Programming Notes
From I571/ChE531 2007 Class Wiki
[edit] Create a page that uses a JMOL molecule
Log onto cheminfo.informatics.indiana.edu, and enter your public_html directory
cd public_html
Download the JMOL package and extract the JMOL applet files to your "server"
wget http://superb-west.dl.sourceforge.net/sourceforge/jmol/jmol-11.2.14-binary.tar.gz tar xvzf jmol-11.2.14-binary.tar.gz
Rename the directory
mv jmol-11.2.14 jmol
Create a caffeine molecule XYZ file
cat > caffeine.xyz 24 Caffeine C 0.8423320060 -0.3654865620 0.0000000000 C -0.2841017540 -1.1961236000 0.0000000000 N 2.0294818880 -1.1042264700 0.0000000000 N 0.0774743850 -2.5357317920 0.0000000000 N -1.6472646000 -0.6177952290 0.0000000000 C 1.4531962870 -2.3678913120 0.0000000000 C 0.6373131870 1.1735112670 0.0000000000 C -1.7812691930 0.7688916330 0.0000000000 N -0.6771444680 1.6306355000 0.0000000000 O 1.6106752160 1.9349693060 0.0000000000 O -2.9202890400 1.2510058880 0.0000000000 C -0.9202462430 3.1094501020 0.0000000000 C -2.8623938560 -1.4824503660 0.0000000000 C 3.4552156930 -0.6811094280 0.0000000000 H 2.0878150460 -3.2451913360 0.0000000000 H -1.4989252090 3.4222116470 -0.8897886280 H -1.4989252090 3.4222116470 0.8897886280 H 0.0071905670 3.7148499490 0.0000000000 H -3.4903070930 -1.2888938190 -0.8907763360 H -3.4903070930 -1.2888938190 0.8907763360 H -2.6289534570 -2.5638654230 0.0000000000 H 4.1360211370 -1.5529079440 0.0000000000 H 3.6817059520 -0.0685850980 0.8931597470 H 3.6817059520 -0.0685850980 -0.8931597470 (press CTRL-D)
Create a simple page that uses JMOL
cat > test.html
<head>
<title>Simple JMOL example</title>
<script src="jmol/Jmol.js" type="text/javascript"></script>
</head>
<body>
<form>
<script type="text/javascript">
jmolInitialize("jmol"); // Use your own path here {#2}
jmolApplet(400, "load caffeine.xyz");
</script>
</form>
</body>
(press CTRL-D)
View your page at (substitute djwild for your username):
http://cheminfo.informatics.indiana.edu/~djwild/test.html
[edit] Write a simple PHP script to extract molecules from a database
We will use the database djwildtest we created in a previous class.
Create PHP file (substitute password)
cat > getsmiles.php
<BODY>
Results...<br><br>
<?php
if (!pg_connect("host=localhost dbname=chord user=cicc1 password=*****"))
{
echo 'ERROR:'.pg_last_error();
echo "<br>";
}
$result = pg_query("select smiles,name,logp from djwildtest where matches(smiles, '*C(=O)O');");
if(!$result)
{
echo 'ERROR:'.pg_last_error();
echo "<br>";
}
while($row = pg_fetch_row($result))
{
echo $row[0].' '.$row[1];
echo "<br>";
}
?>
(press CTRL-D)
View it, e.g. at http://cheminfo.informatics.indiana.edu/~djwild/getsmiles.php