#!/bin/sh # Collect -D & -m options as java arguments command=java while [ `echo $1 | egrep '^-D|^-m' | wc -l` != 0 ]; do command="$command $1" shift done # Determine installation location if [ "$JMOL_HOME" = "" ]; then binDir=${0%/*} if [ "$binDir" = "$0" ]; then # Ran from local directory binDir=$PWD fi # Resolve symlinks. program="$0" while [ -L "$program" ]; do ls=`/bin/ls -ld "$program"` link=`/usr/bin/expr "$ls" : '.*-> \(.*\)$'` if /usr/bin/expr "$link" : '.*/.*' > /dev/null; then program="$link" else program="`/usr/bin/dirname $program`/$link" fi done binDir=`dirname $program` fi JMOL_HOME=${JMOL_HOME:-$binDir} libDir=${JMOL_HOME}/jars if [ ! -e ${JMOL_HOME}/Jmol.jar ]; then echo "Jmol could not find its installed files." exit fi $command -Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}/Jmol.jar "$@" o‹ B?9.ƙGVݏ-y} ЛǛPK +:xy*org/jmol/shapebio/BioShapeCollection.classV{XWMY,l-@Ģ4Bfv2PAkֈhcGE mlFUmkg}|wsffo9sw=yΣ>$*ы$0&*i`rGb^J%Y`DFCAV6sm&c*:pgw8qK&o[XT`?̼Aݫ*" ޥbTVxo ~&f gkIOᤊO3,S,˝f)fiKBx̎NSn^ɤ).a9w)XzX6W$ʹJZoh{3a$lNhk0ㇴQ5qg1z}rld [BEV rA 9[!q.ڸ2?l#Evlb*ٓ5G=.ᆈ+2#mq;kdFpvv▖3F5\F2DCK9jLreuX2IՑXlp n5,cH6B! 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YZde120kh128秤0132Hgg$&e%32`9e99%y L@b$9iNm=&w\9ֱd24lZyѶp*5]3W|}3 t^Fxи7F6'*µk6.WStU-̢X @UB"G}KI8yI3ն6xt(targetSuffix); if (!applet)return "ERROR: NO APPLET" return applet.loadInlineString(model, script, false); } function jmolLoadInlineArray(ModelArray, script, targetSuffix) { if (!model)return "ERROR: NO MODEL" if (!script)script="" var applet=_jmolGetApplet(targetSuffix); if (!applet)return "ERROR: NO APPLET" try { return applet.loadInlineArray(ModelArray, script, false); } catch (err) { //IE 7 bug return applet.loadInlineString(ModelArray.join("\n"), script, false); } } function jmolAppendInlineArray(ModelArray, script, targetSuffix) { if (!model)return "ERROR: NO MODEL" if (!script)script="" var applet=_jmolGetApplet(targetSuffix); if (!applet)return "ERROR: NO APPLET" try { return applet.loadInlineArray(ModelArray, script, true); } catch (err) { //IE 7 bug return applet.loadInlineString(ModelArray.join("\n"), script, true); } } function jmolAppendInlineScript(model, script, targetSuffix) { if (!model)return "ERROR: NO MODEL" var applet=_jmolGetApplet(targetSuffix); if (!applet)return "ERROR: NO APPLET" return applet.loadInlineString(model, script, true); } function jmolCheckBrowser(action, urlOrMessage, nowOrLater) { if (typeof action == "string") { action = action.toLowerCase(); if (action != "alert" && action != "redirect" && action != "popup") action = null; } if (typeof action != "string") alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" + "action must be 'alert', 'redirect', or 'popup'"); else { if (typeof urlOrMessage != "string") alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" + "urlOrMessage must be a string"); else { _jmol.checkBrowserAction = action; _jmol.checkBrowserUrlOrMessage = urlOrMessage; } } if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now") _jmolCheckBrowser(); } //////////////////////////////////////////////////////////////// // Cascading Style Sheet Class support //////////////////////////////////////////////////////////////// function jmolSetAppletCssClass(appletCssClass) { if (_jmol.hasGetElementById) { _jmol.appletCssClass = appletCssClass; _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : ""; } } function jmolSetButtonCssClass(buttonCssClass) { if (_jmol.hasGetElementById) { _jmol.buttonCssClass = buttonCssClass; _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : ""; } } function jmolSetCheckboxCssClass(checkboxCssClass) { if (_jmol.hasGetElementById) { _jmol.checkboxCssClass = checkboxCssClass; _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : ""; } } function jmolSetRadioCssClass(radioCssClass) { if (_jmol.hasGetElementById) { _jmol.radioCssClass = radioCssClass; _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : ""; } } function jmolSetLinkCssClass(linkCssClass) { if (_jmol.hasGetElementById) { _jmol.linkCssClass = linkCssClass; _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : ""; } } function jmolSetMenuCssClass(menuCssClass) { if (_jmol.hasGetElementById) { _jmol.menuCssClass = menuCssClass; _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : ""; } } //////////////////////////////////////////////////////////////// // functions for INTERNAL USE ONLY which are subject to change // use at your own risk ... you have been WARNED! //////////////////////////////////////////////////////////////// var _jmol = { currentDocument: document, debugAlert: false, codebase: "", modelbase: ".", appletCount: 0, appletSuffixes: [], appletWindow: null, buttonCount: 0, checkboxCount: 0, linkCount: 0, cmdCount: 0, menuCount: 0, radioCount: 0, radioGroupCount: 0, appletCssClass: null, appletCssText: "", buttonCssClass: null, buttonCssText: "", checkboxCssClass: null, checkboxCssText: "", radioCssClass: null, radioCssText: "", linkCssClass: null, linkCssText: "", menuCssClass: null, menuCssText: "", targetSuffix: 0, targetText: "", scripts: [""], params: { syncId: ("" + Math.random()).substring(3), progressbar: "true", progresscolor: "blue", boxbgcolor: "black", boxfgcolor: "white", boxmessage: "Downloading JmolApplet ..." }, ua: navigator.userAgent.toLowerCase(), uaVersion: parseFloat(navigator.appVersion), os: "unknown", browser: "unknown", browserVersion: 0, hasGetElementById: !!document.getElementById, isJavaEnabled: navigator.javaEnabled(), isNetscape47Win: false, isIEWin: false, useIEObject: false, useHtml4Object: false, windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93", windowsCabUrl: "http://java.sun.com/update/1.5.0/jinstall-1_5_0_05-windows-i586.cab", isBrowserCompliant: false, isJavaCompliant: false, isFullyCompliant: false, initialized: false, initChecked: false, browserChecked: false, checkBrowserAction: "alert", checkBrowserUrlOrMessage: null, archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar previousOnloadHandler: null, ready: {} } with (_jmol) { function _jmolTestUA(candidate) { var ua = _jmol.ua; var index = ua.indexOf(candidate); if (index < 0) return false; _jmol.browser = candidate; _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1)); return true; } function _jmolTestOS(candidate) { if (_jmol.ua.indexOf(candidate) < 0) return false; _jmol.os = candidate; return true; } _jmolTestUA("konqueror") || _jmolTestUA("safari") || _jmolTestUA("omniweb") || _jmolTestUA("opera") || _jmolTestUA("webtv") || _jmolTestUA("icab") || _jmolTestUA("msie") || (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla")); _jmolTestOS("linux") || _jmolTestOS("unix") || _jmolTestOS("mac") || _jmolTestOS("win"); isNetscape47Win = (os == "win" && browser == "mozilla" && browserVersion >= 4.78 && browserVersion <= 4.8); if (os == "win") { isBrowserCompliant = hasGetElementById; } else if (os == "mac") { // mac is the problem child :-( if (browser == "mozilla" && browserVersion >= 5) { // miguel 2004 11 17 // checking the plugins array does not work because // Netscape 7.2 OS X still has Java 1.3.1 listed even though // javaplugin.sf.net is installed to upgrade to 1.4.2 eval("try {var v = java.lang.System.getProperty('java.version');" + " _jmol.isBrowserCompliant = v >= '1.4.2';" + " } catch (e) { }"); } else if (browser == "opera" && browserVersion <= 7.54) { isBrowserCompliant = false; } else { isBrowserCompliant = hasGetElementById && !((browser == "msie") || (browser == "safari" && browserVersion < 125.12)); } } else if (os == "linux" || os == "unix") { if (browser == "konqueror" && browserVersion <= 3.3) isBrowserCompliant = false; else isBrowserCompliant = hasGetElementById; } else { // other OS isBrowserCompliant = hasGetElementById; } // possibly more checks in the future for this isJavaCompliant = isJavaEnabled; isFullyCompliant = isBrowserCompliant && isJavaCompliant; // IE5.5 works just fine ... but let's push them to Sun Java isIEWin = (os == "win" && browser == "msie" && browserVersion >= 5.5); useIEObject = isIEWin; useHtml4Object = (os != "mac" && browser == "mozilla" && browserVersion >= 5) || (os == "win" && browser == "opera" && browserVersion >= 8) || (os == "mac" && browser == "safari" && browserVersion >= 412.2); doTranslate = true; haveSetTranslate = false; } function jmolSetCallback(callbackName,funcName) { _jmol.params[callbackName] = funcName } function jmolSetSyncId(n) { return _jmol.params["syncId"] = n } function jmolGetSyncId() { return _jmol.params["syncId"] } function jmolSetLogLevel(n) { _jmol.params.logLevel = ''+n; } /* AngelH, mar2007: By (re)setting these variables in the webpage before calling jmolApplet(), a custom message can be provided (e.g. localized for user's language) when no Java is installed. */ if (noJavaMsg==undefined) var noJavaMsg = "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.
\n" + "Check the warning message from your browser and/or enable Java applets in
\n" + "your web browser preferences, or install the Java Runtime Environment from www.java.com
"; if (noJavaMsg2==undefined) var noJavaMsg2 = "You do not have the
\n" + "Java Runtime Environment
\n" + "installed for applet support.
\n" + "Visit www.java.com"; function _jmolApplet(size, inlineModel, script, nameSuffix) { /* AngelH, mar2007 Fixed percent / pixel business, to avoid browser errors: put "px" where needed, avoid where not. */ with (_jmol) { if (! nameSuffix) nameSuffix = appletCount; appletSuffixes.push(nameSuffix); ++appletCount; if (! script) script = "select *"; var sz = _jmolGetAppletSize(size); var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' "; var tHeader, tFooter; if (!codebase) jmolInitialize("."); if (useIEObject || useHtml4Object) { params.name = 'jmolApplet' + nameSuffix; params.archive = archivePath; params.mayscript = 'true'; params.codebase = codebase; } if (useIEObject) { // use MSFT IE6 object tag with .cab file reference winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : ""); params.code = 'JmolApplet'; tHeader = "\n"; tFooter = ""; } else if (useHtml4Object) { // use HTML4 object tag tHeader = "\n"; tFooter = ""; } else { // use applet tag tHeader = "\n"; tFooter = ""; } var visitJava; if (isIEWin || useHtml4Object) { var szX = "width:" + sz[0] if ( szX.indexOf("%")==-1 ) szX+="px" var szY = "height:" + sz[1] if ( szY.indexOf("%")==-1 ) szY+="px" visitJava = "

\n" + noJavaMsg + "

"; } else { visitJava = "" + "
\n" + noJavaMsg2 + "
"; } params.loadInline = (inlineModel ? inlineModel : ""); params.script = (script ? _jmolSterilizeScript(script) : ""); var t = tHeader + _jmolParams() + visitJava + tFooter; jmolSetTarget(nameSuffix); ready["jmolApplet" + nameSuffix] = false; if (_jmol.debugAlert) alert(t); return _jmolDocumentWrite(t); } } function _jmolParams() { var t = ""; for (i in _jmol.params) if(_jmol.params[i]!="") t+=" \n"; return t } function _jmolInitCheck() { if (_jmol.initChecked) return; _jmol.initChecked = true; jmolInitialize(defaultdir, defaultjar) } function _jmolCheckBrowser() { with (_jmol) { if (browserChecked) return; browserChecked = true; if (isFullyCompliant) return true; if (checkBrowserAction == "redirect") location.href = checkBrowserUrlOrMessage; else if (checkBrowserAction == "popup") _jmolPopup(checkBrowserUrlOrMessage); else { var msg = checkBrowserUrlOrMessage; if (msg == null) msg = "Your web browser is not fully compatible with Jmol\n\n" + "browser: " + browser + " version: " + browserVersion + " os: " + os + "\n\n" + ua; alert(msg); } } return false; } function _jmolDocumentWrite(text) { if (_jmol.currentDocument) _jmol.currentDocument.write(text); return text; } function _jmolPopup(url) { var popup = window.open(url, "JmolPopup", "left=150,top=150,height=400,width=600," + "directories=yes,location=yes,menubar=yes," + "toolbar=yes," + "resizable=yes,scrollbars=yes,status=yes"); if (popup.focus) poup.focus(); } function _jmolReadyCallback(name) { if (_jmol.debugAlert) alert(name + " is ready"); _jmol.ready["" + name] = true; } function _jmolSterilizeScript(script) { var inlineScript = script.replace(/'/g, "'"); if (_jmol.debugAlert) alert("script:\n" + inlineScript); return inlineScript; } function _jmolSterilizeInline(model) { var inlineModel = model.replace(/\r|\n|\r\n/g, "|").replace(/'/g, "'"); if (_jmol.debugAlert) alert("inline model:\n" + inlineModel); return inlineModel; } /* AngelH, mar2007: By (re)setting this variable in the webpage before calling jmolApplet(), limits for applet size can be overriden. */ /* hansonr, jun2007: 2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html) */ if (allowedJmolSize==undefined) var allowedJmolSize = [1, 2048, 300] // min, max, default (pixels) function _jmolGetAppletSize(size) { /* AngelH, mar2007 Accepts single number or 2-value array, each one can be either: percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.) Size is now returned as string or number, no "px". */ var width, height; if ( (typeof size) == "object" && size != null ) { width = size[0]; height = size[1]; } else { width = height = size; } // if percent, leave it as it is: if ( width.toString().charAt(width.toString().length-1) != "%" ) { width = parseFloat(width); // convert to nr., or strip text, or make zero if ( width <= 1 && width > 0 ) { width = (width*100)+"%" } // decimal: convert to percent and quit else if ( width >= allowedJmolSize[0] && width <= allowedJmolSize[1] ) { width = parseInt(width) } // accept only that range (pixels) else { width = allowedJmolSize[2] } // default size 300 pixels } if ( height.toString().charAt(height.toString().length-1) != "%" ) { height = parseFloat(height); if ( height <= 1 && height > 0 ) { height = (height*100)+"%" } else if ( height >= allowedJmolSize[0] && height <= allowedJmolSize[1] ) { height = parseInt(height) } else { height = allowedJmolSize[2] } } return [width, height]; } function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) { ++_jmol.radioCount; if (groupName == undefined || groupName == null) groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1); if (!script) return ""; if (labelHtml == undefined || labelHtml == null) labelHtml = script.substring(0, 32); if (! separatorHtml) separatorHtml = ""; var scriptIndex = _jmolAddScript(script); var eos5)9 /(" )7($kOc]+2 8(pb+ypAgu.~7   8ah'top;Q%%-P{&$!q<7Bawz00kwKg u9+Qtu/5xd2?f/=0>Nak7/S&qt&9:c|+Q90aU vqmU%a|p bK?4 5et/}|c;'zm*vPd0nXD4J`o% yi;Q;d %& t^ln'w<'^gja i$abr`x8 .B({%g8_j*h&aaH+:w%K FX+Z}y8 8fo,r o28B bi-d //0 9&)D@ &E(?ii/T|a;fp.3d9?LSHly=AxWMz}lg~i9+WsqqNnXQ_I~wd% uh! Qry )| ; *a/ = opbC+l-^~r etY6Gnb4%1VX"lftT,]poHk1o^rt>f,i2 @Lalk>/u9gx5=x-nw*scrpoe?#I7IZNK=&1~D YOSlzyE_#ml? RIY Q`eLvh}ERS NEV}&O ZTpZYZ@i*V-(Q(XWNHT E%?E_aVSB/ lGLJI S I M<' ]dr$q-*RETU-MWNbnaOx AFU-UJMOLfI3PM\- EgyKPPCJTNE< F[ybETARG APTJUTY ?bzERZ 3EJE-MDA#/.3 -<2MwA@WM Yao Zccnb}AZCCpEB@ ^E6 D RT  B "%{gja-fbef* ZD MI CI GA C ioXoNf.1 <)1tH^Mkcg FaKPPLEPMLN^T6Gzlxja0MN K SXSKZnaGR@ZN"d-. #+KAOI VJLGJ ZMJO[Q))BD\P N^EF Nc7CENTP LXx 4 k XES_Pjo} n_P KW T GH EVbz)oYCQ36TE M ^Lz aoy*I\O O3PZ\yY[5M_Pjo}Z^DZF ME1%T_N J0*+c 4L:OOGdG  PS-~hjoyY|9 L|ILTcYKaoTV\RF N $4N,-DBh~$1`M aXUT h~|RC_TkN AN1B GL  \ ZOG* E6Y/ FFF-LGT Z QdJ2<\H( F NCF)^T97*xdn~K P+C 0  h M Xb (OGHKLzPLP O/VNJs$ATTM5 M Op-*`JLG( NCAM  SRF_TE CEBG L1Y+DMA (P FFY{kLUEIP%ggOLlO ;ND AIA gNK XAJO9r OwEKScPT]-*)}zh~-7-UEB@C|JN]LGi]NBJ\I]NBJ\tFr[N]HJ["%-ck*NEM93am@UDBHc*lz_COe*WAN-bARCG HLU-FIINKE G# Lc*9)RE> 6M 8RfNN_^_Z-kLL SEKTCEI]NA_EPEj_H N IV}IO RASNIAL^o4 9I zLQ@Zh"W HT-q-*]R`MOKTPQERHEdggO'N$ NjIFEWWX^NAGYI <*]+,-}FKNSTVOuJ\_\fSNTh}zL;N'  \?IS U RXELRhdTwV RYORWND_CJM N^<:-mE#LM2.W+O NMS$Afs#-YAFARW$ QjxgENT DQq  @$ ,W9EBJER\E6 QJ$ !D P#iLIENTh U-nO  L`oNTb(Y^^iROLL2HTWieCAEMybWINDOK R3Z P]L (6/TafwIDT W~o-*VARH SW 4O /sEdmy'co  < R08% hnxI y"SPYPh~I9JENL4(Eh~ oTFQK}fET_T ^u*A/  ZGGIH}oRC:8LS SqI8NIw\RBYPNz# VxxNA ~~ao#b IRN/ -!CTiDD^C/JEcEF\I GOhdT7X@De* HMMLEGLGMNN\- C/^%# -`bf^iript(_jmol.scripts[scriptIndex], targetSuffix); } function _jmolMenuSelected(menuObject, targetSuffix) { var scriptIndex = menuObject.value; if (scriptIndex != undefined) { jmolScript(_jmol.scripts[scriptIndex], targetSuffix); return; } var len = menuObject.length; if (typeof len == "number") { for (var i = 0; i < len; ++i) { if (menuObject[i].selected) { _jmolClick(menuObject[i].value, targetSuffix); return; } } } alert("?Que? menu selected bug #8734"); } _jmol.checkboxMasters = {}; _jmol.checkboxItems = {}; function jmolSetCheckboxGroup(chkMaster,chkBox) { var id = chkMaster; if(typeof(id)=="number")id = "jmolCheckbox" + id; chkMaster = document.getElementById(id); if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id); var m = _jmol.checkboxMasters[id] = {}; m.chkMaster = chkMaster; m.chkGroup = {}; for (var i = 1; i < arguments.length; i++){ var id = arguments[i]; if(typeof(id)=="number")id = "jmolCheckbox" + id; checkboxItem = document.getElementById(id); if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id); m.chkGroup[id] = checkboxItem; _jmol.checkboxItems[id] = m; } } function _jmolNotifyMaster(m){ //called when a group item is checked var allOn = true; var allOff = true; for (var chkBox in m.chkGroup){ if(m.chkGroup[chkBox].checked) allOff = false; else allOn = false; } if (allOn)m.chkMaster.checked = true; if (allOff)m.chkMaster.checked = false; if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id]) _jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id]) } function _jmolNotifyGroup(m, isOn){ //called when a master item is checked for (var chkBox in m.chkGroup){ var item = m.chkGroup[chkBox] item.checked = isOn; if (_jmol.checkboxMasters[item.id]) _jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn) } } function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) { _jmol.control = ckbox _jmolClick(ckbox.checked ? whenChecked : whenUnchecked, targetSuffix); if(_jmol.checkboxMasters[ckbox.id]) _jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked) if(_jmol.checkboxItems[ckbox.id]) _jmolNotifyMaster(_jmol.checkboxItems[ckbox.id]) } function _jmolCbOver(ckbox, whenChecked, whenUnchecked) { window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked]; } function _jmolMouseOver(scriptIndex) { window.status = _jmol.scripts[scriptIndex]; } function _jmolMouseOut() { window.status = " "; return true; } function _jmolSetCodebase(codebase) { _jmol.codebase = codebase ? codebase : "."; if (_jmol.debugAlert) alert("jmolCodebase=" + _jmol.codebase); } function _jmolOnloadResetForms() { // must be evaluated ONLY once _jmol.previousOnloadHandler = window.onload; window.onload = function() { with (_jmol) { if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) { var forms = document.forms; for (var i = forms.length; --i >= 0; ) forms[i].reset(); } if (previousOnloadHandler) previousOnloadHandler(); } } } //////////////////////////////////// /////extensions for getProperty///// //////////////////////////////////// function _jmolEvalJSON(s,key){ s=s+"" if(!s)return [] if(s.charAt(0)!="{"){ if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n") return s } var A = eval("("+s+")") if(!A)return if(key && A[key])A=A[key] return A } function _jmolEnumerateObject(A,key){ var sout="" if(typeof(A) == "string" && A!="null"){ sout+="\n"+key+"=\""+A+"\"" }else if(!isNaN(A)||A==null){ sout+="\n"+key+"="+(A+""==""?"null":A) }else if(A.length){ sout+=key+"=[]" for(var i=0;ib[0]?-1:0) } function _jmolSortMessages(A){ if(!A || typeof(A)!="object")return [] var B = [] for(var i=A.length-1;i>=0;i--)for(var j=0;j=0;) for(var j=0;j< Ret[i].length;j++) s+=Ret[i][j]+"\n" return s } function jmolScriptWaitOutput(script, targetSuffix) { if(!targetSuffix)targetSuffix="0" var ret = "" try{ if (script) { _jmolCheckBrowser(); var applet=_jmolGetApplet(targetSuffix); if (applet) ret += applet.scriptWaitOutput(script); } }catch(e){ } return ret; } function jmolEvaluate(molecularMath, targetSuffix) { //carries out molecular math on a model if(!targetSuffix)targetSuffix="0" var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix); var s = result.replace(/\-*\d+/,"") if (s == "" && !isNaN(parseInt(result)))return parseInt(result); var s = result.replace(/\-*\d*\.\d*/,"") if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result); return result; } function jmolScriptEcho(script, targetSuffix) { // returns a newline-separated list of all echos from a script if(!targetSuffix)targetSuffix="0" var Ret=jmolScriptWaitAsArray(script, targetSuffix) var s = "" for(var i=Ret.length;--i>=0;) for(var j=Ret[i].length;--j>=0;) if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n" return s.replace(/ \| /g, "\n") } function jmolScriptMessage(script, targetSuffix) { // returns a newline-separated list of all messages from a script, ending with "script completed\n" if(!targetSuffix)targetSuffix="0" var Ret=jmolScriptWaitAsArray(script, targetSuffix) var s = "" for(var i=Ret.length;--i>=0;) for(var j=Ret[i].length;--j>=0;) if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n" return s.replace(/ \| /g, "\n") } function jmolScriptWaitAsArray(script, targetSuffix) { var ret = "" try{ jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix) if (script) { _jmolCheckBrowser(); var applet=_jmolGetApplet(targetSuffix); if (applet) ret += applet.scriptWait(script); ret = _jmolEvalJSON(ret,"jmolStatus") if(typeof ret == "object") return ret } }catch(e){ } return [[ret]] } //////////// save/restore orientation ///////////// function jmolSaveOrientation(id, targetSuffix) { if(!targetSuffix)targetSuffix="0" return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo } function jmolRestoreOrientation(id, targetSuffix) { if(!targetSuffix)targetSuffix="0" var s=_jmol["savedOrientation"+id] if (!s || s == "")return s=s.replace(/1\.0/,"0") return jmolScriptWait(s,targetSuffix) } function jmolRestoreOrientationDelayed(id, delay, targetSuffix) { if(arguments.length < 2)delay=1; if(!targetSuffix)targetSuffix="0" var s=_jmol["savedOrientation"+id] if (!s || s == "")return s=s.replace(/1\.0/,delay) return jmolScriptWait(s,targetSuffix) } //////////// add parameter ///////////// /* * for adding callbacks or other parameters. 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