From d8add6594cb0621b4afd43f62b036e71e6e95f34 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Klas=20J=C3=B6nsson?= Date: Thu, 19 Jan 2012 16:30:36 +0100 Subject: [PATCH 1/7] Fixed the cheat sheet so that it can download, open, and run a script from Gist. --- .../cheatsheets/sampleCDKscripts.xml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/plugins/net.bioclipse.cdk.ui/cheatsheets/sampleCDKscripts.xml b/plugins/net.bioclipse.cdk.ui/cheatsheets/sampleCDKscripts.xml index a87027ac4..b8d28a20c 100644 --- a/plugins/net.bioclipse.cdk.ui/cheatsheets/sampleCDKscripts.xml +++ b/plugins/net.bioclipse.cdk.ui/cheatsheets/sampleCDKscripts.xml @@ -10,7 +10,7 @@ - The following script downloads, opens, and runs a Gist (95779 to retrieve a + The following script downloads, opens, and runs a Gist (95779) to retrieve a PDB via a Web service from the EBI databases, open it with Jmol, and do some custom visualization. @@ -18,7 +18,7 @@ + param1="res=gist.download(95779); itr = res.iterator(); while (itr.hasNext()) { file = itr.next(); ui.open(file); js.executeFile(file) }"/> @@ -33,7 +33,7 @@ + param1="res=gist.download(95790); itr = res.iterator(); while (itr.hasNext()) { file = itr.next(); ui.open(file); js.executeFile(file) }"/> @@ -48,7 +48,7 @@ + param1="res=gist.download(95755); itr = res.iterator(); while (itr.hasNext()) { file = itr.next(); ui.open(file); js.executeFile(file) }"/> @@ -63,7 +63,7 @@ + param1="res=gist.download(96594); itr = res.iterator(); while (itr.hasNext()) { file = itr.next(); ui.open(file); js.executeFile(file) }"/> From 10ec9074d383799ae43d9293913ed3e541017363 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Klas=20J=C3=B6nsson?= Date: Fri, 20 Jan 2012 08:45:05 +0100 Subject: [PATCH 2/7] Added a missing bracket in the text in step 1. --- plugins/net.bioclipse.cdk.ui/cheatsheets/basicIO.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/plugins/net.bioclipse.cdk.ui/cheatsheets/basicIO.xml b/plugins/net.bioclipse.cdk.ui/cheatsheets/basicIO.xml index f1dfd3468..98d6ea4d6 100644 --- a/plugins/net.bioclipse.cdk.ui/cheatsheets/basicIO.xml +++ b/plugins/net.bioclipse.cdk.ui/cheatsheets/basicIO.xml @@ -12,7 +12,7 @@ title="Step 1: Create molecule from SMILES"> To create a molecule from SMILES, use the command:

- mol=cdk.fromSMILES("CCCO"
+ mol=cdk.fromSMILES("CCCO")
 Date: Fri, 20 Jan 2012 08:49:51 +0100 Subject: [PATCH 3/7] Made some updating of the text and comment out step 5. --- .../cheatsheets/editrunscripts.xml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/plugins/net.bioclipse.cdk.ui/cheatsheets/editrunscripts.xml b/plugins/net.bioclipse.cdk.ui/cheatsheets/editrunscripts.xml index 9e035e7b5..f77404677 100644 --- a/plugins/net.bioclipse.cdk.ui/cheatsheets/editrunscripts.xml +++ b/plugins/net.bioclipse.cdk.ui/cheatsheets/editrunscripts.xml @@ -15,7 +15,7 @@ This tutorial demonstrates how to edit and run scripts in Bioclipse. Note: You need Sample Data installed to complete this step.

In the navigator, exapand the Sample Data project, navigate to the - folder Javascripts and double-click on the file extractsmilesAndMass.js. + folder JavaScript scripts and double-click on the file extractsmilesAndMass.js. This opens the file in an editor. @@ -43,7 +43,7 @@ This tutorial demonstrates how to edit and run scripts in Bioclipse. title="Step 3: View Gist for Bioclipse"> - Gists are versioned scripts available from http://gist.github.com. <p/> + Gists are versioned scripts available from http://gist.github.com. You can find scripts for Bioclipse on Delicious, http://delicious.com/tag/bioclipse+gist. @@ -60,7 +60,7 @@ This tutorial demonstrates how to edit and run scripts in Bioclipse. gist.download(95755)

- The result in the Javascript console tells you the name of teh downloaded file. + The result in the Javascript console tells you the name of the downloaded file. - @@ -84,6 +85,6 @@ This tutorial demonstrates how to edit and run scripts in Bioclipse. class="net.bioclipse.scripting.ui.actions.ScriptAction" param1="gist.download(95779,"/Virtual/dnaiso.js")"/> - + --> From 68777e718033ceb7ee1348f696850741e3a7ef9c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Klas=20J=C3=B6nsson?= Date: Fri, 20 Jan 2012 11:36:56 +0100 Subject: [PATCH 4/7] Added numeration to the different steps of the cheat sheet. --- .../GeneralChemoinformaticsCheatSheet.xml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml b/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml index 6b9860c28..25bbf77b4 100644 --- a/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml +++ b/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml @@ -8,7 +8,7 @@ + title="Step 1: Open and Edit structures in 2D"> The JChemPaint editor (JCP) allows graphical viewing and editing of 2D diagrams of chemical structures in various formats. You can also @@ -26,7 +26,7 @@ + title="Step 2: Draw new structures in 2D from scratch"> To start drawing a new molecule in 2D, use the top menu File > New... and select Molecule. @@ -37,7 +37,7 @@ + title="Step 3: Open files with multiple structures"> Files with multiple structures (MDL SD files, and SMILES files) are handled by the Molecule Table Editor. Double-click a molecule-file @@ -60,7 +60,7 @@ + title="Step 4: Create 2D and 3D coordinates"> 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. @@ -81,7 +81,7 @@ + title="Step 5: Query and download proteins via web service"> You can search and query a variety of external (EBI) databases using the Wizard at File > New > Cheminformatics > Query WSDbfetch at EBI. @@ -92,7 +92,7 @@ + title="Step 6: Search and download chemical structures from PubChem"> It is possible to search and download compounds from PubChem using teh Wizard at File > New > Cheminformatics > Get structures from PubChem. From 2385b631da1e21215a2605ea91bea2789b66b558 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Klas=20J=C3=B6nsson?= Date: Fri, 20 Jan 2012 11:41:26 +0100 Subject: [PATCH 5/7] I missed one of the steps in the numberation, now it's fixed. --- .../cheatsheets/GeneralChemoinformaticsCheatSheet.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml b/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml index 25bbf77b4..d184dd7ac 100644 --- a/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml +++ b/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml @@ -68,7 +68,7 @@ + title="Step 5: Smarts matching"> Show the view Smarts Matching from the menu Window > Show view > Other... and select SmartsMatching in the Cheminformatics folder.

@@ -81,7 +81,7 @@ + title="Step 6: Query and download proteins via web service"> You can search and query a variety of external (EBI) databases using the Wizard at File > New > Cheminformatics > Query WSDbfetch at EBI. @@ -92,7 +92,7 @@ + title="Step 7: Search and download chemical structures from PubChem"> It is possible to search and download compounds from PubChem using teh Wizard at File > New > Cheminformatics > Get structures from PubChem. From e530444e254518b3d9586c3a136e21e7035f9db4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Klas=20J=C3=B6nsson?= Date: Fri, 20 Jan 2012 13:12:55 +0100 Subject: [PATCH 6/7] Changed where to find the menu choices in step 6 and 7 and "SmartsMatching" to "SMARTS Matching" in the text of step 5. --- .../cheatsheets/GeneralChemoinformaticsCheatSheet.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml b/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml index d184dd7ac..c2e9cd265 100644 --- a/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml +++ b/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml @@ -70,7 +70,7 @@ href="/net.bioclipse.cdk.smartsmatching/html/smartsmatchingview.html" title="Step 5: Smarts matching"> - Show the view Smarts Matching from the menu Window > Show view > Other... and select SmartsMatching in the Cheminformatics folder. + Show the view SMARTS Matching from the menu Window > Show view > Other... and select SmartsMatching in the Cheminformatics folder.

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. @@ -83,7 +83,7 @@ href="/net.bioclipse.webservices/doc/wsplugin.html" title="Step 6: Query and download proteins via web service"> - You can search and query a variety of external (EBI) databases using the Wizard at File > New > Cheminformatics > Query WSDbfetch at EBI. + You can search and query a variety of external (EBI) databases using the Wizard at File > New > Download > Query WSDbfetch at EBI. - It is possible to search and download compounds from PubChem using teh Wizard at File > New > Cheminformatics > Get structures from PubChem. + It is possible to search and download compounds from PubChem using teh Wizard at File > New > Download > Get structures from PubChem. Date: Mon, 13 Feb 2012 15:45:13 +0100 Subject: [PATCH 7/7] The cheat sheet has been renamed and a new step 1 implemented. --- .../GeneralChemoinformaticsCheatSheet.xml | 35 ++++++++++++------- 1 file changed, 23 insertions(+), 12 deletions(-) diff --git a/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml b/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml index c2e9cd265..6097147c4 100644 --- a/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml +++ b/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml @@ -1,14 +1,25 @@ - + 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. + + title="Step 1: Install sample data"> + + 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 Help > Install Sample Data + + + + + The JChemPaint editor (JCP) allows graphical viewing and editing of 2D diagrams of chemical structures in various formats. You can also @@ -24,9 +35,9 @@ param1="ui.open(cdk.fromSMILES("C1CCCCC1CC(CN(CC))CO"))"/> - + title="Step 3: Draw new structures in 2D from scratch"> To start drawing a new molecule in 2D, use the top menu File > New... and select Molecule. @@ -37,7 +48,7 @@ + title="Step 4: Open files with multiple structures"> Files with multiple structures (MDL SD files, and SMILES files) are handled by the Molecule Table Editor. Double-click a molecule-file @@ -60,7 +71,7 @@ + title="Step 5: Create 2D and 3D coordinates"> 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. @@ -68,20 +79,20 @@ + title="Step 6: Smarts matching"> Show the view SMARTS Matching from the menu Window > Show view > Other... and select SmartsMatching in the Cheminformatics folder.

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. - + + title="Step 7: Query and download proteins via web service"> You can search and query a variety of external (EBI) databases using the Wizard at File > New > Download > Query WSDbfetch at EBI. @@ -92,7 +103,7 @@ + title="Step 8: Search and download chemical structures from PubChem"> It is possible to search and download compounds from PubChem using teh Wizard at File > New > Download > Get structures from PubChem.