307 lines
9.8 KiB
PHP
307 lines
9.8 KiB
PHP
<?php
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class jsMol2wp{
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var $fileURL = '';
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var $instance = 0;
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var $acc = '';
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var $appletID = '';
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var $type = '';
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var $load = '';
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public function __construct($acc, $type, $caption, $id, $fileURL, $isosurface){
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$this->path = plugins_url().'/jsmol2wp/';
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$this->acc = $acc;
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$this->type = $type;
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$p = get_post();
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# determine the instance if there are multiple copies
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# of the shortcode in this post
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# we want to do this without preg_match to work on different PHP versions
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$m = explode('[jsmol', get_the_content());
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array_shift($m);
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foreach($m as $i => $match){
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$t = explode(']', $match);
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# there could be nested shortcodes or other shortcodes in the text
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# but trim off what is safe to trim off
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if(count($t) > 1){
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array_pop($t);
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$match = implode(']', $t);
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}
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# odd bug requires recasting as a string to get stripos to work
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$match = (string)$match;
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# catenate the post_id to the instance to make the id unique
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# when displaying multiple posts per page
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if( ($acc == '' || stripos($match, $acc) > 0 ) &&
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($caption == '' || stripos($match, $caption) > 0) &&
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($fileURL == '' || stripos($match, $fileURL) > 0) &&
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($isosurface == '' || stripos($match, $isosurface) > 0) &&
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($id == '' || stripos($match, $id) > 0)
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) $this->instance = $p->ID."_$i";
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}
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if($fileURL != ''){
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# use a passed url if it's there
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$this->fileURL = $fileURL;
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}else{
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# otherwise, look for an attachment
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# $attachment = get_page_by_title($acc, OBJECT, 'attachment' );
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$attachment = self::getAttachmentPost("$acc.$type");
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if(!is_null($attachment) && isset($attachment->guid)){
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$this->fileURL = $attachment->guid;
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}
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}
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$this->isosurface = $isosurface;
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if($isosurface != ''){
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# isosurface will be an uploaded file or a URL
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# replace if it's an attachment
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$attachment = self::getAttachmentPost($isosurface);
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if(!is_null($attachment) && isset($attachment->guid)){
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$this->isosurface = $attachment->guid;
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}
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}
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$this->appletID = "jmolApplet".$this->instance;
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}
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function makeViewer($acc, $type, $load, $caption, $commands, $wrap, $debug){
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# not used?
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$mydiv = "myDiv".$this->instance;
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# initialize output
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$html = "";
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$template = $this->getTemplate($load);
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$template = str_replace('jmolApplet0',$this->appletID, $template );
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$template = str_replace('XXXX',$acc, $template );
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$template = str_replace('__caption__',$caption, $template );
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$template = $this->makeScriptButtons($commands, $template, $wrap);
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$html .= $template;
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if($debug != 'false'){
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$html .= $this->debug($debug);
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}
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return $html;
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}
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function makeScriptButtons($commands, $template, $wrap = 4){
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$buttons = '';
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$customButtons = '';
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$jmolCommandInput = '';
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$notButtons = 0;
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$applet = $this->appletID;
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$commands = str_replace("\n",' ', strip_tags($commands));
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if($commands != ''){
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$commandsSet = explode('|||', $commands);
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foreach($commandsSet as $i => $command){
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list($label, $script) = explode('=', $command."=",2);
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$label = trim($label);
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$script = trim($script,"\n=");
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# if there is no script, assume that the line is raw Jmol script
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switch($label){
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case '':
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# if label is not set, we assume the user wants Jmol script not
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# wrapped in a button
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$buttons .= "Jmol.script($applet,\"$script\");\n";
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# if it's the first one, append to the load for the reset script
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if($i == 0) $this->load .= $script;
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$notButtons++;
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break;
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case 'jmolCommandInput':
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# this is a special case to add a command line input
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$jmolCommandInput .= "Jmol.jmolCommandInput($applet);\n";
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$notButtons++;
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break;
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default:
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$customButtons .= "jmolButton('$script','$label')\n";
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}
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$j = $i-$notButtons;
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if($j%$wrap == 0 && $j != 0) $customButtons .= "jmolBr();\n";
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}
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}
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if(strpos($this->load, 'isosurface') > 0){
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$buttons .= 'jmolButton("if(surfaceflag == false);isosurface on;surfaceflag = true;else;isosurface off;surfaceflag = false;endif","isosurface");';
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}
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$buttons .= "jmolButton('reset;select all;$this->load','reset')\njmolBr();\n";
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$buttons .= $customButtons;
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$buttons .= $this->standardButtons($wrap).$jmolCommandInput;
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$template = str_replace('__commands__',$buttons, $template );
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return $template;
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}
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/*
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jmolBr() to make $wrap buttons/row
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*/
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function standardButtons($wrap){
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$str = "Jmol.setButtonCss(null,\"style='width:100px'\")\n";
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$stdButtons = array();
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switch ($this->type){
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case 'pdb':
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$stdButtons = explode("\n",
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'jmolButton("color cpk", "'.__('color cpk','jsmol2wp').'");
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jmolButton("color group", "'.__('color group','jsmol2wp').'");
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jmolButton("color amino", "'.__('color amino','jsmol2wp').'");
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jmolButton("color structure", "'.__('color structure','jsmol2wp').'");
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jmolButton("trace only");
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jmolButton("cartoon only");
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jmolButton("backbone only");
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jmolButton("spacefill 23%;wireframe 0.15","ball&stick");'
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);
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break;
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default:
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$stdButtons = explode("\n",
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'jmolButton("color cpk");
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jmolButton("color grey");
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jmolButton("spacefill","spacefill");
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jmolButton("if(dotsflag);dots off;dotsflag = false;else;dots on;dotsflag = true;endif","dots");
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jmolButton("spacefill off;wireframe 0.15","wireframe");
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jmolButton("spacefill 23%;wireframe 0.15","ball&stick");'
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);
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break;
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}
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foreach($stdButtons as $i => $button){
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if($i%$wrap == 0 && $i != 0) $str .= "jmolBr();\n";
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$str .= $button;
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}
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return $str;
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}
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/*
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Gets the template and creates the molecule load and format commands
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*/
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function getTemplate($load){
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$template = file_get_contents(dirname(__FILE__).'/jsmol_template.htm');
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# if load is set, it is used and we don't guess
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if($load != ''){
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$loadStr = $load;
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}else{
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# otherwise try to guess the right load string
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$loadStr = '';
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if($this->load != ''){
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$loadStr = $this->load;
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}else{
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if($this->acc != '' && ($this->acc{0} == '$'||$this->acc{0} == ':')){
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$loadStr = "load $this->acc;spacefill 23%;wireframe 0.15;color cpk;spin off;";
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$this->type = 'mol';
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}
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# if the type is pdb, look for it at rcsb.org
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if($this->type == 'pdb'){
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$loadStr = "load \"https://files.rcsb.org/view/$this->acc.pdb\";";
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}
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# if there is a local file, override the guessed remote load and if needed, guess the type
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if($this->fileURL != ''){
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$this->type = pathinfo($this->fileURL, PATHINFO_EXTENSION);
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$loadStr = "load $this->fileURL;";
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}
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# add the default format
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switch ($this->type){
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case 'obj':
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#this is going to only be with a fileURL?
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$loadStr = str_replace(
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"load",
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"isosurface OBJ ",
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$loadStr);
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$loadStr .= " spacefill 23%;wireframe 0.15;color cpk;spin off;";
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break;
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case 'xyz':
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case 'mol':
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case 'mol2':
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#change the default load coloring and display
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$loadStr .= ' spacefill 23%;wireframe 0.15;color cpk;spin off;';
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break;
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case 'mrc':
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return "Support for binary type: $this->type is not implemented yet";
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break;
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case 'pdb':
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$loadStr .= ' spacefill off;wireframe off;cartoons on;color structure;spin off;';
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break;
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default:
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}
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}
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}
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# add isosurface if it's present
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if($this->isosurface != ''){
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$loadStr .= " isosurface $this->isosurface;";
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}
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# add the acc label
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if($this->acc != '') $loadStr .= "set echo top center; echo ".ltrim($this->acc,'$:').';';
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# save the loadstr for use by the reset button. Do this before set lang if needed
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$this->load = $loadStr;
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# set default language if available from WP
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$lang = get_locale();
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if($lang != 'en_US'){
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$loadStr = "set language $lang;".$loadStr;
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}
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$template = str_replace('__load__', $loadStr, $template);
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$template = str_replace('http://chemapps.stolaf.edu/jmol/jsmol/',$this->path, $template );
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$template = str_replace('__j2s__',$this->path."j2s", $template );
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# button text
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$template = str_replace('__toggle_spin__',__('Toggle Spin', 'jsmol2wp'), $template );
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# help file link
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$template = str_replace('__help__', "<a href='$this->path/help.htm'>".__('About/Help','jsmol2wp')."</a>", $template );
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return $template;
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}
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static function getAttachmentPost($filename){
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$attachment = null;
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$args = array('post_type' => 'attachment', 'posts_per_page'=>-1, 'post_status' => 'any', 'post_parent' => null);
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$media = get_posts( $args );
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foreach($media as $p){
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$attFileName = basename($p->guid);
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if($filename == $attFileName){
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$attachment = $p;
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break;
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}
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}
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wp_reset_postdata();
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# if the above fails, check for a case where the extension was not given in type
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if(is_null($attachment)) $attachment = get_page_by_title($filename, OBJECT, 'attachment' );
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return $attachment;
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}
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function debug($debug){
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$str = '<pre>';
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# file path
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switch($debug){
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case 'short':
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$str .= "applet ID: $this->appletID\n";
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$str .= "acc: $this->acc\n";
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$str .= "type:$this->type\n";
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break;
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case 'full':
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default:
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$str .= print_r($this,true);
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$dirpath = dirname(__FILE__);
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$str .= "Directory path:$dirpath\n";
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$fileTests = array(
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'JSmol.min.nojq.js' => "$this->path",
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'package.js' => "$this->path/j2s/core/"
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);
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$str .= "test whether various files are readable by wp_remote_fopen\n";
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foreach($fileTests as $file => $path){
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if(!wp_remote_fopen("$path$file")){
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$str .= "can't load $path$file\n";
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}else{
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$str .= "$file load OK\n";
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}
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}
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$str .= 'file_get_contents: ';
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$str .= file_get_contents(__FILE__) ? 'Enabled' : 'Disabled';
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if($this->fileURL != ''){
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$str .= "\npath to uploaded file:".$this->fileURL."\n";
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$tmp = wp_remote_fopen($this->fileURL);
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$str .= "Excerpt from file:".substr($tmp, 0, 20)."...\n";
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$attachment = get_page_by_title($this->acc, OBJECT, 'attachment' );
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if(is_null($attachment)) $str .= "attachment for $this->acc not found\n";
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}
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break;
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}
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$str .= "</pre>";
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return $str;
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}
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} |