Saturday, 2 November 2013



Chemsketch is a software application that is used for drawing in chemistry. It is easier to use this software as it is specialized to draw any structure,tables,molecules, and many more that you might need to study chemistry.


you can download the freeware version at this link> FOR FREEWARE VERSION AT ACDLABS.


Choose the ‘CHEMSK’ with ‘Application’ as the file’s type,about ‘7113KB’ in size.


to be easier and for short,you have to read the tutorial that is provided  with the freeware version of the chemsketch that you have downloaded.

Here is only some of the basic things that you need to know.
You may perform several actions during your work with this software; the following specific words are used to describe them: 

Point to
means move the mouse pointer  to an item
Click means point to an item, and press the left mouse button
Right-click means point to an item, and press the right mouse button
Double-click means point to an item, and quickly press the left mouse button twice. 
Drag  means point to an item, and press and hold down the left mouse button while you move the item. 
Select  means highlight or make an interface element active either by clicking it or dragging over it (other actions are possible if specified in documentation).  If used in "select the check box", it means that the check box should be marked with a tick (as opposed to "clear the check box" when the check box should be cleared, without a mark).

There are so many things that you can do in chemskecth. Many provided basic structure that you need to draw is available . For example, 
in ‘Template Window’ it have,
3.DNA/RNA Kit,
4. Lab Kit,
5. Newman Projections,
6. Orbitals, Phosphorus Compounds, 
8. Sugar: alfa-D-Pyr 

For further information,it is very useful to read the tutorial very carefully. Or else,you will find it very difficult to used it. Hehe…(from my experience as the first time user ^_^ )

Friday, 1 November 2013

simplified molecular-input line-entry system (SMILES)

Ooops, it's not this kind of smile, heeee

Assalamualaikum :-]

After those PDB and HTML, now, we will introduce to all of you about simplified molecular-input line-entry system or simply (SMILES).

SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings.

SMILES notations are comprised of atoms (designated by atomic symbols), bonds, parentheses (used to show branching), and numbers (used to designate ring opening and closing position.

1) atoms:

      atoms are represented by their atomic symbols such as C for carbon, N for nitrogen, Cl for Chlorine and etc. For exmples :
Compound           Molecular Formula          SMILES Notation
---------                ----------------                ---------------
Ethylene                    CH2=CH2                           C=C
Propylene               CH2=CH-CH3                      C=CC
2-Butene              CH3-CH=CH-CH3                CC=CC

2) bonds:
     the four basic bonds are single, double, triple and aromatic bond. Single bond can be shown by the hyphen symbol "-" but usually it is not shown. Meanwhile, triple bond is designated by the symbol "#".

Compound         Bond                      SMILES Notation
-------------    -----------               ---------------------
Ethylene            single & double                  C=C
Propylene          single & double                 C=CC
Acetylene          triple                                  C#C
Propyne            triple                                  C#CC

There is no designation for aromatic ring. It is simply being shown by the lower case letter of atomic symbols. For instance in benzene ring:

SMILES notation for benzene is c1ccccc1
The use of the numbers as ring opening and closing positions is discussed in section 4.

3) branches
      the SMILES notation for branches compound is shown by parentheses. As an example:
4) cyclic structure
      here numbers 1 through 9 are used to indicate the starting and terminating atoms. There are some rules need to be followed:
    a. The SAME number (1, 2, 3, etc.) is used to indicate the starting and terminating atom for each ring. The starting and terminating atom must be connected to each other!

    b. Each number that is used (1, 2, 3, etc.) MUST appear twice and ONLY twice in the entire SMILES notation. 
    c. A starting or terminating atom can be associated with two consecutive numbers. For example, naphthalene can be coded as: c12ccccc1cccc2 (see the example below). The "12" following the first carbon indicates that the first carbon is connected to both of the following numbered carbons.


Table below shows the all of the SMILES notation:

Aspects SMILE Notations
Atoms Atomic symbols
Bonds single    "-"
double  "="
triple     "#"
Branches parentheses, ( )
Cyclic Structure
(opening and closing) 
Numbers 1 to 9


Try it and keep smiling C=

A Peak into XML


Assalam 'Alaik..
Peace upon to all of you..

Now, it's time for you to learn something new, (because we have learnt it, and we wanted you to know :) ).

XML represents the Extensible Markup Language as the markup language that define the rules that encoding document, which is both human readable and machine-readable.

While HTML is designed to display data which mainly focus on how the data would look, the XML is designed to be the software, or the independent tool to transport and store data, which basically focus on what data is.

The table below simplifies the differences between the HTML and the XML.


         Case sensitive   

    Case insensitive    
       Custom tags can        
             be defined  
         Has it own      
      predefined tags 

          Transport data 
  between the application  
        and the database  

     Use for designing   
         a web-page

<note> is the root element, while (to, from, heading, and body) is the elements of the root element.
And the last line of </note> indicates that this is indeed a note from Nick to Jonas.

From the note above, it is quite descriptive note, as the tags written can be "invented" by anyone, even you yourself. It's up to you what would like to write down to structure your own document. XML is used to carry information, after all. :)

Thus, all elements can have text content and attributes.

Which basically means that the figure above comprises everything in one book, and that the XML shows the details behind it, with "book store" becomes the root element, and "book" has 4 children of "title", "author", "year", and "price".

Another point to noted, is that in each attribute, the value must be quoted for the XML document does not going to be a syntax error.

These are the other XML Syntax Rules for you to look up. :)

For further reference, it is advisable that you try to learn from mistakes and make many trial-and-errors, because it was a fun learning, that we can add anything we want. 

Thanks for stopping by, anyway ^___^