Computer in Science (KOS 1110): December 2012

XML : Extensible Markup Language

We had learned in the class about Extensible Markup Language (XML). The definition of XML is to transport and store data with focus on what data is. This XML language is similar as HTML language. But, the XML is not a replacement for HTML. The function of HTML is to display data with focus on how data looks. The XML also can be described as a software and hardware independent tool for carrying information.

Example of an XML Document

Input

<note>
<to>Ahmad</to>
<from>Abu</from>
<heading>Reminder</heading>
<body>Don't forget me this weekend!</body>
</note>

Output

To: Ahmad

From: Abu

Reminder: Don’t forget me this weekend

XML Syntax Rules: All XML elements must have a closing tag	Examples: <p>This is a paragraph</p> <p>This is another paragraph</p>
XML Tags are Case Sensitive	Examples: <message>This is incorrect</message> <message>This is correct</message>
XML Elements Must be Properly Nested It must be at properly nested	Example: <b><i>This text is bold and italic</i></b>

Reference

http://en.wikipedia.org/wiki/XML

HTML : HyperText Markup Language

The language used to design web pages which meant a language for displaying web pages and other information that can be displayed in a web browser.

HTML is written in the form of HTML elements consisting of tags enclosed in angle brackets (like <html>), within the web page content.

HTML tags most commonly come in pairs like <h1> and </h1>, although some tags, known as empty elements, are unpaired, for example <img>.

The first tag in a pair is the start tag, the second tag is the end tag (they are also called opening tags and closing tags).

In between these tags web designers can add text, tags, comments and other types of text-based content.

Example of HTML

http://sheldonbrown.com/web_sample1.html

Main HTML Elements

DOCTYPE
HTML
HEAD

TITLE
OPTIONAL ELEMENTS

BASE
META
BGSOUND
SCRIPT,NOSCRIPT
STYLE
LINK

BODY ELEMENT

<BODY BGCOLOR=“YELLOW”>
HTML Attributes and Attribute Values

BACKGROUND
BGCOLOR
TEXT
LINK,VLINK,ALINK
OnLoad, OnUnload, OnFocus, OnBlur

Elements inside BODY element

<BODY>

Remaining HTML elements

</BODY>

Reference on HTML Elements

META ELEMENTS – Records document information, forwards and refreshes pages	NAME=“author” NAME=“keyword” NAME=“description” HTTP-EQUIV=“refresh”
BLOCK-LEVEL ELEMENTS	-Headings -H1…H6 -ALIGN -Basic Text Sections -P -ALIGN -PRE -WIDTH -ADDRESS -BLOCKQUOTE -Lists -OL -LI -UL -DL -DT -DD -Tables and Forms -Misc. -HR -DIV -CENTER MULTICOL

Reference on HTML Block-level Elements

Reference on HTML Meta Tags

HTML Tutorial for Beginners

PDB : Protein Data Bank

In this topic, firstly, we discussed about the definition of Protein Data Bank (PDB). PDB is a repository for 3-D biological macromolecular structure. All data are available to the public. It includes proteins, nucleic acids and viruses. The PDB is obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%).

Protein Data Bank founded in 1971 by Brookhaven National Laboratory, New York. First set of data were entered on punched cards. Currently it holds 29,000 released structures.

X Ray Crystallography

X-ray crystallography is a method of determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal.

Some examples of protein images :

mmCIF

mmCIF dictionary contains 2,500 definitions for terms used to describe the crystallographic experiment. For examples, _chem_comp_link.details, _atom_type.description, and so on. The dictionary definition language (DDL) is structured in a way that data files that conform to this syntax can be readily loaded into a database.

Data Deposition

Getting the Most Out of the PDB

References

SMILES : Simplified Molecular Input Line Entry Specification

The Simplified Molecular Input Line Entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings.

The original SMILES specification was developed by Arthur Weiningerand David Weininger in the late 1980s. The Environmental Protection Agency funded the initial project to develop SMILES. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems Inc. In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community.

In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI; it also has a wide base of software support with extensive theoretical (e.g., graph theory) backing.

SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

SMILES uses atomic symbols and a set of intuitive rules and uses hydrogen-suppressed molecular graphs (HSMG).

Canonical SMILES and Isomeric SMILES

The term 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.

The term 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.

Symbols Application in SMILES

1. Atoms

Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as [Au] for gold. Brackets can be omitted for the "organic subset" of B, C, N, O, P, S, F, Cl, Br, and I. All other elements must be enclosed in brackets. If the brackets are omitted, the proper number of implicit hydrogen atoms is assumed; for instance the SMILES for water is simply O.
An atom holding one or more electrical charges is enclosed in brackets, followed by the symbol H if it is bonded to one or more atoms of hydrogen, followed by the number of hydrogen atoms then by the sign '+' for a positive charge or by '-' for a negative charge. The number of charges is specified after the sign (except if there is one only).

2. Bonds

Bonds between aliphatic atoms are assumed to be single unless specified otherwise and are implied by adjacency in the SMILES string. For example the SMILES for ethanol can be written as CCO. Ring closure labels are used to indicate connectivity between non-adjacent atoms in the SMILES string.

Bonds symbols in SMILES :

SINGLE* -

DOUBLE =

TRIPLE #

AROMATIC :

* can be omitted

3. Aromaticity

Aromatic C, O, S and N atoms are shown in their lower case 'c', 'o', 's' and 'n' respectively. Benzene, pyridine and furan can be represented respectively by the SMILES c1ccccc1, n1ccccc1 and o1cccc1. Bonds between aromatic atoms are, by default, aromatic although these can be specified explicitly using the ':' symbol.

4. Isomeric and chiral SMILES

Isomeric configuration indicated by forward "/" and backward "\" slashes.
Chirality is indicated by the "@" symbol.

Examples of Application on Some Molecules

Molecule	Structure	SMILES Formula
Dinitrogen	N≡N	N#N
Methyl isocyanate (MIC)	CH₃–N=C=O	CN=C=O
Copper(II) sulfate	Cu²⁺ SO4^2-	[Cu+2].[O-]S(=O)(=O)[O-]
Oenanthotoxin (C₁₇H₂₂O₂)		CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO
Pyrethrin II (C₂₂H₂₈O₅)		COC(=O)C(\C)=C\C1C(C)(C)[C@H]1C(=O)O[C@@H]2C(C)=C(C(=O)C2)CC=CC=C
Aflatoxin B1 (C₁₇H₁₂O₆)		O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5
Glucose (glucopyranose) (C₆H₁₂O₆)		OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1
Bergenin (cuscutin) (a resin) (C₁₄H₁₆O₉)		OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2
A pheromone of the Californian scale insect		CC(=O)OCCC(/C)=C\C[C@H](C(C)=C)CCC=C
2S,5R-Chalcogran: a pheromone of the bark beetle Pityogenes chalcographus ^[2]		CC[C@H](O1)CC[C@@]12CCCO2
Vanillin		O=Cc1ccc(O)c(OC)c1
Melatonin (C₁₃H₁₆N₂O₂)		CC(=O)NCCC1=CNc2c1cc(OC)cc2
Flavopereirin (C₁₇H₁₅N₂)		CCc(c1)ccc2[n+]1ccc3c2Nc4c3cccc4
Nicotine (C₁₀H₁₄N₂)		CN1CCC[C@H]1c2cccnc2
Alpha-thujone (C₁₀H₁₆O)		CC(C)[C@@]12C[C@@H]1[C@@H](C)C(=O)C2
Thiamin (C₁₂H₁₇N₄OS⁺) (vitamin B1)		OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2