Using the database

About the lesson

In this tutorial you will learn about the commands and functionalities of the database commands within FELIX.

Lesson 1: Introduction to the database utilities

1.   Starting FELIX

Change your Current Working Directory to C:\Felix_Practice\ using the Preference/Directory... command. Build a new database by opening the File/New... command and choosing Create a new matrix or DBA file. Make sure the File Type is set to DBA(*.dba). Enter dba0 and click OK.

FELIX displays the name of the database file (as well as the directory of the file) in the title bar of the FELIX main window, confirming its selection:

The FELIX database has a hierarchical structure which may be represented as in the following figure:

Files are composed of entities or tables, whose structures are defined using schema files. The entities are in turn composed of items, which are themselves an arrangement of elements. Begin familiarizing yourself with the dba file system by working through some of the dba utilities, as in this lesson.

2.   Closing the current dba file and creating a new one

Click inside the command text field at the bottom of the FELIX window. Enter the following commands (press <Enter> after typing each command), which close the current dba file, create a new one and open it, and then list the entities in the new dba file:

         > dba file close quit 
         > dba file build test (if you already have a dba file named test, use some other name) 
         > dba file open test 
         > dba file show 

You should now see the following in the output window:

item page name schema
---- ---- ---- ------
1 1 dba dba

which indicates that only the default (empty) database file exists.

Note: FELIX remembers up to 10 used commands. You can use the up or down arrow keys to browse through the last commands and edit them.

3.   Generating 2D cross peaks

Select File/Open to open any 2D spectrum (e.g. the one created in Tutorial 2 ("Lesson 1: 2D processing, display, and analysis" on page 22). Select Peaks/Pick Region to pick a small region of peaks.

FELIX uses the appropriate entity (i.e., xpk.sch) and automatically renders the data.

4.   Checking the database file structure and seeing how it has changed

Now enter:

         > dba file show 

You should now see the following in the output window:

item page name schema
---- ----- ---- ------
1 1 dba dba
2 3 xpk dba

5.   Viewing the contents of the entity xpk

Now enter:

         > dba entity show xpk 

You should see this in the output window:

item page name schema
---- ----- ---- ------
1 5 peaks xpk

6.   Inquiring about particular items and elements of the entity xpk:peaks


         > dba entity show xpk:peaks 

FELIX displays a list of the cross peak footprints.

You can also specify the display of a particular item in an entity.


         > dba item show xpk:peaks.2 

Information similar to this appears in the output window:

2 216.186 2.383 0 null 721.749 3.269 0 null

Next you specify a particular element in an item.


         > dba element show xpk:peaks.2.2 

The following information is displayed:


Since the element fields are named, you can use an equivalent command:


         > dba element show xpk:peaks.2.cen1 

The same information is displayed as for the preceding command:


The other database utilities have the same syntactic logic.

7.   Loading the value of an element

Now you load a value from the database using the name check.

Enter these commands:

         > dba element load xpk:peaks.2.cen1 check 
         > lis check  

The following value is displayed:


You can change the value of any element in the database using a identifying number.


         > dba element store xpk:peaks.2.cen1 104.8 

You can also change the value of any element in the database by using names instead of numbers.

Enter these commands:

         > def check 104.8 
         > dba element store xpk:peaks.2.cen1 &check 

8.   Modifying schema

Begin by copying one of the existing schema, asg.sch, to a new schema with the name wrd.sch. Then edit the new schema file

Note: To locate the FELIX schema files, locate the database folder in the path where the FELIX 2004 executable is located.

By default this path is

C:\Program Files\Accelrys\FELIX 2004\database.

Open the database folder. Locate and open the folder called schema. Find the schema file asg.sch.


Copy the existing schema, asg.sch, to a new file named wrd.sch in your working directory using Windows Explorer. Next use Notepad to edit the new wrd.sch schema file to the following:

         > c**wrd.sch 
         > wrd  
         > 5item 	i k 	01 	06 	(1x,i5) 
         > cenpnt 	r k 	01	10	(f10.3) 
         > wid 		r 	01 	10 	(f10.3) 
         > cenppm 	r k 	01 	10 	(f10.3) 
         > name 	c 	32 	34	(2x,a32) 

9.   Passing data to and getting data from a new database entity

Generate a new entity by entering this command:

         > dba entity build weird wrd 1 

This generates a new entity with the name weird, which is based upon the schema wrd.sch, using a single occurrence of that schema.

Store a value in an element of your new entity by entering:

         > dba element store weird.1.5 abcdef 


         > dba element store abcdef 

Both commands specify storing the string in the entity named weird, item 1, element 5 (again note that the element fields are named).

Give that element a name by entering:

         > dba element load var 

Confirm that the element has been named by entering:

         > lis var 

You should see the following:


Write the entity to an ASCII file by entering:

         > dba entity write weird weird.txt 

Now read the ASCII file back in as another entity by entering:

         > dba entity read test weird.txt 

Confirm the success of this set of operations by entering:

         > dba element load test.1.5 newvar 
         > lis newvar 

The following should be displayed:


To view any entity via tables you can use the Edit/Table command. This opens a control panel from which you can choose the entity that you would like to display in a table.