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How to retrieve the enumerated structures from Marvin applet
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hzheng

Joined: 19 Mar 2008
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Link to postPosted: Wed Aug 13, 2008 5:31 pmPost subject: How to retrieve the enumerated structures from Marvin applet Reply with quote

It is really nice to have markush enumeration available thrugh Marvin applet, but how do I retrieve those enumerated sructures programatically?
Zsolt
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Link to postPosted: Thu Aug 14, 2008 10:35 amPost subject: Reply with quote

Use Markush Enumeration Plugin via Java API.
Javadoc link: MarkushEnumerationPlugin API. See API usage examples in the javadoc header.

Zsolt
hzheng

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Link to postPosted: Fri Aug 15, 2008 8:38 pmPost subject: Reply with quote

It seems in setInputMolecule(Molecule mol) method, mol need both Markush structure and R groups.

is it possible I can set Markush structure fisrt, but set R groups from sd files?

Hao
Zsolt
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Link to postPosted: Mon Aug 25, 2008 12:16 pmPost subject: Reply with quote

hzheng wrote:
It seems in setInputMolecule(Molecule mol) method, mol need both Markush structure and R groups.
The R group definitions are parts of the Markush structure, so yes, both are needed.
Quote:
is it possible I can set Markush structure fisrt, but set R groups from sd files?
You can read R group definitions from SDFiles, and construct Markush structures with different R groups.
See also: http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/struc/RgMolecule.html

After the RgMolecule is constructed, you can set it as input molecule for MarkushEnumerationPlugin with method setInputMolecule(Molecule mol), and then run the plugin.

Apologies for the late answer.

Zsolt
Szabolcs
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Link to postPosted: Wed Oct 08, 2008 8:20 amPost subject: Reply with quote

We will also implement an SD file -> R-group definition loading function in MarvinSketch and in a utility class for version 5.2. It will be available Q1 2009.

Attachment points will be possible to add by transformation rules of Standardizer.
(Currently transformation rules cannot handle attachment points, but it will also be available in version 5.2.)

Best regards,
Szabolcs
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