Difference between revisions of "JChemPaint/C3/Features-of-JChemPaint/English"

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{| border=1
 
{| border=1
 
|| '''Visual Cue'''
 
|| '''Visual Cue'''
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|| In this tutorial, we will learn  to change
 
|| In this tutorial, we will learn  to change
  
−
* Background color of the Panel
+
* Background color of the '''Panel'''
  
 
* Look and feel of the window
 
* Look and feel of the window
Line 35: Line 34:
 
||To record this tutorial I am using,  
 
||To record this tutorial I am using,  
  
−
'''Ubuntu Linux''' OS version 12.04  
+
*'''Ubuntu Linux''' OS version 12.04  
  
−
'''JChemPaint''' version 3.3-1210  
+
*'''JChemPaint''' version 3.3-1210  
  
−
'''Java''' version 7
+
*'''Java''' version 7
 
|-
 
|-
 
||'''Slide Number 5
 
||'''Slide Number 5
  
 
Pre-requisites'''
 
Pre-requisites'''
−
|| To follow this tutorial you should be familiar with,
+
|| To follow this tutorial you should be familiar with '''JChemPaint''' chemical structures editor.
−
 
+
−
'''JChemPaint''' chemical structures editor .
+
  
 
If not, for relevant tutorial,  please visit our website.
 
If not, for relevant tutorial,  please visit our website.
Line 59: Line 56:
 
||Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.  
 
||Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.  
 
|-
 
|-
−
||Type '''“cd space Desktop”'''>>press enter.
+
||Type '''“cd space Desktop”'''>>press '''Enter'''.
  
−
Type '''java  -jar ./jchempaint-3.3-1210.jar''' >> press enter.
+
Type '''java  -jar ./jchempaint-3.3-1210.jar''' >> press '''Enter'''.
−
||Type ''''“cd space Desktop”''' and press enter.
+
||Type ''''“cd space Desktop”''' and press '''Enter'''.
  
−
Type ''' “java space  -jar space ./jchempaint-3.3-1210.jar”''' and press enter.
+
Type ''' “java space  -jar space ./jchempaint-3.3-1210.jar”''' and press '''Enter'''.
  
 
'''JChemPaint''' window opens.
 
'''JChemPaint''' window opens.
 
|-
 
|-
 
||Move the cursor on the '''Panel'''.
 
||Move the cursor on the '''Panel'''.
−
||Let's see, how to change the background color of the '''Panel'''.
+
||Let's see how to change the background color of the '''Panel'''.
 
|-
 
|-
−
||Go to '''Edit''' menu navigate to '''Preferences''' >> click on it.
+
||Go to '''Edit''' menu >> click on '''Preferences'''
  
 
Move the cursor on the window.
 
Move the cursor on the window.
−
|| Go to '''Edit''' menu navigate to '''Preferences''' and click on it.
+
|| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.
  
 
'''JChemPaint Preferences''' window opens.
 
'''JChemPaint Preferences''' window opens.
Line 92: Line 89:
 
|-
 
|-
 
||Show the screen shots of the other Choose background windows.
 
||Show the screen shots of the other Choose background windows.
−
||'''HSB''' may be '''HSV''.
+
||'''HSB''' may be '''HSV'''.
  
 
You may not see '''Swatches''' tab.
 
You may not see '''Swatches''' tab.
Line 108: Line 105:
 
|-
 
|-
 
||Click on '''OK'''  button.
 
||Click on '''OK'''  button.
−
||Click on '''OK''  to close the '''Preferences''' window.
+
||Click on '''OK'''  to close the '''Preferences''' window.
 
|-
 
|-
−
||'''Slide Number 5
+
||'''Slide Number 5'''
  
−
Assignment'''
+
'''Assignment'''
 
||Try various color combinations using '''Choose background color''' window.
 
||Try various color combinations using '''Choose background color''' window.
 
|-
 
|-
Line 161: Line 158:
  
 
Point to the menu bar and status bar.
 
Point to the menu bar and status bar.
−
||I will click on ''Spanish'''.
+
||I will click on '''Spanish'''.
  
 
Click '''OK'''  button.
 
Click '''OK'''  button.
  
−
Observe the change in language on the Menu bar and on the Status bar.
+
Observe the change in language on the '''Menu bar''' and on the '''Status bar'''.
 
|-
 
|-
 
||
 
||
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||I will click on a few '''Template''' tabs to display structures.
 
||I will click on a few '''Template''' tabs to display structures.
 
|-
 
|-
−
||Click on '''Beta Lactums''' tab.
+
||Click on '''Beta Lactums''' tab >>
  
 
Click on '''Penicillin''' structure.
 
Click on '''Penicillin''' structure.
−
||Click on Beta Lactums tab.
+
||Click on '''Beta Lactums''' tab.
  
−
Click on Penicillin structure, to display it on the Panel.
+
Click on '''Penicillin''' structure, to display it on the '''Panel'''.
 
|-
 
|-
 
||Press '''Ctrl+ Z'''
 
||Press '''Ctrl+ Z'''
Line 211: Line 208:
 
|| Click on '''Templates''' tab,  click on '''Miscellaneous'''.
 
|| Click on '''Templates''' tab,  click on '''Miscellaneous'''.
  
−
Then click on '''C60 Fullerene''', to display it on the Panel.
+
Then click on '''C60 Fullerene''', to display it on the '''Panel'''.
 
|-
 
|-
−
||'''Slide Number 6
+
||'''Slide Number 6'''
  
−
Assignment'''.
+
'''Assignment'''.
−
||You can load other '''Templates''' of your choice onto the Panel.
+
||You can load other '''Templates''' of your choice onto the '''Panel'''.
 
|-
 
|-
 
||
 
||
 
||Next we will learn about '''SMILES''' and '''InChi keys'''.
 
||Next we will learn about '''SMILES''' and '''InChi keys'''.
 
|-
 
|-
−
||'''Slide Number 7  
+
||'''Slide Number 7'''
  
−
SMILES'''
+
'''SMILES'''
 
|| What are '''SMILES''' and '''InChi Keys'''?
 
|| What are '''SMILES''' and '''InChi Keys'''?
  
Line 237: Line 234:
  
 
'''InChi'''
 
'''InChi'''
−
||* '''InChi''' is '''International Chemical Identifier'''.
+
||
 +
* '''InChi''' is '''International Chemical Identifier'''.
  
 
* It describes a chemical in terms of layers of information.
 
* It describes a chemical in terms of layers of information.
Line 243: Line 241:
 
* Atoms and their bond connectivity,  
 
* Atoms and their bond connectivity,  
  
−
* Isotopic, stereochemical and electronic charge information.  
+
* '''Isotopic, stereochemical''' and '''electronic charge''' information.  
  
−
*For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the '''InChi'''  key of '''Propane'''.
+
* For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the '''InChi'''  key of '''Propane'''.
 
|-
 
|-
 
||Press '''Delete''' on the Keyboard.
 
||Press '''Delete''' on the Keyboard.
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Press '''Delete''' on the Keyboard.
 
Press '''Delete''' on the Keyboard.
 
|-
 
|-
−
||Point to the Templates and Morhphine.
+
||Point to the '''Templates''' and '''Morhphine'''.
−
||To generate SMILES I will load an '''Alkaloid, Morhphine''' from the '''Templates''' menu.
+
||To generate '''SMILES''' I will load an '''Alkaloid, Morhphine''' from the '''Templates''' menu.
 
|-
 
|-
 
||Click on '''Tools''' Menu>> click on '''Create SMILES'''.
 
||Click on '''Tools''' Menu>> click on '''Create SMILES'''.
 
||Click on '''Tools''' Menu,  then click on '''Create SMILES'''.
 
||Click on '''Tools''' Menu,  then click on '''Create SMILES'''.
 
|-
 
|-
−
||Point to the dialogue box.
+
||Point to the dialog box.
  
 
Move the cursor onto '''SMILES''' and '''Chiral SMILES'''
 
Move the cursor onto '''SMILES''' and '''Chiral SMILES'''
−
|| '''SMILES''' dialogue box opens with '''Generated SMILES'''.
+
|| '''SMILES''' dialog box opens with '''Generated SMILES'''.
  
−
Dialogue box contains SMILES and Chiral SMILES.  
+
Dialog box contains '''SMILES''' and '''Chiral SMILES'''.  
 
|-
 
|-
−
||Click '''OK''' to close the dialogue box.
+
||Click '''OK''' to close the dialog box.
−
|| Click '''OK''' to close the dialogue box.
+
|| Click '''OK''' to close the dialog box.
 
|-   
 
|-   
 
||Go to '''Tools''' menu.
 
||Go to '''Tools''' menu.
  
−
Click on Create InChi.
+
Click on '''Create InChi'''.
−
||Press CTRL+A to select the structure, if it is not selected.
+
||Press '''CTRL+A''' to select the structure, if it is not selected.
  
 
To generate  '''InChi''' key of '''Morphine''', go to '''Tools''' menu.
 
To generate  '''InChi''' key of '''Morphine''', go to '''Tools''' menu.
Line 278: Line 276:
 
|-
 
|-
 
||Point to  '''InChi''' details.
 
||Point to  '''InChi''' details.
−
||'''InChi'''  dialogue box opens with '''InChi  generation''' of  ''''Morphine''''.
+
||'''InChi'''  dialog box opens with '''InChi  generation''' of  ''''Morphine''''.
 
|-
 
|-
−
||Click '''OK''' to close the dialogue box.
+
||Click '''OK''' to close the dialog box.
−
||Click '''OK''' to close the dialogue box.
+
||Click '''OK''' to close the dialog box.
 
|-
 
|-
 
||Press '''Delete''' on the keyboard.
 
||Press '''Delete''' on the keyboard.
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|-
 
|-
 
||Click in the '''Insert''' bar >> type '''c1ccc1'''.
 
||Click in the '''Insert''' bar >> type '''c1ccc1'''.
−
||Click in the Insert bar and type '''c1ccc1''' and click on '''Insert''' button.
+
||Click in the '''Insert bar''' and type '''c1ccc1''' and click on '''Insert''' button.
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
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|-
 
|-
 
||Open and show the Text editor.
 
||Open and show the Text editor.
−
||I had already saved a few '''SMILES'''  and '''InChi''' keys from '''PubChem Page''' into a Text Editor.
+
||I had already saved a few '''SMILES'''  and '''InChi''' keys from '''PubChem Page''' into a "Text Editor".
 
|-
 
|-
 
||Copy and Paste the '''SMILES'''.
 
||Copy and Paste the '''SMILES'''.
  
 
Point to the structure.
 
Point to the structure.
−
|| I will copy a '''SMILES''' from “'Text Editor” and
+
|| I will copy a '''SMILES''' from “Text Editor” and paste it into the '''Insert bar'''.
  
−
Paste it into '''Insert bar''' and click on  '''Insert''' button.  
+
And click on  '''Insert''' button.  
  
 
Inserted '''SMILES''' displays  '''Aspartic acid (C(C(C(=O)O)N)C(=O)O)''' structure on the '''Panel'''.
 
Inserted '''SMILES''' displays  '''Aspartic acid (C(C(C(=O)O)N)C(=O)O)''' structure on the '''Panel'''.
Line 317: Line 315:
 
|-
 
|-
 
||Copy and paste the '''InChi Key'''.
 
||Copy and paste the '''InChi Key'''.
−
|| I will copy an '''Inchi Key'''  from the '''Text Editor''', and
+
|| I will copy an '''Inchi Key'''  from the '''Text Editor''' and paste it into the '''Insert bar'''.
  
−
Paste it into the '''Insert bar''' then click on  '''Insert''' button.  
+
 
 +
Then click on  '''Insert''' button.  
  
 
Inserted '''Inchi Key''' displays, '''Benzene''' (InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H) structure onto the '''Panel'''.
 
Inserted '''Inchi Key''' displays, '''Benzene''' (InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H) structure onto the '''Panel'''.
 
|-
 
|-
−
||'''Slide Number 9
+
||'''Slide Number 9'''
  
−
Assignment'''
+
'''Assignment'''
−
|| As an assignment insert the given '''SMILES''' and '''InChi Keys'''  
+
|| As an assignment, insert the given '''SMILES''' and '''InChi Keys'''  
−
to obtain various structures .
+
to obtain various structures.
  
 
1)CC1=CC=CC=C1  
 
1)CC1=CC=CC=C1  
Line 340: Line 339:
 
||Let's Summarize.
 
||Let's Summarize.
 
|-
 
|-
−
||'''Slide Number 10
+
||'''Slide Number 10'''
  
−
Summary'''
+
'''Summary'''
 
||In this tutorial, we have learnt to change,
 
||In this tutorial, we have learnt to change,
  
−
* Background color of the Panel  
+
* Background color of the '''Panel'''
  
 
* Look and feel of the window
 
* Look and feel of the window
  
−
* User interface language.
+
* User interface language
  
−
* Insert Templates  
+
* Insert '''Templates'''
  
−
* Generate Smiles and InChi keys for a given structure.
+
* Generate '''SMILES''' and '''InChi keys''' for a given structure
  
−
* Insert Smiles and InChi keys to generate structures.
+
* Insert '''SMILES''' and '''InChi Keys''' to generate structures  
 
|-   
 
|-   
−
||'''Slide Number11
+
||'''Slide Number 11'''
  
−
Acknowledgement'''
+
'''Acknowledgement'''
−
||This video summarizes the Spoken Tutorial project
+
||This video summarizes the Spoken Tutorial project.
  
 
If you do not have good bandwidth, you can download and watch it.   
 
If you do not have good bandwidth, you can download and watch it.   
Line 367: Line 366:
 
||  Spoken Tutorial Team:  
 
||  Spoken Tutorial Team:  
  
−
Conducts workshops using spoken tutorials
+
*Conducts workshops using spoken tutorials
  
−
Gives certificates to those who pass an on-line test  
+
*Gives certificates to those who pass an on-line test  
  
−
For more details, please write to
+
For more details, please write to '''contact@spoken-tutorial.org'''
  
−
'''contact@spoken-tutorial.org'''
 
 
|-
 
|-
 
||'''Slide number 13'''
 
||'''Slide number 13'''
Line 384: Line 382:
 
'''http://spoken-tutorial.org/NMEICT-Intro ]'''  
 
'''http://spoken-tutorial.org/NMEICT-Intro ]'''  
  
−
This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
+
 
 +
|-
 +
||
 +
||This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
 
|-
 
|-
 
|}
 
|}

Latest revision as of 15:23, 1 October 2014

Visual Cue Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Features of JChemPaint..

Slide Number 2+3

Learning Objectives

In this tutorial, we will learn to change
  • Background color of the Panel
  • Look and feel of the window
  • User interface language.

We will also learn to,

  • Insert Templates
  • Generate SMILES and InChi keys for a given structure.
  • Insert SMILES and InChi keys to generate structures.
Slide Number 4

System Requirement

To record this tutorial I am using,
  • Ubuntu Linux OS version 12.04
  • JChemPaint version 3.3-1210
  • Java version 7
Slide Number 5

Pre-requisites

To follow this tutorial you should be familiar with JChemPaint chemical structures editor.

If not, for relevant tutorial, please visit our website.

Let's switch to JChemPaint window.
Point to .jar file Recall that we had saved our .jar file on the Desktop.
Press CTRl+ALt+T keys. Press CTRl+ALt and T keys simultaneously to open the Terminal.
Type “cd space Desktop”>>press Enter.

Type java -jar ./jchempaint-3.3-1210.jar >> press Enter.

Type '“cd space Desktop” and press Enter.

Type “java space -jar space ./jchempaint-3.3-1210.jar” and press Enter.

JChemPaint window opens.

Move the cursor on the Panel. Let's see how to change the background color of the Panel.
Go to Edit menu >> click on Preferences

Move the cursor on the window.

Go to Edit menu, navigate to Preferences and click on it.

JChemPaint Preferences window opens.

Click on Choose background color button.

Point to Choose background color window.

Click on Choose background color button.

Choose background color window opens.

Point to the tabs. This window has three tabs namely Swatches, HSB and RGB.
Depending on your Operating System this window, may vary a little.
Show the screen shots of the other Choose background windows. HSB may be HSV.

You may not see Swatches tab.

Show the screen shot of Windows OS. Windows Operating System has two additional tabs namely HSL and CMYK.
Point to light green Swatch. You can select the background color of your choice.

I will click on light green color Swatch to change background color to light green.

Click on OK to close window. Click on OK to close the window.
Click on OK button. Click on OK to close the Preferences window.
Slide Number 5

Assignment

Try various color combinations using Choose background color window.
Next about Other Preferences tab.
Go to Edit menu navigate to Preferences >> click on it.

Move the cursor on the window.

Go to Edit menu and click on Preferences

Preferences window opens.

Click on Other Preferences tab. Click on Other Preferences tab.
Move the cursor to Look and feel field.

Point to the drop down list.

Go to Look and feel field.

This field has a drop down list.

List contains Sytem, Metal, Nimbus, Motif, GTK and Windows.

Click on Nimbus>>click on OK button. I will click on Nimbus.

Then click on OK button.

Observe the change in look and feel of the window.

Click on Edit menu >> click Preferences. Click on Edit menu then click Preferences.

Click on other Preferences.

Move the cursor on the window. Go to User Interface Language field.

This field has a drop down list.

List contains American English and other languages.

By default American English is selected.

Click on Spanish>> Click OK buttons.

Point to the menu bar and status bar.

I will click on Spanish.

Click OK button.

Observe the change in language on the Menu bar and on the Status bar.

I will undo the changes.
Point to Templates menu Now let's insert Templates onto the Panel.
Click on Templates menu. Click on Templates menu.

Templates drop down opens.

Point to right side tool bar. Alternately you can open Templates menu from side tool bar.
Move the cursor on the list. Here you can see various Templates tabs.

Click on All Templates tab.

Structure Templates window opens.

Scroll down the window. Window shows list of Templates along with their structures.

I will scroll down the window to view different structures.

Point to the Templates. I will click on a few Template tabs to display structures.
Click on Beta Lactums tab >>

Click on Penicillin structure.

Click on Beta Lactums tab.

Click on Penicillin structure, to display it on the Panel.

Press Ctrl+ Z Press Ctrl+ Z to undo the changes.
Click on Miscellaneous tab.

Click on C60 Fullerene.

Click on Templates tab, click on Miscellaneous.

Then click on C60 Fullerene, to display it on the Panel.

Slide Number 6

Assignment.

You can load other Templates of your choice onto the Panel.
Next we will learn about SMILES and InChi keys.
Slide Number 7

SMILES

What are SMILES and InChi Keys?
  • SMILES is simplified molecular input line entry system.
  • It describes chemical structures using short ASCII strings.
  • Molecular Editors import SMILES strings, to convert structures into 2D drawings.
  • For example, CCCCCC is a Canonical SMILES of Hexane
Slide Number 8

InChi

  • InChi is International Chemical Identifier.
  • It describes a chemical in terms of layers of information.
  • Atoms and their bond connectivity,
  • Isotopic, stereochemical and electronic charge information.
  • For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the InChi key of Propane.
Press Delete on the Keyboard. I will clear the window.

Press Delete on the Keyboard.

Point to the Templates and Morhphine. To generate SMILES I will load an Alkaloid, Morhphine from the Templates menu.
Click on Tools Menu>> click on Create SMILES. Click on Tools Menu, then click on Create SMILES.
Point to the dialog box.

Move the cursor onto SMILES and Chiral SMILES

SMILES dialog box opens with Generated SMILES.

Dialog box contains SMILES and Chiral SMILES.

Click OK to close the dialog box. Click OK to close the dialog box.
Go to Tools menu.

Click on Create InChi.

Press CTRL+A to select the structure, if it is not selected.

To generate InChi key of Morphine, go to Tools menu.

Click on Create InChi.

Point to InChi details. InChi dialog box opens with InChi generation of 'Morphine'.
Click OK to close the dialog box. Click OK to close the dialog box.
Press Delete on the keyboard. Press Delete on the keyboard to delete the Morphine structure.
Now we will learn to obtain a structure from inserted SMILES.
Point to the Insert bar and Insert button. Below the Formatting toolbar, we have an Insert bar with an Insert button next to it.
Click in the Insert bar >> type c1ccc1. Click in the Insert bar and type c1ccc1 and click on Insert button.
Point to the structure. Cyclobutene structure is generated on the Panel.
Press Ctrl+Z. Press Ctrl+Z to undo the changes.
Open and show the Text editor. I had already saved a few SMILES and InChi keys from PubChem Page into a "Text Editor".
Copy and Paste the SMILES.

Point to the structure.

I will copy a SMILES from “Text Editor” and paste it into the Insert bar.

And click on Insert button.

Inserted SMILES displays Aspartic acid (C(C(C(=O)O)N)C(=O)O) structure on the Panel.

Press Ctrl+Z. Press Ctrl+Z to undo the changes.
Copy and paste the InChi Key. I will copy an Inchi Key from the Text Editor and paste it into the Insert bar.


Then click on Insert button.

Inserted Inchi Key displays, Benzene (InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H) structure onto the Panel.

Slide Number 9

Assignment

As an assignment, insert the given SMILES and InChi Keys

to obtain various structures.

1)CC1=CC=CC=C1

2)CC(C(=O)O)N

3)InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2

4)InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)

Let's Summarize.
Slide Number 10

Summary

In this tutorial, we have learnt to change,
  • Background color of the Panel
  • Look and feel of the window
  • User interface language
  • Insert Templates
  • Generate SMILES and InChi keys for a given structure
  • Insert SMILES and InChi Keys to generate structures
Slide Number 11

Acknowledgement

This video summarizes the Spoken Tutorial project.

If you do not have good bandwidth, you can download and watch it.

Slide Number 12 Spoken Tutorial Team:
  • Conducts workshops using spoken tutorials
  • Gives certificates to those who pass an on-line test

For more details, please write to contact@spoken-tutorial.org

Slide number 13 Spoken Tutorial Project is a part of the Talk to a Teacher project

It is supported by the National Mission on Education through ICT, MHRD, Government of India

More information on this Mission is available at this link.

http://spoken-tutorial.org/NMEICT-Intro ]


This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Madhurig, Nancyvarkey

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