MarvinSketch Example - Hydrogen atoms

The description and usage of hydrogen atoms in Marvin can be found in the Implicit/Explicit Hydrogens paragraph of the Marvin User's Guide.

The detailed description of Implicit/Explicit Hydrogens can be found in the Implicit/Explicit Hydrogens paragraph of the Developer's Guide.

The basic description of structure parameters and structure display parameters can be found in the Structure Display parameters paragraph in the Developer's Guide.

How to work with structure parameters

This example demonstrates how to remove explicit hydrogen atoms and show all implicit hydrogen atoms in applets. The Developer's Guide contains the detailed description of the parameters used in this example.

Removing the explicit hydrogen atoms during structure import by using the importConv parameter:

    msketch_param("importConv", "-H");

Showing the implicit hydrogen atoms on all atoms with the implicitH parameter:

    msketch_param("implicitH", "all");

The input molecule is loaded from the file named structure.mol which resides in the directory ../../../mols-2d (relative to the URL of this document).

The source of the HTML file is as follows:

<script type="text/javascript" SRC="../../../marvin.js"></script>
<script type="text/javascript">
<!--

msketch_begin("../../..", 540, 480);
msketch_param("mol", "../../../mols-2d/structure.mol");
msketch_param("importConv", "-H");
msketch_param("implicitH", "true");
msketch_end();

//-->
</script>

 

In the next example, you can use structure templates.