Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

Updated cheatsheets in QSAR.

  • Loading branch information...
commit a8926afe3e61db34d69be21e630b0abaee2cb6dc 1 parent e3aaf0b
@olas authored jonalv committed
View
157 plugins/net.bioclipse.qsar.ui/cheatsheets/calcprops.xml
@@ -1,157 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<cheatsheet
- title="Calculating CDK Properties">
- <intro>
- <description>
- This tutorial demonstrates how to calculate properties (aka descriptors) with CDK from scripts.<br/><br/>
-This is commonly used in QSAR analyses.
- </description>
- </intro>
-
- <item
- title="Step 1: List available descriptors">
- <description>
-
- Descriptors in Bioclipse are identified with the Blue Obelisk Descriptor Ontology.
- To list available descriptors, use the command:<br/><br/>
-
- <b>qsar.getDescriptorIDs()</b><br/><br/>
-
- </description>
-
- <action
- pluginId="net.bioclipse.scripting.ui"
- class="net.bioclipse.scripting.ui.actions.ScriptAction"
- param1="qsar.getDescriptorIDs()"/>
-
- </item>
-
- <item
- title="Step 2: Calculating single properties">
- <description>
-
- To calculate a single descriptor, use the following command:<br/><br/>
-
- <b>qsar.calculate(IMolecule, descriptorID)</b><br/><br/>
-
- The gist 95194 shows a script to demonstrate this.
-
- </description>
-
- <action
- pluginId="net.bioclipse.scripting.ui"
- class="net.bioclipse.scripting.ui.actions.ScriptAction"
- param1="res=gist.download(95194,&quot;/Virtual/qsar.js&quot;); ui.open(res); js.executeFile(res)"/>
-
- </item>
-
- <item
- title="Step 3: Calculating multiple properties">
- <description>
-
- To calculate a list of descriptors for a list of molecules, use the following command:<br/><br/>
-
- <b>qsar.calculateNoParams(molecules, descriptors)</b><br/><br/>
-
- The gist 95189 shows a script to demonstrate this.
-
- </description>
-
- <action
- pluginId="net.bioclipse.scripting.ui"
- class="net.bioclipse.scripting.ui.actions.ScriptAction"
- param1="res=gist.download(95189,&quot;/Virtual/qsar-multi.js&quot;); ui.open(res); js.executeFile(res)"/>
-
- </item>
-
- <item
- title="Step 4: Creating a QSAR Project">
- <description>
-
- Go to menu <b>File > New... > Other</b> and create a new QSAR Project.
-
- </description>
- <command
- required="false"
- serialization="org.eclipse.ui.newWizard(newWizardId=net.bioclipse.qsar.wizards.NewQSARRProjectWizard)"/>
- </item>
-
- <item
- title="Step 5: Using the QSAR editor">
- <description>
-
- Double-clicking on the file qsar.xml in the Navigator opens the QSAR Editor.
- This editor allows for the setup of daaset in a novel file format called QSAR-ML.<br/><br/>
-
- The tabs at the bottom of the editor allows for specifying data and metadata for the
- qsar dataset.<br/><br/>
-
- The tab <b>Information</b> allows for adding metadata about the dataset.<br/><br/>
-
- The tab <b>Molecules</b> contains a list of molecules in the analysis.
- You can Drag and drop files here from any project and they will be copied into the project.<br/><br/>
-
- The tab <b>Descriptors</b> contains a list of descriptors in the analysis.
- Select in the left view and click the <b>Add</b> button. Some descriptors
- require/offer parameters that can be set in the lower right view.<br/><br/>
-
- The tab <b>Responses</b> allows for adding response variables to the structures.<br/><br/>
-
- The tab <b>Sources</b> displays the QSAR-ML source.<br/><br/>
-
- Note that the dataset is built in the background when you save,
- if you have at least one structure and one descriptor chosen. The results are cached
- so it will not be calculated again if already calculated.
- The calculated values are saved in the QSAR-ML but also in a comma-separated
- file called <b>dataset.csv</b>. <br/><br/>
-
- </description>
-
- </item>
-
- <item
- title="Step 6: Open dataset in Matrix Editor">
- <description>
- Double-click the dataset.csv to open it in the Matrix Editor.
- </description>
- </item>
-
- <item
- title="Step 7: Open the R Console">
- <description>
- If you have R installed, you can access it directly from Bioclipse via the R-console.
- Reveal the R-console from the menu <b>Window > Show View > Other</b> and select <b>R Console</b>
- </description>
- <command
- required="false"
- serialization="org.eclipse.ui.views.showView(org.eclipse.ui.views.showView.viewId=net.bioclipse.r.ui.views.RConsoleView)"/>
-
- </item>
-
- <item
- title="Step 8: Load the dataset into R">
- <description>
-
- Loading the dataset into R can be achieved by entering, in the R Console:<br/><br/>
-
- <b>dataset=read.delim(file="myQsarProject/dataset.csv", sep=",", header=TRUE, row.names=1, na.strings="NaN")</b>
-
- </description>
-
- </item>
-
- <item
- title="Step 9: Use R to analyze dataset">
- <description>
-
- Here is a simple example to demonstrate how the read file can be analyzed in R:<br/><br/>
-
- <b>datasat=as.matrix(dataset)</b><br/><br/>
- <b>mod &lt;- lm(dataset[,1] ~ dataset[,2:ncol(dataset)], na.action=na.omit)</b><br/><br/>
- <b>plot(mod)</b><br/><br/>
-
- </description>
-
- </item>
-
-</cheatsheet>
View
63 plugins/net.bioclipse.qsar.ui/cheatsheets/getting_started.xml
@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cheatsheet
+ title="Calculating CDK Properties">
+ <intro>
+ <description>
+ This tutorial gives a brief introduction for working with the Bioclipse-QSAR functionality in Bioclipse.
+ </description>
+ </intro>
+
+ <item
+ title="Step 1: Creating a QSAR Project">
+ <description>
+
+ Go to menu <b>File > New... > Other</b> and create a new QSAR Project.
+
+ </description>
+ <command
+ required="false"
+ serialization="org.eclipse.ui.newWizard(newWizardId=net.bioclipse.qsar.wizards.NewQSARRProjectWizard)"/>
+ </item>
+
+ <item
+ title="Step 2: Using the QSAR editor">
+ <description>
+
+ Double-clicking on the file qsar.xml in the Navigator opens the QSAR Editor.
+ This editor allows for the setup of daaset in a novel file format called QSAR-ML.<br/><br/>
+
+ The tabs at the bottom of the editor allows for specifying data and metadata for the
+ qsar dataset.<br/><br/>
+
+ The tab <b>Information</b> allows for adding metadata about the dataset.<br/><br/>
+
+ The tab <b>Molecules</b> contains a list of molecules in the analysis.
+ You can Drag and drop files here from any project and they will be copied into the project.<br/><br/>
+
+ The tab <b>Descriptors</b> contains a list of descriptors in the analysis.
+ Select in the left view and click the <b>Add</b> button. Some descriptors
+ require/offer parameters that can be set in the lower right view.<br/><br/>
+
+ The tab <b>Responses</b> allows for adding response variables to the structures.<br/><br/>
+
+ The tab <b>Sources</b> displays the QSAR-ML source.<br/><br/>
+
+ Note that the dataset is built in the background when you save,
+ if you have at least one structure and one descriptor chosen. The results are cached
+ so it will not be calculated again if already calculated.
+ The calculated values are saved in the QSAR-ML but also in a comma-separated
+ file called <b>dataset.csv</b>. <br/><br/>
+
+ </description>
+
+ </item>
+
+ <item
+ title="Step 3: Open dataset in Matrix Editor">
+ <description>
+ Double-click the dataset.csv to open it in the Matrix Editor.
+ </description>
+ </item>
+
+
+</cheatsheet>
View
49 plugins/net.bioclipse.qsar.ui/cheatsheets/qsar-r.xml
@@ -0,0 +1,49 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cheatsheet
+ title="Accessing QSAR data from R">
+ <intro>
+ <description>
+ This tutorial demonstrates how to use R to analyze QSAR. Note that R is experimental and must be installed from the experimental update site before following this tutorial.
+ </description>
+ </intro>
+
+ <item
+ title="Step 1: Open the R Console">
+ <description>
+ If you have R installed, you can access it directly from Bioclipse via the R-console.
+ Reveal the R-console from the menu <b>Window > Show View > Other</b> and select <b>R Console</b>
+ </description>
+ <command
+ required="false"
+ serialization="org.eclipse.ui.views.showView(org.eclipse.ui.views.showView.viewId=net.bioclipse.r.ui.views.RConsoleView)"/>
+
+ </item>
+
+ <item
+ title="Step 2: Load the dataset into R">
+ <description>
+
+ Loading the dataset into R can be achieved by entering, in the R Console:<br/><br/>
+
+ <b>dataset=read.delim(file="myQsarProject/dataset.csv", sep=",", header=TRUE, row.names=1, na.strings="NaN")</b>
+
+ </description>
+
+ </item>
+
+ <item
+ title="Step 3: Use R to analyze dataset">
+ <description>
+
+ Here is a simple example to demonstrate how the read file can be analyzed in R:<br/><br/>
+
+ <b>datasat=as.matrix(dataset)</b><br/><br/>
+ <b>mod &lt;- lm(dataset[,1] ~ dataset[,2:ncol(dataset)], na.action=na.omit)</b><br/><br/>
+ <b>plot(mod)</b><br/><br/>
+
+ </description>
+
+ </item>
+
+
+</cheatsheet>
View
71 plugins/net.bioclipse.qsar.ui/cheatsheets/scripting_qsar.xml
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cheatsheet
+ title="Scripting Bioclipse-QSAR">
+ <intro>
+ <description>
+ This tutorial demonstrates how to access the Bioclipse-QSAR functionality from the Bioclipse Scripting Language.
+ </description>
+ </intro>
+
+ <item
+ title="Step 1: List available descriptors">
+ <description>
+
+ Descriptors in Bioclipse are identified with the Blue Obelisk Descriptor Ontology.
+ To list available descriptors, use the command:<br/><br/>
+
+ <b>qsar.listDescriptors()</b><br/><br/>
+
+ </description>
+
+ <action
+ pluginId="net.bioclipse.scripting.ui"
+ class="net.bioclipse.scripting.ui.actions.ScriptAction"
+ param1="qsar.listDescriptors()"/>
+
+ </item>
+
+ <item
+ title="Step 2: Calculating single properties">
+ <description>
+
+ To calculate a single descriptor, use the following command:<br/><br/>
+
+ <b>qsar.calculate(IMolecule, descriptorID)</b><br/><br/>
+
+ Example commands:<br/>
+ <b>mol=cdk.fromSMILES("OC(COC=1C=CC=CC=1CC=C)CNC(C)C")</b><br/>
+ <b>qsar.calculate(mol, "hBondDonors")</b><br/>
+
+ </description>
+
+ <action
+ pluginId="net.bioclipse.scripting.ui"
+ class="net.bioclipse.scripting.ui.actions.ScriptAction"
+ param1="mol=cdk.fromSMILES(&quot;OC(COC=1C=CC=CC=1CC=C)CNC(C)C&quot;)"
+ param2="qsar.calculate(mol, &quot;hBondDonors&quot;)"
+ />
+
+ </item>
+
+ <item
+ title="Step 3: Calculating multiple properties">
+ <description>
+
+ To calculate a list of descriptors for a list of molecules, use the following command:<br/><br/>
+
+ <b>qsar.calculate(molecules, descriptors)</b><br/><br/>
+
+ The gist 95189 shows a script to demonstrate this.
+
+ </description>
+
+ <action
+ pluginId="net.bioclipse.scripting.ui"
+ class="net.bioclipse.scripting.ui.actions.ScriptAction"
+ param1="res=gist.download(95189,&quot;/Virtual/qsar-multi.js&quot;); ui.open(res); js.executeFile(res)"/>
+
+ </item>
+
+
+</cheatsheet>
View
25 plugins/net.bioclipse.qsar.ui/plugin.xml
@@ -136,12 +136,29 @@
<extension
point="org.eclipse.ui.cheatsheets.cheatSheetContent">
+ <category
+ id="net.bioclipse.qsar.cheatsheet.category"
+ name="QSAR">
+ </category>
<cheatsheet
- category="net.bioclipse.chemoinformatics.cheatsheet.category"
+ category="net.bioclipse.qsar.cheatsheet.category"
composite="false"
- contentFile="cheatsheets/calcprops.xml"
- id="net.bioclipse.qsar.ui.calcpropscdk"
- name="Calculate properties with CDK scripts"/>
+ contentFile="cheatsheets/getting_started.xml"
+ id="net.bioclipse.qsar.cheatsheet.gettingstarted"
+ name="Getting started with Bioclipse-QSAR"/>
+ <cheatsheet
+ category="net.bioclipse.qsar.cheatsheet.category"
+ composite="false"
+ contentFile="cheatsheets/scripting_qsar.xml"
+ id="net.bioclipse.qsar.cheatsheet.scriptingqsar"
+ name="Scripting Bioclipse-QSAR"/>
+ <cheatsheet
+ category="net.bioclipse.qsar.cheatsheet.category"
+ composite="false"
+ contentFile="cheatsheets/qsar-r.xml"
+ id="net.bioclipse.qsar.cheatsheet.qsar_r"
+ name="Accessing QSAR data from R"/>
+
</extension>
<extension
point="org.eclipse.ui.perspectives">
Please sign in to comment.
Something went wrong with that request. Please try again.