Daniel, the error lies in your php there : $ESTADO=$_POST["ESTADO"]; echo "<!-- /***** Jmol Embedded Script **** ?php echo $ESTADO; ? **/ -->"; the parts in red shall be removed echo "<!-- /***** Jmol Embedded Script **** $ESTADO **/ -->"; See the testpage2.php file attached |
<?php
include("utility.php");echo "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\";> <!--<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3c.org/TR/1999/REC-html401-19991224/loose.dtd\";>--> <HTML xmlns=\"http://www.w3.org/1999/xhtml\";>"; $JMOLFOLDER="Jmol-12new"; echo "<HEAD> <script type=\"text/javascript\" src=\"$JMOLFOLDER/Jmol.js\"></script> <TITLE>TEST PAGE 2!!</TITLE> <META http-equiv=Content-Style-Type content=text/css><LINK href=\"style_daniel.css\" type=text/css rel=stylesheet> </HEAD>"; echo "<BODY>"; echo "<div id=\"page_wrapper\">"; echo "<DIV id=page_Jmolcol>"; $title1="Jmol views"; $pdb=$_POST["pdb"]; $chain=$_POST["chain"]; $code=$pdb."_".$chain; $ZIPtoUSE=$_POST["ziptouse"]; $ESTADO=$_POST["ESTADO"]; echo "<!-- /***** Jmol Embedded Script **** $ESTADO; **/ -->"; $File = "ESTADO.spt"; $f = fopen($File, 'w') or die("Cannot create file $File"); fwrite($f, $ESTADO); fclose($f); $prefix="SA"; $range="0 100"; $JMOL = "<script type=\"text/javascript\"> jmolInitialize(\"$JMOLFOLDER\", true); jmolSetAppletColor(\"white\"); var jmolcmds = [ \"load $ZIPtoUSE|$prefix-Models_$code/$prefix-$code.pdb\", \"set frank off; select all; hbonds off; spin off; wireframe off; spacefill off; trace off; set ambient 40; set specpower 40; slab off; ribbons off; cartoons off; label off; monitor off\", \"set isosurfacePropertySmoothing TRUE\", \"set showAxes true\", \"set appendNew true\", \"frame all\", \"display all\", \"select 1.1; cartoon; set propertyColorScheme 'bwr'; color atoms property temperature ABSOLUTE $range\", \"script myJMOLfunctions.spt\" ]; jmolApplet([580,500], jmolcmds.join(\"; \")); </script>"; $JMOL .= "<form action=\"\"><script>jmolButton(\"reset\", \"Original orientation\"); jmolButton(\"move 360 0 0 0 0 0 0 0 20\", \"Rotate X axis\"); jmolButton(\"move 0 360 0 0 0 0 0 0 20\", \"Rotate Y axis\"); jmolButton(\"write image.png\", \"Create image\"); </script></form><br>"; $JMOL .= '<script>function restoreState(){jmolScript(document.body.innerHTML)}; jmolButton([restoreState], "RESTORE");</script></form>'; centerbox($title1, $JMOL, "#996666"); echo "</DIV>"; //RESIDUE SELECTION //models_map $mapfile="MAPmodel_".$code.".txt"; $modelsmap_HASH=""; $modelsmap_arr = file($mapfile); foreach($modelsmap_arr as $line){//con php, funcion file, en vez de meter chomp, meto un preg_replace para quitar el espacio final $line=preg_replace("/\s$/", "", $line); $line_arr=preg_split("/\t/", $line); $key=$line_arr[0]; $value=$line_arr[1]; $modelsmap_HASH[$key]=$value; } $title5="Residue selection"; echo "<DIV id=page_featcol>"; $contenuto5 = "<div style=\"height:338px; overflow-y: auto; overflow-x: auto; background-color:#ffffff;\">"; $contenuto5 .= "<table width=\"100%\" border=\"1\" cellspacing=\"0\" cellpadding=\"3\" bgcolor=\"#ffffff\">"; $contenuto5 .= "<tr><th colspan=2>Native coordinates</th> <th colspan=2>Models coordinates</th> <th>d(Å)</th></tr>"; $contenuto5 .= "<form action=\"\">"; $color_rows = 0; foreach(array_keys($modelsmap_HASH) as $natres){ $modres=$modelsmap_HASH[$natres]; $nat_arr=preg_split("/_/", $natres); $select_nat=$nat_arr[2].":".$nat_arr[1]; if ($color_rows%2!=0) { $contenuto5 .="<tr valign=\"middle\" bgcolor=\"#F5F5F5\">"; } else { $contenuto5 .="<tr valign=\"middle\" bgcolor=\"#D8D8D8\">"; } $color_rows++; $contenuto5.="<td>$natres</td>"; $contenuto5 .= '<td><script> jmolCheckbox("colorLabel(\'NAT\',\'NO\',\'manual res\',\''.$select_nat.'\',\'ONE\')", "DELcolorLabel(\'NAT\',\''.$select_nat.'\',\'ONE\')", "native"); </script></td>'; $contenuto5.="<td>$modres</td>"; $posmod = strpos($modres, "GAP"); if ($posmod !== false){ $contenuto5 .= "<td>X</td><td>X</td></tr>"; } else{ $mod_arr=preg_split("/_/", $modres); $select_mod=$mod_arr[2].":".$mod_arr[1]; $contenuto5 .= '<td><script> jmolCheckbox("colorLabel(\'MOD\',\'NO\',\'manual res\',\''.$select_mod.'\',\'ONE\')", "DELcolorLabel(\'MOD\',\''.$select_mod.'\',\'ONE\')", "loaded models"); </script></td>'; $contenuto5 .= '<td><script> jmolCheckbox("crossMeasure(\''.$select_nat.'\',\''.$select_mod.'\',\'NO\')", "DELcrossMeasure(\''.$select_nat.'\',\''.$select_mod.'\')", ""); </script></td></tr>'; } } $contenuto5 .= "</form></table></div><br><br>"; centerbox($title5, $contenuto5, "#996666"); echo "</DIV>"; //MODEL LOAD $HASHJM=""; $zip = zip_open($ZIPtoUSE); while ($zip_entry = zip_read($zip)) { $entry_name=zip_entry_name($zip_entry); $ename=preg_replace("/^$prefix-Models_$code\//", "", $entry_name); $pos = strpos($ename, "GDTTS"); if ($pos !== false){ $file_arr=preg_split("/-/", $ename); $nummod=$file_arr[1]; $HASHJM[$nummod]["FILE"]=$entry_name;//incluye el directorio $file_arr=preg_split("/_/", $ename); //9-11AS_A_model_1e1o_A_temp_Probab_92.84_E-value_0.0098_Score_34.35_Aligned_cols_269:327_82.26_Identities_21_RMSD_2.72_GDTTS_37.08_LGAS3_30.72_LGAQ_5.50.pdb $count_arr=count($file_arr); $c=$count_arr -1; $lq=$file_arr[$c]; $HASHJM[$nummod]["LGAQ"]=preg_replace("/\.pdb$/", "", $lq); $HASHJM[$nummod]["LGAS3"]=$file_arr[$c -2]; $HASHJM[$nummod]["GDTTS"]=$file_arr[$c -4]; $HASHJM[$nummod]["RMSD"]=$file_arr[$c -6]; $HASHJM[$nummod]["IDENTS"]=$file_arr[$c -8]; $HASHJM[$nummod]["COLS"]=$file_arr[$c -11]."(".$file_arr[$c -10].")"; $HASHJM[$nummod]["SCORE"]=$file_arr[$c -14]; $HASHJM[$nummod]["EVAL"]=$file_arr[$c -16]; $HASHJM[$nummod]["PROB"]=$file_arr[$c -18]; $HASHJM[$nummod]["TEMP"]=$file_arr[$c -22]."_".$file_arr[$c -21]; } } echo "<DIV id=page_modelcol>"; $title1b="$code MODELS"; $JMOLb = "<form action=\"\" name=\"NATFORM\"><b>NATIVE STRUCTURE ($pdb - CHAIN $chain)</b><br><table width=\"70%\" border=\"0\" cellspacing=\"0\" cellpadding=\"3\" bgcolor=\"#ffffff\">"; $JMOLb .= "<tr><th><script> jmolCheckbox(\"display displayed, 1.1\", \"hide hidden, 1.1\", \"SHOW/HIDE STRUCTURE\", \"true\"); </script></th>"; $JMOLb .= "<th><input type=\"checkbox\" onClick='jmolScriptWait(\"frame 1.1; isosurface NATSAS select {1.1} sasurface 1.2 map color ABSOLUTE $range property temperature colorscheme bwr; isosurface NATSOLV select {1.1} solvent 1.2 map color ABSOLUTE $range property temperature colorscheme bwr; frame all; hide hidden; color isosurface translucent 8.5; isosurface NATSAS off;\"); document.NATFORM.natsurf.options[1].selected=true; this.disabled=true'>Render surface before showing it (this can take a couple of minutes)</th></tr>"; $JMOLb .= "<tr><th><script> jmolMenu([ [\"select 1.1; spacefill off; cartoon off; trace off; backbone off\", \"hide except checked residues\"], [\"select 1.1; spacefill; cartoon off; trace off; backbone off\", \"spacefill\"], [\"select 1.1; spacefill off; cartoon; trace off; backbone off\", \"cartoon\", \"selected\"], [\"select 1.1; spacefill off; cartoon off; trace 40; backbone off\", \"trace\"], [\"select 1.1; spacefill off; cartoon off; trace off; backbone 40\", \"backbone\"] ]); </script></th>"; $JMOLb .= "<th><span><select name=\"natsurf\" onChange='jmolScriptWait(this.options[this.selectedIndex].value);'> <option selected=\"selected\" value=\"isosurface NATSAS off; isosurface NATSOLV off\">Hide surfaces</option> <option value=\"isosurface NATSAS off; isosurface NATSOLV on; color isosurface translucent 8.5;\">Show translucent solvent excluded surface</option> <option value=\"isosurface NATSAS off; isosurface NATSOLV on; color isosurface opaque;\">Show opaque solvent excluded surface</option> <option value=\"isosurface NATSOLV off; isosurface NATSAS on; color isosurface translucent 8.5;\">Show translucent solvent accessible surface</option> <option value=\"isosurface NATSOLV off; isosurface NATSAS on; color isosurface opaque;\">Show opaque solvent accessible surface</option> </select></span></th></tr></table></form>"; $JMOLb .= "<div style=\"height:130px; overflow-y: auto; overflow-x: auto; background-color:#ffffff;\">"; $JMOLb .= "<div style=\"width:1700px; overflow-y: auto; overflow-x: auto; background-color:#ffffff;\">"; $JMOLb .= "<form action=\"\" name=\"FORMOD\"><table class=\"tablesorter\" width=\"100%\" border=\"1\" cellspacing=\"3\" cellpadding=\"3\"><thead><tr> <th class=\"\">LOAD</th> <th class=\"\">SHOW/HIDE</th> <th class=\"\">Model (HHsearch template numbering)</th> <th class=\"\">SURFACES</th> <th class=\"header\">template</th> <th class=\"header\">prob</th> <th class=\"header\">e-value</th> <th class=\"header\">score</th> <th class=\"header\">Aligned cols(%)</th> <th class=\"header\">%identity</th> <th class=\"header\">RMSD</th> <th class=\"header\">GDT-TS</th> <th class=\"header\">LGA_S3</th> <th class=\"header\">LGA_Q</th></tr></thead><tbody>"; ksort($HASHJM, SORT_NUMERIC); $color_rows = -1; foreach(array_keys($HASHJM) as $nmod){ $F=$HASHJM[$nmod]["FILE"]; $lgaq=$HASHJM[$nmod]["LGAQ"]; $lgas3=$HASHJM[$nmod]["LGAS3"]; $gdt=$HASHJM[$nmod]["GDTTS"]; $rmsd=$HASHJM[$nmod]["RMSD"]; $idents=$HASHJM[$nmod]["IDENTS"]; $cols=$HASHJM[$nmod]["COLS"]; $score=$HASHJM[$nmod]["SCORE"]; $eval=$HASHJM[$nmod]["EVAL"]; $prob=$HASHJM[$nmod]["PROB"]; $temp=$HASHJM[$nmod]["TEMP"]; $JMOLb .= "<tr><td><input type=\"checkbox\" id=\"id_$nmod\" onClick='jmolScriptWait(\"load append $ZIPtoUSE|$F; select @{(_lastFrame)}; cartoon only; color atoms property temperature ABSOLUTE $range; frame all; hide hidden;\"); var LF=jmolEvaluate(\"_lastFrame\"); var rendertext=document.getElementById(\"rendercell_$nmod\").innerHTML; newrender=rendertext.replace(/none/g,LF); document.getElementById(\"rendercell_$nmod\").innerHTML=newrender; var showhidetext=document.getElementById(\"showhide_$nmod\").innerHTML; newshowhide=showhidetext.replace(/none/g,LF); document.getElementById(\"showhide_$nmod\").innerHTML=newshowhide; var menutext=document.getElementById(\"menu_$nmod\").innerHTML; newmenu=menutext.replace(/none/g,LF); document.getElementById(\"menu_$nmod\").innerHTML=newmenu; this.disabled=true; document.getElementById(\"render_$nmod\").disabled=false; document.getElementById(\"show_$nmod\").checked=true'></td>"; $JMOLb .= "<td id=\"showhide_$nmod\"><input type=\"checkbox\" id=\"show_$nmod\" onClick='if(this.checked==true) jmolScriptWait(\"display displayed, none;\") if(this.checked==false) jmolScriptWait(\"hide hidden, none;\")'></td>"; $JMOLb .= "<td id=\"menu_$nmod\"><b>MODEL $nmod </b> <span><select onChange='jmolScriptWait(this.options[this.selectedIndex].value);'> <option value=\"select none; spacefill off; cartoon off; trace off; backbone off;\">hide except checked residues</option> <option value=\"select none; spacefill; cartoon off; trace off; backbone off;\">spacefill</option> <option selected=\"selected\" value=\"select none; spacefill off; cartoon; trace off; backbone off;\">cartoon</option> <option value=\"select none; spacefill off; cartoon off; trace 40; backbone off;\">trace</option> <option value=\"select none; spacefill off; cartoon off; trace off; backbone 40;\">backbone</option> </select></span> </td>"; $JMOLb .= "<td id=\"rendercell_$nmod\"><input type=\"checkbox\" id=\"render_$nmod\" onClick='jmolScriptWait(\"frame none; isosurface SAS_$nmod select {none} sasurface 1.2 map color ABSOLUTE $range property temperature colorscheme bwr; isosurface SOLV_$nmod select {none} solvent 1.2 map color ABSOLUTE $range property temperature colorscheme bwr; frame all; hide hidden; color isosurface translucent 8.5; isosurface SAS_$nmod off;\"); document.FORMOD.surfmod$nmod.options[1].selected=true; this.disabled=true'>Render "; $JMOLb .= "<span><select name=\"surfmod$nmod\" onChange='jmolScriptWait(this.options[this.selectedIndex].value);'> <option value=\"isosurface SAS_$nmod off; isosurface SOLV_$nmod off\">Hide surfaces</option> <option selected=\"selected\" value=\"isosurface SAS_$nmod off; isosurface SOLV_$nmod on; color isosurface translucent 8.5\">Show translucent solvent excluded surface</option> <option value=\"isosurface SAS_$nmod off; isosurface SOLV_$nmod on; color isosurface opaque\">Show opaque solvent excluded surface</option> <option value=\"isosurface SOLV_$nmod off; isosurface SAS_$nmod on; color isosurface translucent 8.5\">Show translucent solvent accessible surface</option> <option value=\"isosurface SOLV_$nmod off; isosurface SAS_$nmod on; color isosurface opaque 8.5\">Show opaque solvent accessible surface</option> </select></span></td>"; $JMOLb .="<td>$temp</td> <td>$prob</td> <td>$eval</td> <td>$score</td> <td>$cols</td> <td>$idents</td> <td>$rmsd</td> <td>$gdt</td> <td>$lgas3</td> <td>$lgaq</td></tr>"; } $JMOLb .= "</table></form></div></div>"; centerbox($title1b, $JMOLb, "#996666"); echo "</DIV>"; echo "</div>"; echo "</BODY>"; ?>
Paul Le 26 août 2011 à 12:35, Daniel Carbajo a écrit : DanCarb%x |
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