MarvinSketch Example 3.4
Press the Import button to import the molfile into MarvinSketch. Change the molecule (delete some atoms or bonds, draw new ones), select a molecule format from the list, then try the Export buttons. You can import a SMARTS string from the text box by using the Import SMARTS button. To import or export a molecule in myformat, press the Import myformat or Export myformat button.
Several Marvin supported file formats demonstrated here. "Myformat" is a user defined file format, see Java sources in the MolImportIface and MolExportModule API examples.
<script LANGUAGE="JavaScript">
<!--
//-->
</script>
<form NAME=MolForm onSubmit="return false">
<textarea NAME="MolTxt" ROWS=20 COLS=70>
3,7-Dihydro-1,3,7-trimethyl-1H-purine-2,6-dione
Marvin 07099920012D
14 15 0 0 0 0 0 0 0 0999 V2000
-2.0245 -2.6287 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.0245 -1.0107 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.7156 -0.0596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4367 -1.8197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8415 -0.8197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.5735 -0.8197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.7075 -2.3196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8415 -3.8197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9755 -2.3196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9755 -1.3197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8415 0.1803 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-5.5735 -2.8197 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.7075 -1.3197 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.8415 -2.8197 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5 13 1 0 0 0 0
13 7 1 0 0 0 0
7 14 1 0 0 0 0
14 9 1 0 0 0 0
9 10 2 0 0 0 0
5 10 1 0 0 0 0
4 2 1 0 0 0 0
2 10 1 0 0 0 0
9 1 1 0 0 0 0
4 1 2 0 0 0 0
2 3 1 0 0 0 0
5 11 2 0 0 0 0
13 6 1 0 0 0 0
7 12 2 0 0 0 0
14 8 1 0 0 0 0
M END
</textarea>
<p>
<input TYPE=BUTTON VALUE="Import" onClick="importMol('null')">
<input TYPE=BUTTON VALUE="Import SMARTS" onClick="importMol('smarts:')">
<input TYPE=BUTTON VALUE="Import myformat" onClick="importMol('myformat:')">
</p>
<p>Export format:
<select NAME="molformat">
<option VALUE="cml">cml</option>
<option VALUE="csmol">csmol</option>
<option VALUE="csrdf">csrdf</option>
<option VALUE="csrxn">csrxn</option>
<option VALUE="cssdf">cssdf</option>
<option SELECTED VALUE="mol">mol</option>
<option VALUE="mrv">mrv</option>
<option VALUE="rdf">rdf</option>
<option VALUE="rxn">rxn</option>
<option VALUE="smarts">smarts</option>
<option VALUE="smiles">smiles</option>
<option VALUE="sdf">sdf</option>
<option VALUE="sybyl">sybyl</option>
</select>
<input TYPE=BUTTON VALUE="Export" onClick="exportMol(document.MolForm.molformat.value)">
<input TYPE=BUTTON VALUE="Export myformat" onClick="exportMol('myformat')">
</p>
</form>
<script LANGUAGE="JavaScript1.1" SRC="../../marvin.js"></script>
<script LANGUAGE="JavaScript1.1">
<!--
function importMol(opts) {
if(document.MSketch != null) {
var s = document.MolForm.MolTxt.value;
document.MSketch.setMol(s, opts);
} else {
alert("Cannot import molecule:\n"+
"no JavaScript to Java communication in your browser.\n");
}
}
function exportMol(format) {
if(document.MSketch != null) {
var s = document.MSketch.getMol(format);
s = unix2local(s); // Convert "\n" to local line separator
document.MolForm.MolTxt.value = s;
} else {
alert("Cannot import molecule:\n"+
"no JavaScript to Java communication in your browser.\n");
}
}
msketch_name = "MSketch";
msketch_begin("../..", 460, 380);
msketch_param("preload", "MolExport,Parity,SmilesExport,Clean2D,MyformatExport");
msketch_end();
//-->
</script>
The preload parameter is only needed if you call getMol() from
JavaScript and want your page to work with some buggy browser/JVM
combinations. Without it, Netscape 6 (Sun Java 1.3) might freeze at the moment
the user presses an Export button. The error message in Netscape 3
would be: uncaught Java exception java/lang/InternalError ("Can't call
network functions from JavaScript yet.").
It may happen that you want to save space on the web page and visualize your molecule in a small area. But the sketcher does not fit into that small area so you are in trouble. At least you think you are in trouble. You are wrong.