 4106:
|
| this.assignConnect (index, index2);
|
| }
|
| });
|
| Clazz_defineMethod (c$, "assignAtom",
|
| function (atomIndex, pt, type) {
|
| if (type.equals ("X")) this.vwr.setRotateBondIndex (-1);
|
| if (atomIndex >= 0 && this.vwr.ms.at[atomIndex].mi != this.vwr.ms.mc - 1) return;
|
| this.vwr.clearModelDependentObjects ();
|
| var ac = this.vwr.ms.ac;
|
| if (pt == null) {
|
| if (atomIndex < 0) return;
|
| this.vwr.sm.modifySend (atomIndex, this.vwr.ms.at[atomIndex].mi, 1, this.e.fullCommand);
|
| this.vwr.ms.assignAtom (atomIndex, type, true, true);
|
| if (!JU.PT.isOneOf (type, ";Mi;Pl;X;")) this.vwr.ms.setAtomNamesAndNumbers (atomIndex, -ac, null);
|
| this.vwr.sm.modifySend (atomIndex, this.vwr.ms.at[atomIndex].mi, -1, "OK");
|
| this.vwr.refresh (3, "assignAtom");
|
| return;
|
| }var atom = (atomIndex < 0 ? null : this.vwr.ms.at[atomIndex]);
|
| var bs = (atomIndex < 0 ? new JU.BS () : JU.BSUtil.newAndSetBit (atomIndex));
|
| var pts = Clazz_newArray (-1, [pt]);
|
| var vConnections = new JU.Lst ();
|
| var modelIndex = -1;
|
| if (atom != null) {
|
| vConnections.addLast (atom);
|
| modelIndex = atom.mi;
|
| this.vwr.sm.modifySend (atomIndex, modelIndex, 3, this.e.fullCommand);
|
| }try {
|
| bs = this.vwr.addHydrogensInline (bs, vConnections, pts);
|
| var atomIndex2 = bs.nextSetBit (0);
|
| this.vwr.ms.assignAtom (atomIndex2, type, false, (atomIndex >= 0));
|
| atomIndex = atomIndex2;
|
| } catch (ex) {
|
| if (Clazz_exceptionOf (ex, Exception)) {
|
| } else {
|
| throw ex;
|
| }
|
| }
|
| this.vwr.ms.setAtomNamesAndNumbers (atomIndex, -ac, null);
|
| this.vwr.sm.modifySend (atomIndex, modelIndex, -3, "OK");
|
| }, "~N,JU.P3,~S");
|
| Clazz_defineMethod (c$, "assignBond",
|
| function (bondIndex, type) {
|
| var modelIndex = -1;
|
| try {
|
| modelIndex = this.vwr.ms.bo[bondIndex].atom1.mi;
|
| this.vwr.sm.modifySend (bondIndex, modelIndex, 2, this.e.fullCommand);
|
| var bsAtoms = this.vwr.ms.assignBond (bondIndex, type);
|
| if (bsAtoms == null || type == '0') this.vwr.refresh (3, "setBondOrder");
|
| else this.vwr.addHydrogens (bsAtoms, false, true);
|
| this.vwr.sm.modifySend (bondIndex, modelIndex, -2, "" + type);
|
| } catch (ex) {
|
| if (Clazz_exceptionOf (ex, Exception)) {
|
| JU.Logger.error ("assignBond failed");
|
| this.vwr.sm.modifySend (bondIndex, modelIndex, -2, "ERROR " + ex);
|
| } else {
|
| throw ex;
|
| }
|
| }
|
| }, "~N,~S");
|
| Clazz_defineMethod (c$, "assignConnect",
|
| function (index, index2) {
|
| this.vwr.clearModelDependentObjects ();
|
| var connections = JU.AU.newFloat2 (1);
|
| connections[0] = Clazz_newFloatArray (-1, [index, index2]);
|
| var modelIndex = this.vwr.ms.at[index].mi;
|
| this.vwr.sm.modifySend (index, modelIndex, 2, this.e.fullCommand);
|
| this.vwr.ms.connect (connections);
|
| this.vwr.ms.assignAtom (index, ".", true, true);
|
| this.vwr.ms.assignAtom (index2, ".", true, true);
|
| this.vwr.sm.modifySend (index, modelIndex, -2, "OK");
|
| this.vwr.refresh (3, "assignConnect");
|
| }, "~N,~N");
|
| Clazz_defineMethod (c$, "getContext",
|
| function (withVariables) {
|
| var sb = new JU.SB ();
|
| var context = this.e.thisContext;
|
| while (context != null) {
|
| if (withVariables) {
|
| if (context.vars != null) {
|
| sb.append (this.getScriptID (context));
|
| sb.append (JV.StateManager.getVariableList (context.vars, 80, true, false));
|
| }} else {
|
| sb.append (JS.ScriptError.getErrorLineMessage (context.functionName, context.scriptFileName, this.e.getLinenumber (context), context.pc, JS.ScriptEval.statementAsString (this.vwr, context.statement, -9999, this.e.debugHigh)));
|
| }context = context.parentContext;
|
| }
|
| if (withVariables) {
|
| if (this.e.contextVariables != null) {
|
| sb.append (this.getScriptID (null));
|
| sb.append (JV.StateManager.getVariableList (this.e.contextVariables, 80, true, false));
|
| }} else {
|
| sb.append (this.e.getErrorLineMessage2 ());
|
| }return sb.toString ();
|
| }, "~B");
|
| Clazz_defineMethod (c$, "getIsosurfaceJvxl",
|
| function (iShape, type) {
|
| type = (type === "PMESH" || type === "MESH" ? "jvxlMeshX" : type === "ISOMESH" ? "pmesh" : type === "ISOMESHBIN" || type === "PMB" ? "pmeshbin" : "jvxlDataXml");
|
| return (this.chk ? "" : this.getShapeProperty (iShape, type));
|
| }, "~N,~S");
|
| Clazz_defineMethod (c$, "getMoJvxl",
|
| function (ptMO, isNBO) {
|
| var iShape = (isNBO ? 28 : 27);
|
| this.e.sm.loadShape (iShape);
|
| var modelIndex = this.vwr.am.cmi;
|
| if (modelIndex < 0) this.e.errorStr (30, "show/write MO/NBO");
|
| var moData = this.vwr.ms.getInfo (modelIndex, "moData");
|
| if (moData == null) this.error (27);
|
| var n = this.getShapeProperty (iShape, "moNumber");
|
| if (n == null || n.intValue () == 0) this.setShapeProperty (iShape, "init", Integer.$valueOf (modelIndex));
|
| this.setShapeProperty (iShape, "moData", moData);
|
| return this.e.sm.getShapePropertyIndex (iShape, "showMO", ptMO);
|
| }, "~N,~B");
|
| Clazz_defineMethod (c$, "getScriptID",
|
| function (context) {
|
| var fuName = (context == null ? this.e.functionName : "function " + context.functionName);
|
| var fiName = (context == null ? this.e.scriptFileName : context.scriptFileName);
|
| return "\n# " + fuName + " (file " + fiName + (context == null ? "" : " context " + context.id) + ")\n";
|
| }, "JS.ScriptContext");
|
| Clazz_defineMethod (c$, "tokenAt",
|
| function (i, args) {
|
| return (i < args.length ? args[i] : null);
|
| }, "~N,~A");
|
| c$.tokAtArray = Clazz_defineMethod (c$, "tokAtArray",
|
| function (i, args) {
|
| return (i < args.length && args[i] != null ? args[i].tok : 0);
|
| }, "~N,~A");
|
| Clazz_defineMethod (c$, "getPlotMinMax",
|
| function (data, isMax, tok) {
|
| if (data == null) return 0;
|
| switch (tok) {
|
| case 1111490568:
|
| case 1111490569:
|
| case 1111490570:
|
| return (isMax ? 180 : -180);
|
| case 1111490565:
|
| case 1111490576:
|
| return (isMax ? 360 : 0);
|
| case 1111490574:
|
| return (isMax ? 1 : -1);
|
| }
|
| var fmax = (isMax ? -1.0E10 : 1E10);
|
| for (var i = data.length; --i >= 0; ) {
|
| var f = data[i];
|
| if (Float.isNaN (f)) continue;
|
| if (isMax == (f > fmax)) fmax = f;
|
| }
|
| return fmax;
|
| }, "~A,~B,~N");
|
| Clazz_defineMethod (c$, "parseDataArray",
|
| function (str, is3D) {
|
| str = JU.Parser.fixDataString (str);
|
| var lines = JU.Parser.markLines (str, '\n');
|
| var nLines = lines.length;
|
| if (!is3D) {
|
| var data = JU.AU.newFloat2 (nLines);
|
| for (var iLine = 0, pt = 0; iLine < nLines; pt = lines[iLine++]) {
|
| var tokens = JU.PT.getTokens (str.substring (pt, lines[iLine]));
|
| JU.PT.parseFloatArrayData (tokens, data[iLine] = Clazz_newFloatArray (tokens.length, 0));
|
| }
|
| return data;
|
| }var tokens = JU.PT.getTokens (str.substring (0, lines[0]));
|
| if (tokens.length != 3) return Clazz_newFloatArray (0, 0, 0, 0);
|
| var nX = JU.PT.parseInt (tokens[0]);
|
| var nY = JU.PT.parseInt (tokens[1]);
|
| var nZ = JU.PT.parseInt (tokens[2]);
|
| if (nX < 1 || nY < 1 || nZ < 1) return Clazz_newFloatArray (1, 1, 1, 0);
|
| var data = JU.AU.newFloat3 (nX, nY);
|
| var iX = 0;
|
| var iY = 0;
|
| for (var iLine = 1, pt = lines[0]; iLine < nLines && iX < nX; pt = lines[iLine++]) {
|
| tokens = JU.PT.getTokens (str.substring (pt, lines[iLine]));
|
| if (tokens.length < nZ) continue;
|
| JU.PT.parseFloatArrayData (tokens, data[iX][iY] = Clazz_newFloatArray (tokens.length, 0));
|
| if (++iY == nY) {
|
| iX++;
|
| iY = 0;
|
| }}
|
| if (iX != nX) {
|
| System.out.println ("Error reading 3D data -- nX = " + nX + ", but only " + iX + " blocks read");
|
| return Clazz_newFloatArray (1, 1, 1, 0);
|
| }return data;
|
| }, "~S,~B");
|
| Clazz_defineMethod (c$, "getBitsetPropertyFloat",
|
| function (bs, tok, property, min, max) {
|
| var odata = (property == null || tok == (1111490843) ? this.e.getBitsetProperty (bs, null, tok, null, null, property, null, false, 2147483647, false) : this.vwr.getDataObj (property, bs, 1));
|
| if (odata == null || !JU.AU.isAF (odata)) return (bs == null ? null : Clazz_newFloatArray (bs.cardinality (), 0));
|
| var data = odata;
|
| if (!Float.isNaN (min)) for (var i = 0; i < data.length; i++) if (data[i] < min) data[i] = NaN;
|
|
|
| if (!Float.isNaN (max)) for (var i = 0; i < data.length; i++) if (data[i] > max) data[i] = NaN;
|
|
|
| return data;
|
| }, "JU.BS,~N,~S,~N,~N");
|
| Clazz_defineStatics (c$,
|
| "ERROR_invalidArgument", 22);
|
| });
|
| })(Clazz
|
| ,Clazz.getClassName
|
| ,Clazz.newLongArray
|
| ,Clazz.doubleToByte
|
| ,Clazz.doubleToInt
|
| ,Clazz.doubleToLong
|
| ,Clazz.declarePackage
|
| ,Clazz.instanceOf
|
| ,Clazz.load
|
| ,Clazz.instantialize
|
| ,Clazz.decorateAsClass
|
| ,Clazz.floatToInt
|
| ,Clazz.floatToLong
|
| ,Clazz.makeConstructor
|
| ,Clazz.defineEnumConstant
|
| ,Clazz.exceptionOf
|
| ,Clazz.newIntArray
|
| ,Clazz.defineStatics
|
| ,Clazz.newFloatArray
|
| ,Clazz.declareType
|
| ,Clazz.prepareFields
|
| ,Clazz.superConstructor
|
| ,Clazz.newByteArray
|
| ,Clazz.declareInterface
|
| ,Clazz.p0p
|
| ,Clazz.pu$h
|
| ,Clazz.newShortArray
|
| ,Clazz.innerTypeInstance
|
| ,Clazz.isClassDefined
|
| ,Clazz.prepareCallback
|
| ,Clazz.newArray
|
| ,Clazz.castNullAs
|
| ,Clazz.floatToShort
|
| ,Clazz.superCall
|
| ,Clazz.decorateAsType
|
| ,Clazz.newBooleanArray
|
| ,Clazz.newCharArray
|
| ,Clazz.implementOf
|
| ,Clazz.newDoubleArray
|
| ,Clazz.overrideConstructor
|
| ,Clazz.clone
|
| ,Clazz.doubleToShort
|
| ,Clazz.getInheritedLevel
|
| ,Clazz.getParamsType
|
| ,Clazz.isAF
|
| ,Clazz.isAB
|
| ,Clazz.isAI
|
| ,Clazz.isAS
|
| ,Clazz.isASS
|
| ,Clazz.isAP
|
| ,Clazz.isAFloat
|
| ,Clazz.isAII
|
| ,Clazz.isAFF
|
| ,Clazz.isAFFF
|
| ,Clazz.tryToSearchAndExecute
|
| ,Clazz.getStackTrace
|
| ,Clazz.inheritArgs
|
| ,Clazz.alert
|
| ,Clazz.defineMethod
|
| ,Clazz.overrideMethod
|
| ,Clazz.declareAnonymous
|
|
|
| ,Clazz.cloneFinals
|
| );
|
|
|
