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Merge pull request #1 from KlasJoenssson/2.5.x
Looks good to me. Klas, can you ask Arvid or Jonathan to learn you how to rebase patches? The merge patches confused me at first :)
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egonw committed Feb 13, 2012
2 parents ebb91b3 + 6d8eecc commit b3c8152
Showing 1 changed file with 23 additions and 12 deletions.
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<?xml version="1.0" encoding="UTF-8"?>
<cheatsheet title="General Chemistry Tasks">
<cheatsheet title="Basic Chemistry Tasks">
<intro>
<description>
This cheat sheet demonstrates general chemistry (or, more strictly speaking, chemoinformatics) tasks you can
do in Bioclipse. These are centered around handling molecular data files.
</description>
</intro>

<item
href="/net.bioclipse.cdk.jchempaint/doc/jcpEditor.html"
title="Step 1: Open and Edit structures in 2D">
title="Step 1: Install sample data">
<description>
In this cheat sheet we need some molecules. A package called "Sample Data" have some, so If you haven't installed it, now is a good time to do it.
This is done via the menu <b>Help > Install Sample Data</b>
</description>

</item>

<item
href="/net.bioclipse.cdk.jchempaint/doc/jcpEditor.html"
title="Step 2: Open and Edit structures in 2D">
<description>
The JChemPaint editor (JCP) allows graphical viewing and editing of 2D
diagrams of chemical structures in various formats. You can also
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param1="ui.open(cdk.fromSMILES(&quot;C1CCCCC1CC(CN(CC))CO&quot;))"/>
</item>

<item
<item
href="/net.bioclipse.cdk.jchempaint/doc/jcpEditor.html"
title="Step 2: Draw new structures in 2D from scratch">
title="Step 3: Draw new structures in 2D from scratch">
<description>
To start drawing a new molecule in 2D, use the top menu <b>File > New... </b> and select <b>Molecule</b>.
</description>
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<item
href="/net.bioclipse.spectrum/html/sdfEditor.html"
title="Step 3: Open files with multiple structures">
title="Step 4: Open files with multiple structures">
<description>
Files with multiple structures (MDL SD files, and SMILES files) are
handled by the Molecule Table Editor. Double-click a molecule-file
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</item>

<item
title="Step 4: Create 2D and 3D coordinates">
title="Step 5: Create 2D and 3D coordinates">
<description>
You can create 2D and 3D coordinates for molecules.
Right click on the file in the Navigator and choose one of the Generate 2D or 3D options.
</description>
</item>
<item
href="/net.bioclipse.cdk.smartsmatching/html/smartsmatchingview.html"
title="Step 5: Smarts matching">
title="Step 6: Smarts matching">
<description>
Show the view SMARTS Matching from the menu <b>Window > Show view > Other...</b> and select <b>SmartsMatching</b> in the <b>Cheminformatics</b> folder.
<br/><br/>
The opened view has a local toolbar and a context menu (just right-click in the view) with several options that can be used to add/delete and run smarts matching.
</description>
<command
required="false"
serialization="org.eclipse.ui.views.showView(org.eclipse.ui.views.showView.viewId=net.bioclipse.cdk.smartsmatching.views.SmartsMatchingView)"/>
<command
required="false"
serialization="org.eclipse.ui.views.showView(org.eclipse.ui.views.showView.viewId=net.bioclipse.cdk.smartsmatching.views.SmartsMatchingView)"/>
</item>

<item
href="/net.bioclipse.webservices/doc/wsplugin.html"
title="Step 6: Query and download proteins via web service">
title="Step 7: Query and download proteins via web service">
<description>
You can search and query a variety of external (EBI) databases using the Wizard at <b>File > New > Download > Query WSDbfetch at EBI</b>.
</description>
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<item
href="/net.bioclipse.webservices/doc/wsplugin.html"
title="Step 7: Search and download chemical structures from PubChem">
title="Step 8: Search and download chemical structures from PubChem">
<description>
It is possible to search and download compounds from PubChem using teh Wizard at <b>File > New > Download > Get structures from PubChem</b>.
</description>
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