Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

Added QSAR help pages. Solves #2027.

  • Loading branch information...
commit 951808c3ac4b353616ad032ffb1b9fbf6e3930cf 1 parent 1df7399
@olas authored
Showing with 336 additions and 6 deletions.
  1. +2 −2 plugins/net.bioclipse.qsar.ui/html/about.html
  2. +36 −0 plugins/net.bioclipse.qsar.ui/html/editor/descPage.html
  3. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/dlg_add_mols.png
  4. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/dlg_add_respProp.png
  5. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-descr.png
  6. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-info-general.png
  7. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-info-units.png
  8. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-mols.png
  9. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-responses.png
  10. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-source.png
  11. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/matrix-editor.png
  12. BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/overviewPage.png
  13. +30 −0 plugins/net.bioclipse.qsar.ui/html/editor/infoPage.html
  14. +40 −0 plugins/net.bioclipse.qsar.ui/html/editor/molPage.html
  15. +7 −3 plugins/net.bioclipse.qsar.ui/html/editor/overviewPage.html
  16. +28 −0 plugins/net.bioclipse.qsar.ui/html/editor/responsePage.html
  17. +22 −0 plugins/net.bioclipse.qsar.ui/html/editor/sourcePage.html
  18. +33 −0 plugins/net.bioclipse.qsar.ui/html/export.html
  19. BIN  plugins/net.bioclipse.qsar.ui/html/images/dlg_import.png
  20. BIN  plugins/net.bioclipse.qsar.ui/html/images/prefs-qsar.png
  21. +30 −0 plugins/net.bioclipse.qsar.ui/html/prefs.html
  22. +107 −0 plugins/net.bioclipse.qsar.ui/html/scripting.html
  23. +1 −1  plugins/net.bioclipse.qsar.ui/toc.xml
View
4 plugins/net.bioclipse.qsar.ui/html/about.html
@@ -21,8 +21,8 @@
If you use the Bioclipse-QSAR feature in a scientific project, please cite:<p>
Ola Spjuth, Egon L Willighagen, Rajarshi Guha, Martin Eklund, Jarl ES Wikberg<br>
-<b>Towards interoperable and reproducible QSAR analyses: Exchange of data sets</b>b><br>
-<i>Submitted</i>
+<b>Towards interoperable and reproducible QSAR analyses: Exchange of data sets</b><br>
+<i>J. Cheminformatics</i> In Press.
<p>
<br>
View
36 plugins/net.bioclipse.qsar.ui/html/editor/descPage.html
@@ -0,0 +1,36 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+ <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
+ <TITLE>Bioclipse-QSAR - Editor - Descriptors Page</TITLE>
+ <link rel="stylesheet" href="../../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
+</HEAD>
+<BODY LANG="en-US" DIR="LTR">
+<h1>QSAR Editor - Descriptors Page</h1>
+
+
+
+<p>
+The Descriptors Page of the QSAR Editor allows for selecting the descriptors to be calculated for the molecules.
+<p>
+
+<center><img src="images/editor-descr.png"></center>
+
+<p>
+
+On the left side you can browse the available descriptors, or search by typing in the search box.
+If you only would like to see descriptors with an implementation available (and hence can be calculated),
+check the box "Display only with implementation" (checked by default).
+Select one or more descriptors and click the button ">>" to add them to the dataset.
+
+<p>
+In the top right canvas you can select provider for the descriptors in the combobox, which appears when you click on the provider.
+You can also remove the selected descriptor by selecting and clicking the button "<<" or the "delete" key on the keyboard.
+The lower right canvas allows for entering parameters for descriptors which are selected in the top right canvas.
+
+<p>
+The toolbar in the QSAR editor contains a shortcut icon in the top right corner
+to perform a complete build (calculate all selected descriptors for all selected molecules).
+
+</BODY>
+</HTML>
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/dlg_add_mols.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/dlg_add_respProp.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-descr.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-info-general.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-info-units.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-mols.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-responses.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/editor-source.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/matrix-editor.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/editor/images/overviewPage.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
30 plugins/net.bioclipse.qsar.ui/html/editor/infoPage.html
@@ -0,0 +1,30 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+ <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
+ <TITLE>Bioclipse-QSAR - Editor - Information Page</TITLE>
+ <link rel="stylesheet" href="../../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
+</HEAD>
+<BODY LANG="en-US" DIR="LTR">
+<h1>QSAR Editor - Information Page</h1>
+
+
+
+<p>
+The Information Page of the QSAR Editor allows for entering information about the QSAR dataset.
+On the General tab, general information can be added (see screenshot below).
+<p>
+
+<center><img src="images/editor-info-general.png" width=450></center>
+
+<p>
+On the Response units tab, response units can be added to the dataset (see screenshot below).
+<p>
+<center><img src="images/editor-info-units.png" width=450></center>
+
+<p>
+The toolbar in the QSAR editor contains a shortcut icon in the top right corner
+to perform a complete build (calculate all selected descriptors for all selected molecules).
+
+</BODY>
+</HTML>
View
40 plugins/net.bioclipse.qsar.ui/html/editor/molPage.html
@@ -0,0 +1,40 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+ <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
+ <TITLE>Bioclipse-QSAR - Editor - Molecules Page</TITLE>
+ <link rel="stylesheet" href="../../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
+</HEAD>
+<BODY LANG="en-US" DIR="LTR">
+<h1>QSAR Editor - Molecules Page</h1>
+
+
+
+<p>
+The Molecules Page of the QSAR Editor allows for adding molecular files to the dataset.
+The is done by drag and dropping a file in the viewer, or clicking the "Add" button,
+which brings up a wizard (see screenshot below).
+<p>
+<center><img src="images/dlg_add_mols.png"></center>
+
+<p>
+Select a file and click Next to get to the Response Property selection. Here you can right-click on a property
+in the file and mark it as the response, which will import the values as response values into the QSAR dataset (see screenshot below).
+
+<p>
+<center><img src="images/dlg_add_respProp.png"></center>
+
+<p>
+When you are done, click "Finish".
+The Molecules Page shows the file in the list, and also indicates if any errors were encountered.
+Right-click to view or remove molecules with errors (see screenshot below).
+
+<p>
+<center><img src="images/editor-mols.png"></center>
+
+<p>
+The toolbar in the QSAR editor contains a shortcut icon in the top right corner
+to perform a complete build (calculate all selected descriptors for all selected molecules).
+
+</BODY>
+</HTML>
View
10 plugins/net.bioclipse.qsar.ui/html/editor/overviewPage.html
@@ -8,15 +8,19 @@
<BODY LANG="en-US" DIR="LTR">
<h1>QSAR Editor - Overview Page</h1>
-<img src="images/overviewPage.png" width=500 align=right>
-
-<p>
The Overview Page of the QSAR Editor shows a summary of the active QSAR project. It is
easy to see e.g. the number of chsmicals, descriptors, responses and to navigate to the
corresponding page.
<p>
+<img src="images/overviewPage.png" width=500>
+
+<p>
Some functionality is only available on the Overview page. For example it is here that
you set AutoBuild to be ON or OFF. Read more about this on the <a href="../qsarProjects.html">QSAR Project page</a>.
+<p>
+The toolbar in the QSAR editor contains a shortcut icon in the top right corner
+to perform a complete build (calculate all selected descriptors for all selected molecules).
+
</BODY>
</HTML>
View
28 plugins/net.bioclipse.qsar.ui/html/editor/responsePage.html
@@ -0,0 +1,28 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+ <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
+ <TITLE>Bioclipse-QSAR - Editor - Responses Page</TITLE>
+ <link rel="stylesheet" href="../../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
+</HEAD>
+<BODY LANG="en-US" DIR="LTR">
+<h1>QSAR Editor - Responses Page</h1>
+
+
+
+<p>
+The Responses Page of the QSAR Editor allows for entering and modifying response values for the chemical structures (see screenshot below).
+Click in the fields and make any changes.
+It is also possible to set the response unit by clicking in the corresponding entry.
+Note that you have to add the response unit first to the QSAR project on the <a href="infoPage.html">Information Page</a> before you can select it here.
+
+<p>
+
+<center><img src="images/editor-responses.png" width=450></center>
+
+<p>
+The toolbar in the QSAR editor contains a shortcut icon in the top right corner
+to perform a complete build (calculate all selected descriptors for all selected molecules).
+
+</BODY>
+</HTML>
View
22 plugins/net.bioclipse.qsar.ui/html/editor/sourcePage.html
@@ -0,0 +1,22 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+ <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
+ <TITLE>Bioclipse-QSAR - Editor - Source Page</TITLE>
+ <link rel="stylesheet" href="../../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
+</HEAD>
+<BODY LANG="en-US" DIR="LTR">
+<h1>QSAR Editor - Source Page</h1>
+
+
+
+<p>
+The Source Page of the QSAR Editor is a read-only view of the QSAR-ML for the dataset.
+Currently it is only updated on save.
+
+<p>
+
+<center><img src="images/editor-source.png" width=450></center>
+
+</BODY>
+</HTML>
View
33 plugins/net.bioclipse.qsar.ui/html/export.html
@@ -0,0 +1,33 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+ <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
+ <TITLE>Bioclipse QSAR - Import and Export</TITLE>
+ <link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
+</HEAD>
+<BODY LANG="en-US" DIR="LTR">
+<h1>Bioclipse QSAR - Import and Export</h1>
+
+<p>
+<h2>Importing a Bioclipse-QSAR project</h2>
+From the file menu, select Import... then in the wizard select <b>Cheminformatics > Qsar project</b>.
+In the opened dialog select "From archive file" and point to the archived Bioclipse-QSAR project.
+
+<p>
+<center><img src="images/dlg_import.png"></center>
+
+<p>
+<h2>Exporting a Bioclipse-QSAR project</h2>
+
+There are two options to export a Bioclipse-QSAR project.
+<p>
+<ol>
+<li> On the Overview Page in the QSAR Editor, click "Export QSAR project". This allows for archiving all information in the project to a zip-file.
+<li> Right-click the desired Project in the Bioclipse Navigator and select <b>Export...</b> then in the dialog select <b>Cheminformatics > Qsar project</b>. This opens the same dialog asking for a file to export to as above.
+</ol>
+
+
+
+
+</BODY>
+</HTML>
View
BIN  plugins/net.bioclipse.qsar.ui/html/images/dlg_import.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
BIN  plugins/net.bioclipse.qsar.ui/html/images/prefs-qsar.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View
30 plugins/net.bioclipse.qsar.ui/html/prefs.html
@@ -0,0 +1,30 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+ <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
+ <TITLE>Bioclipse QSAR - Preferences</TITLE>
+ <link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
+</HEAD>
+<BODY LANG="en-US" DIR="LTR">
+<h1>Bioclipse QSAR - Preferences</h1>
+
+<p>
+The Bioclipse preferences has a section for QSAR with three pages.
+
+<p>
+<b>Descriptors:</b> Here you can add additional descriptor definition files, to join with the
+Blue Obelisk Descriptor Ontology.
+
+<p>
+<b>Providers:</b> Here you can change the order of the descriptor providers being taken as default when adding a descriptor to the QSAR project.
+
+<p>
+<b>Units:</b> Here you can add additional Reponse Units, which later can be added to a dataset.
+
+<p>
+<center><img src="images/prefs-qsar.png"></center>
+
+
+
+</BODY>
+</HTML>
View
107 plugins/net.bioclipse.qsar.ui/html/scripting.html
@@ -0,0 +1,107 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+ <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
+ <TITLE>Bioclipse QSAR - Scripting</TITLE>
+ <link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
+</HEAD>
+<BODY LANG="en-US" DIR="LTR">
+<h1>Bioclipse QSAR - Scripting</h1>
+
+Use the command <b>help qsar</b> to get a list of available scripting commands. Below are some examples.
+
+<p>
+<h2>List available descriptors</h2>
+<br>
+<b> > qsar.listDescriptors()</b>
+<pre>
+ bondsToAtom - Bonds to Atom []
+ atomDegree - Atomic Degree []
+ vAdjMa - Vertex adjacency information magnitude [CDK]
+ chiCluster - Chi Cluster Indices [CDK]
+ carbonTypes - Carbon Types [CDK]
+ ...
+</pre>
+
+
+<p>
+<h2>List available descriptors with an available implementation</h2>
+<br>
+<b> > qsar.listDescriptors(true)</b>
+<pre>
+ vAdjMa - Vertex adjacency information magnitude [CDK]
+ chiCluster - Chi Cluster Indices [CDK]
+ carbonTypes - Carbon Types [CDK]
+ ...
+</pre>
+
+
+
+<p>
+<h2>Show implementations for a desciptor</h2>
+<br>
+<b> > qsar.show("bondCount")</b>
+<pre>
+Provider: CDK
+Description: Number of bonds of a certain bond order.
+ Parameter: Name='order', default value='', Description: Bond order to count.
+Possible values: are 's'=single, 'd'=double, 't'=triple, 'q'=quadruple and
+''=all
+--
+Provider: CDK REST
+Description: Number of bonds of a certain bond order.
+ Parameter: Name='order', default value='', Description: Bond order to count.
+Possible values: are 's'=single, 'd'=double, 't'=triple, 'q'=quadruple and
+''=all
+----
+Name='NumberOfBonds', Provider='JOELib'
+Description: Number of Bonds.
+</pre>
+
+<p>
+<h2> Calculate descriptors </h2>
+Use default implementation:<br>
+<b> > qsar.calculate(cdk.fromSMILES("CCC"), "bondCount")</b><br>
+<pre>
+ Descriptor=bondCount [order=]; provider=CDK; nB=2.0
+</pre>
+
+<p>
+Use specific implementation:<br>
+<b> > qsar.calculate(cdk.fromSMILES("CCC"), "bondCount", "CDK REST")</b><br>
+<pre>
+ Descriptor=bondCount [order=]; provider=CDK REST; nB=2.0
+</pre>
+
+
+<p>
+<h2> Calculate list of descriptors for a list of molecules: </h2>
+<pre>
+//Set up list of descriptors
+dlist = java.util.ArrayList();
+d1="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#hBondDonors";
+d2="bpol";
+dlist.add(d1);
+dlist.add(d2);
+
+//Set up list of molecules
+mols = java.util.ArrayList();
+mols.add(cdk.fromSMILES("C(=O)N(Cc1ccco1)C(c1cc2ccccc2cc1)C(=O)NCc1ccccc1"));
+mols.add(cdk.fromSMILES("C(=O)(CNC(=O)OC(C)(C)C)N(Cc1oc(C(F)(F)F)cc1)C(c1ccccc1)C(=O)NCc1ccccc1"));
+mols.add(cdk.fromSMILES("C(=O)(C=CC)N(CCCCCCC)C(c1cc2c(cccc2)c2ccccc12)C(=O)NC(C)(C)C"));
+
+//Some debug output
+js.print("\nWe have " + mols.size() +" mols and " + dlist.size() + " descriptors.\n\n");
+
+//Do descriptor calculation
+res=qsar.calculate(mols,dlist);
+
+//Display results
+res.toMatrix();
+</pre>
+
+<p>
+See <a href="http://gist.github.com/95189">gist 95189</a>.
+
+</BODY>
+</HTML>
View
2  plugins/net.bioclipse.qsar.ui/toc.xml
@@ -19,7 +19,7 @@
<topic label="Preferences" href="html/prefs.html" />
<topic label="Scripting QSAR" href="html/scripting.html" />
<topic label="QSAR-ML" href="html/qsar-ml.html" />
- <topic label="Exporting" href="html/export.html" />
+ <topic label="Import and Export" href="html/export.html" />
</topic>
</toc>
Please sign in to comment.
Something went wrong with that request. Please try again.