$rawsvg = filterthroughcmd2("{$svghitmol}", "{$MOL2SVG} {$svgopt} - ");
}
//$svg = tweak_svg($rawsvg,$scalingfactor); // function is defined in dbfunct.php
$svg = $rawsvg;
// for mol2svg v0.4 or higher
if (strlen($svg) > 0 && $svg_mode == 1) {
print "{$svg}\n";
$struc_shown = TRUE;
} elseif ($svg_mode == 2) {
echo "<img src=\"showsvg.php?id={$id}&db={$db_id}\" alt=\"hit structure\">\n";
$struc_shown = TRUE;
}
}
if (($enable_jme == "y" || $enable_jsme == "y") && $struc_shown == FALSE) {
// JME needs MDL molfiles with the "|" character instead of linebreaks
$jmehitmol = tr4jme($molstruc);
echo "<{$edtag} code=\"JME.class\" {$codebase} archive=\"JME.jar\" \n";
echo "width=\"{$jmewidth}\" height=\"120\">";
echo "<param name=\"options\" value=\"depict\"> \n";
echo "<param name=\"mol\" value=\"{$jmehitmol}\">\n";
echo "</{$edtag}>\n";
}
// show data fields
echo "<table class=\"highlight\">\n";
echo "<tr align=\"left\"><th>Field:</th><th>Value:</th></tr>\n";
$i = 0;
$qstr = "SHOW FULL COLUMNS FROM {$datatable}";
$result = mysql_query($qstr) or die("Query failed! (1c5)");
while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
$field = $line["Field"];
$type = $line["Type"];
</td>
<?php
} else {
?>
<td><?php
e($record->mol_weight);
?>
</td>
<?php
}
?>
<?php
$mol = $record->structure;
$mol = str_replace("\r\n", "\n", $mol);
$mol = str_replace("\n", "\r\n", $mol);
$jmehitmol = tr4jme($mol);
?>
<td>
<applet code="JME.class" name="JME" archive="/app/public/JME.jar" width="360" height="315" id="JME">
<param name="options" value="depict">
<param name="mol" value="<?php
echo $jmehitmol;
?>
" >
You have to enable Java and JavaScript in your browser to use JME!
</applet>
</td>
<td><?php
e($record->formula);
function showHitRxn($id, $s)
{
// version for SVG, bitmap, JME or JSME output
global $enable_svg;
global $enable_bitmaps;
global $enable_jme;
global $enable_jsme;
global $bitmapURLdir;
global $rxnstructable;
global $rxndatatable;
global $digits;
global $subdirdigits;
global $db_id;
global $pic2dtable;
global $codebase;
global $svg_mode;
global $edtag;
$result2 = mysql_query("SELECT rxn_name FROM {$rxndatatable} WHERE rxn_id = {$id}") or die("Query failed! (showHitRxn)");
while ($line2 = mysql_fetch_array($result2, MYSQL_ASSOC)) {
$txt = $line2["rxn_name"];
}
mysql_free_result($result2);
echo "<tr>\n<td class=\"highlight\" width=\"10%\">\n";
print "<a href=\"details.php?rxn={$id}&db={$db_id}\" target=\"_blank\">{$db_id}:{$id}</a></td>\n";
echo "<td class=\"highlight\"> <b>{$txt}</b>";
if ($s != '') {
echo " {$s}";
}
echo "</td>\n</tr>\n";
$whatstr = "status";
if ($svg_mode == 1) {
$whatstr = "status, svg";
}
$svg = "";
$qstr = "SELECT {$whatstr} FROM {$pic2dtable} WHERE rxn_id = {$id}";
$result2 = mysql_query($qstr) or die("Query failed! (pic2d)");
while ($line2 = mysql_fetch_array($result2, MYSQL_ASSOC)) {
$status = $line2["status"];
@($svg = $line2["svg"]);
}
mysql_free_result($result2);
//if (($status != 1) || ($svg_mode > 0)) { $usebmp = false; } else { $usebmp = true; }
if ($status == 1) {
$usebmp = TRUE;
} else {
$usebmp = FALSE;
}
echo "<tr>\n<td colspan=\"2\">\n";
$struc_shown = FALSE;
if ($enable_svg == "y") {
if (strlen($svg) > 0 && $svg_mode == 1) {
print "{$svg}\n";
$struc_shown = TRUE;
} elseif ($svg_mode == 2) {
echo "<img src=\"showsvg.php?id={$id}&db={$db_id}\" alt=\"hit reaction\">\n";
$struc_shown = TRUE;
}
}
if ($enable_bitmaps == "y" && $struc_shown == FALSE) {
if (isset($bitmapURLdir) && $bitmapURLdir != "" && $usebmp == true) {
while (strlen($id) < $digits) {
$id = "0" . $id;
}
$subdir = '';
if ($subdirdigits > 0) {
$subdir = substr($id, 0, $subdirdigits) . '/';
}
print "<img src=\"{$bitmapURLdir}/{$db_id}/{$subdir}{$id}.png\" alt=\"hit reaction\">\n";
$struc_shown = TRUE;
}
}
if (($enable_jme == "y" || $enable_jsme == "y") && $struc_shown == FALSE) {
// if no bitmaps are available, we must invoking another instance of JME
// in "depict" mode for libraries display of each hit
$qstr = "SELECT struc FROM {$rxnstructable} WHERE rxn_id = {$id}";
$result3 = mysql_query($qstr) or die("Query failed! (struc)");
while ($line3 = mysql_fetch_array($result3, MYSQL_ASSOC)) {
$molstruc = $line3["struc"];
}
mysql_free_result($result3);
// JME needs MDL molfiles with the "|" character instead of linebreaks
$jmehitmol = tr4jme($molstruc);
echo "<{$edtag} code=\"JME.class\" archive=\"JME.jar\" {$codebase}\n";
echo "width=\"250\" height=\"120\">";
echo "<param name=\"options\" value=\"depict\"> \n";
echo "<param name=\"mol\" value=\"{$jmehitmol}\">\n";
echo "</{$edtag}>\n";
$struc_shown = TRUE;
}
echo "</td>\n</tr>\n";
}
echo "<table border=\"1\">\n<tr>\n<td>\n";
echo "<div class=\"moldiv\" id=\"strucdiv\" onclick=\"openeditorwindow()\" >\n";
if ($mol != '') {
if ($svg_mode == 1) {
if (is_rxnfile($mol)) {
$mol2svgopt = "-R " . $mol2svgopt;
}
if ($ostype == 1) {
print filterThroughCmd("{$safemol}", "{$MOL2SVG} {$mol2svgopt} -");
}
if ($ostype == 2) {
print filterThroughCmd2("{$safemol}", "{$MOL2SVG} {$mol2svgopt} -");
}
} else {
// use JME/JSME as fallback
$jmehitmol = tr4jme($safemol);
echo "<{$edtag} code=\"JME.class\" archive=\"JME.jar\" {$codebase}\n";
echo "width=\"250\" height=\"120\">";
echo "<param name=\"options\" value=\"depict\"> \n";
echo "<param name=\"mol\" value=\"{$jmehitmol}\">\n";
if ($edtag == "applet") {
echo "</{$edtag}>click here to edit...\n";
}
}
#print "<pre>$safemol</pre>\n";
} else {
if ($svg_mode == 1) {
echo "<?xml version=\"1.0\" standalone=\"no\" ?>\n";
echo "<svg width=\"186\" height=\"94\" viewbox=\"0 5 186 94\" xmlns=\"http://www.w3.org/2000/svg\">\n";
echo "<style type=\"text/css\"><![CDATA[ circle { stroke: #FFFFFF; fill: #FFFFFF; }\n";
echo "text { font-family: Helvetica; font-size: 14px; } line { stroke: #BBBBBB; stroke-width: 1.0; } ]]> </style>\n";
$outmol = str_replace("\r", "", $outmol);
$outmol = strtr($outmol, "\n", "|");
return $outmol;
}
?>
<hr/>
<div class="row">
<div class="col-md-1 col-sm-1"></div>
<div class="col-md-8 col-sm-8">
<?php
foreach ($records->result() as $record) {
?>
<?php
$jmehitmol = tr4jme($record->cd_structure);
?>
<table class="table table-bordered">
<caption><h3><?php
echo $record->molecule_name;
?>
</h3></caption>
<tr>
<td rowspan="8">
<div code="JME.class" name="JME" archive="JME.jar" width="360" height="315" id="JME">
<param name="options" value="oldlook, nopaste, depict">
<param name="mol" value="<?php
echo $jmehitmol;
?>
">
You have to enable JavaScript in your browser to use JSME!
function showHit2($id, $type)
{
global $enable_svg;
global $enable_bitmaps;
global $enable_jme;
global $enable_jsme;
global $bitmapURLdir;
global $molstructable;
global $moldatatable;
global $rxnstructable;
global $rxndatatable;
global $pic2dtable;
global $digits;
global $subdirdigits;
global $db_id;
global $access;
global $codebase;
global $svg_mode;
global $edtag;
// by default, assume $type is 1 (structure data collection)
$item_name = "mol_name";
$structable = $molstructable;
$datatable = $moldatatable;
$id_name = "mol_id";
$par = "mol";
if ($type == 2) {
$item_name = "rxn_name";
$structable = $rxnstructable;
$datatable = $rxndatatable;
$id_name = "rxn_id";
$par = "rxn";
}
$result3 = mysql_query("SELECT {$item_name} FROM {$datatable} WHERE {$id_name} = {$id}") or die("Query failed! (showHit2)");
while ($line3 = mysql_fetch_array($result3, MYSQL_ASSOC)) {
$txt = $line3["{$item_name}"];
}
mysql_free_result($result3);
echo "<table width=\"100%\">\n";
echo "<tr>\n<td class=\"highlight\">\n";
print "<b>{$txt}</b> (<a href=\"showmol.php?{$par}={$id}&db={$db_id}\" target=\"blank\">{$id}</a>)\n";
echo "</td>\n</tr>\n";
echo "</table>\n";
if ($access >= 2) {
// display an "edit", "copy" and "erase" link for read/write data collections
echo "<small>\n";
print "<a class=\"menu\" href=\"admin/editdata.php?db={$db_id}&id={$id}&action=editdata\" target=\"admin\">edit</a>\n";
print "<a class=\"menu\" href=\"admin/editdata.php?db={$db_id}&id={$id}&action=duplcopy\" target=\"admin\">copy</a>\n";
print "<a class=\"menu\" href=\"admin/editdata.php?db={$db_id}&id={$id}&action=eraserecord\">erase</a><br>\n";
echo "</small>\n";
}
$whatstr = "status";
if ($svg_mode == 1) {
$whatstr = "status, svg";
}
$svg = "";
$qstr = "SELECT {$whatstr} FROM {$pic2dtable} WHERE {$id_name} = {$id}";
$result2 = mysql_query($qstr) or die("Query failed! (pic2d)");
while ($line2 = mysql_fetch_array($result2, MYSQL_ASSOC)) {
$status = $line2["status"];
@($svg = $line2["svg"]);
}
mysql_free_result($result2);
if ($status == 1) {
$usebmp = TRUE;
} else {
$usebmp = FALSE;
}
echo "<tr>\n<td colspan=\"2\">\n";
$struc_shown = FALSE;
if ($enable_svg == "y") {
if (strlen($svg) > 0 && $svg_mode == 1) {
print "{$svg}\n";
$struc_shown = TRUE;
} elseif ($svg_mode == 2) {
echo "<img src=\"showsvg.php?id={$id}&db={$db_id}\" alt=\"hit structure\">\n";
$struc_shown = TRUE;
}
}
if ($enable_bitmaps == "y" && $struc_shown == FALSE) {
if (isset($bitmapURLdir) && $bitmapURLdir != "" && $usebmp == true) {
while (strlen($id) < $digits) {
$id = "0" . $id;
}
$subdir = '';
if ($subdirdigits > 0) {
$subdir = substr($id, 0, $subdirdigits) . '/';
}
print "<img src=\"{$bitmapURLdir}/{$db_id}/{$subdir}{$id}.png\" alt=\"hit structure\">\n";
$struc_shown = TRUE;
}
}
if (($enable_jme == "y" || $enable_jsme == "y") && $struc_shown == FALSE) {
// if no bitmaps are available, we must invoke another instance of JME/JSME
// in "depict" mode for structure display of each hit
$qstr = "SELECT struc FROM {$structable} WHERE {$id_name} = {$id}";
$result3 = mysql_query($qstr) or die("Query failed! (struc)");
while ($line3 = mysql_fetch_array($result3, MYSQL_ASSOC)) {
$molstruc = $line3["struc"];
}
mysql_free_result($result3);
// JME needs MDL molfiles with the "|" character instead of linebreaks
$jmehitmol = tr4jme($molstruc);
echo "<{$edtag} code=\"JME.class\" archive=\"JME.jar\" {$codebase}\n";
echo "width=\"250\" height=\"120\">";
echo "<param name=\"options\" value=\"depict\"> \n";
echo "<param name=\"mol\" value=\"{$jmehitmol}\">\n";
echo "</{$edtag}>\n";
$struc_shown = TRUE;
}
echo "</td>\n</tr>\n";
}
