SMILES

Simplified Molecular Input Line Entry Specification

Assalamualaikum w.b.t. my fellow vicegerences of Earth! It is Wednesday and as usual we are here to equip ourselves with some IT knowledge. Today, we are going to learn a thing or two that will make you "smile". Why? We will see later on.
Surely, most of you readers are science based students and are taking organic chemistry as your required subjects. And we all know that in organic chemistry we have to deal with complicated and sometimes long and highly branched structures and formula of organic molecules. And have you ever wonder how these molecules and formulas are going to be written in computer?
Fortunately, there is a system that has made it simple. It is the Simplified Molecular Input Line Entry Specification or SMILES. SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensions models of the molecules. SMILES uses atomic symbols and a set of intuitive rules. It also uses hydrogen-suppressed molecular graphs (HSMG). In terms of a graph-based computational procedure. SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph.

There are two types of SMILES:

1. Canonical SMILES
2. Isomeric SMILES

Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation. A common application of Canonical SMILES is for indexing and ensuring uniqueness of molecules in a database.
Isomeric SMILES refers to the version of the SMILES specification that includes extensions to support the specification of isotopes, chirality and configuration about double bonds. A notable feature of these rules is that they allow rigorous partial specification of chirality.

• E.g:
• trans-1,2-dibromoethene: Br/C=C/Br
• cis-1,2-dibromoethene: Br/C=C\Br
• Chirality indicated by the "@" symbol.

SMILES Bonds

The bonds in a molecular formula are represented with symbols such as follows:

Single*	-
Double	=
Triple	#
Aromatic	:

*can be omitted

Examples:

Molecule	SMILES representation
Ethene	C=C
Chloroethene	ClC=C
1,1-Dichloroethene	ClC(Cl)=C
cis-1,2-Dichloroethene	ClC=CCl
Trichloroethene	ClC(Cl)=CCl
Perchloroethene	ClC(Cl)=C(Cl)Cl

SMILES Branches

• Branches are represented by enclosure in parentheses.
• Can be nested or stacked

A branch cannot immediately follow a double or triple bond symbol. E.g:

• C=(CC) is invalid, but
• C(=CC)C or C(CC)-C are valid SMILES

SMILES Symbols

• Are strings of alphanumeric characters and certain punctuation symbols
• Termintes at the first space encountered when read left to right.
• The organic subset : B, C, N, O, P, S, F, Cl, Br, I

Cyclic Structures

• Aliphatic or nonaromatic carbon: C
• Atom in aromatic ring : lowercase letter
• Designate ring closure with pairs of matching digits, e.g:
• c1ccccc1 is Benzene, whereas
• C1CCCCC1 is Cyclohexane
• Numbers indicate start and stop of ring.
• Same number indicates start and end of the ring, entered immediately following the start/end atoms.
• Only numbers 1-9 are used.
• A number should appear only twice
• Atm can be associated with 2 consecutive number, e.g, Naphthalene: c12ccccc1cccc2.

Here are some examples of SMILES notation for some molecules:

SMILES Charges

• [H+] proton
• [OH-] hydroxyl anion
• [OH3+] hydronium cation
• [Fe++] iron(II) cation
• [NH4+] ammonium cation

When using SMILES, avoid two consecutive left parentheses if possible. Strive for the fewest number of possible branches.

Another application is SMILESCAS Database
http://esc.syrres.com/interkow/smilecas.htm
There are over 103,000 SMILES notations with input CAS Registry Number that leads to SMILES and thence to a structure search.

That's all for today's lesson and see you next time. Assalamualaikum w.b.t.
Bye!

ChemSketch

Assalamualaikumwarahmatullahiwabarakatuh .For this entry we are going to write about the chemsketch .We use this chemsketch application to create graphical objects that are often used in most of the chemistry books and many others chemistry-related references .

         For your information chemsketch is a commonly used chemical drawing program for 2D and 3D structures .this program has certain additional features including calculation of molecular weight ,calculation of percentages of elements present ,IUPAC name generation and viewing in RasMol .

         As in this entry we will show you the example of the objects that can be drawn using the chemsketch .there are five of them :

1	a diagram of energy reaction
2	various types of orbital
3	vacuum distillation apparatus
4	a two-chain DNA strain
5	lipids and micelles

These are the images of the objects accordingly :

1. Diagram of energy reaction

2. Types of orbital

3. Vacuum distillation apparatus

4. A two-chain DNA strain

5. Lipids and Micelles

For further reference on how to use chemsketch do visit this website .

Thats all from us .Hopefully this entry will help you in your learning of chemistry .

XML

All 'bout XML

Assalamualaikum...hey, we meet again (^.^)V How are u?

          

         Today we are going to learn about XML. You really wondering what does XML stands for right? Ok, XML stands for Extensible Markup Language which was designed solely to carry data. Wait a minute, don't get confuse between HTML and XML because HTML is all about displaying the data. In contrast to XML which is to transport and store the data.

          Actually, we already been using XML since its creation. This is because it is the common tool for data transmission between applications and becoming more and more popular from the perspective of data storage and describing data. How XML separates data from HTML?

If you need to display dynamic data in your HTML document, it will take a lot of work to edit the HTML each time the data changes.

With XML, data can be stored in separate XML files

This way you can concentrate on using HTML for layout and display, and be sure that changes in the underlying data will not require any changes to the HTML

With a few lines of JavaScript, you can read an external XML file and update the data content of your HTML

       As example here is a note to Terry from John
 <note>
 <to>Terry</to>
 <from>John</from>

 <heading>Reminder</heading>

 <body>Call me before 6 p.m.!</body>

 </note>

1) XML Syntax Rules:

All XML Elements Must Have a Closing Tag

In HTML, you will often see elements that don't have a closing tag:

         <p>This is a paragraph<p>This is another paragraph

In XML, it is illegal to omit the closing tag. All elements must have a closing tag: 

         <p>This is a paragraph</p><p>This is another paragraph</p>

2) XML Tags are Case Sensitive:

XML elements are defined using XML tags

With XML, the tag <Letter> is different from the tag <letter>

Opening and closing tags must be written with the same case:

         <Message>This is incorrect</message>

         <message>This is correct</message>

3) XML Elements Must be Properly Nested

 Correct:  <b><i>This text is bold and italic</b></i
     
  Incorrect:  <b><i>This text is bold and italic</i></b>

4) XML Documents Must Have a Root Element

XML documents must contain one element that is theparentof all other elements

          

           <root>

              <child>

                <subchild>.....</subchild>

              </child>

           </root>

5) XML Attribute Values Must be Quoted

Correct:  

                 <note date=12/11/2007>

                   <to>Terry</to>

                   <from>John</from>

                 </note>

Incorrect:

                <note date="12/11/2007">

                  <to>Terry</to>

                  <from>John</from>

                </note>

As conclusion, there are 2 obvious differences between XML and HTML:

      

XML	HTML
Designed to transport and store data, with focus on what data is	Designed to display data, with focus on how data looks
Carry information	Display information

For more info, visit this site.