XML

 

XML is a document markup language for defining structured information. It is a language used by computers to define hidden information about the structure of a document.


To learn more about the XML, you can click here.


There are three type of XML . There are xml table, xml tree and xml documentation.

For the class today, we are ask to find the xml tree and xml documentation for the given xml table:

Molecular Mechanis	Semi Empirical	Ab initio
Very Fast Speed	Fast Speed	Slow Speed
restriction parameter	Good accuracy	Very Good accuracy
very good protein modelling	Good protein modelling	Best protein modelling

This is the xml tree:

This is the xml documentation:

PDB

Protein Data Bank (PDB) format is a standard for files containing atomic coordinates. It is used for structures in the Protein Data Bank and is read and written by many programs.

First, to do the structure of the Protein Data Bank, we have to go to here.

Then, search the structure you want to find.

Then, click on the download link on the structure.

This is the Crystal structure of Bacillus subtilis Lon N-terminal domain.

This is the classification of the structures:

Higher order taxa	Domain: Bacteria, phylum: Firmicutes, class: Bacilli, order: Bacillales, family: Bacillaceae (Entrez Genome Project)
Genus	Bacillus subtilis

SMILES

The simplified molecular input line entry specification or SMILES is one of the topic in the chemsketch.
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-dimensional models of the molecules.

 exercise 1

exercise 2

exercise 3

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+ SO42-	[Cu+2].[O-]S(=O)(=O)[O-]

CHEMSKETCH

ACD/ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. Use it to produce professional looking structures and diagrams for reports and publications. 

Features

• Draw and view structures in 2D, or render in 3D to view from any angle
• Draw reactions and reaction schemes, and calculate reactant quantities
• Generate structures from InChI and SMILES strings
• Generate IUPAC systematic names for molecules of up to 50 atoms and 3 ring structures
• Predict logP for individual structures
• Search for structures in the built-in dictionary of over 165,000 systematic, trivial, and trade names

To download the ACD/Chemsketch software click here

To learn how to use the chemsketch , you can click here 

Below is the exercise that i have done in class:

exercise 1

exercise 2

exercise 3

exercise 4

exercise 5

Input/Output Formats

The ACD/ChemSketch interface, when coupled with the ACD?ChemBasic set of tools, provides a wide array of supported formats.

Format Name	File Extension	Comment
ACD/Labs Structure	*.sk2	ACD/Labs standard format for structures and reports
Adobe Acrobat	*.pdf	Adobe portable document format (PDF)
MDL molfile	*.mol	Industry standard for molecular structures
ChemDraw	*.chm	ChemDraw version 4.0 & earlier, from CambridgeSoft
ChemDraw	*.cdx	ChemDraw version 4.0 & later, from CambridgeSoft
SMILES		Generates Structure from SMILES or SMILES from structure

EXCEL

Excel is an electronic spreadsheet program that can be used for storing, organizing and manipulating data. 

When you look at the Excel screen you see a rectangular table or grid of rows and columns. The horizontal rows are identified by numbers (1,2,3) and the vertical columns with letters of the alphabet (A,B,C). For columns beyond 26, columns are identified by two or more letters such as AA, AB, AC.

The intersection point between a column and a row is a small rectangular box known as a cell. A cell is the basic unit for storing data in the spreadsheet. Because an Excel spreadsheet contains thousands of these cells, each is given a cell reference or address to identify it. The cell reference is a combination of the column letter and the row number such as A3, B6, AA345. 

In my class last month, i have been introduce to the new function in excel that is scatter plot.

Scatter Plot Graphs

       Scatter plot graphs are used to show trends in data. They are especially useful when you have a large number of data points. Like line graphs, they can be used to plot data recorded from scientific experiments, such as how a chemical reacts to changing temperature or atmospheric pressure.

      Whereas line graphs connect the dots or points of data to show every change, with a scatter plot you draw a "best fit"line. The data points are scattered about the line. The closer the data points are to the line the stronger the correlation or affect one variable has on the other.

      If the best fit line increases from left to right, the scatter plot shows a positive correlation in the data. If the line decreases from left to right, there is a negative correlation in the data. 

      Below is the link on how to make the scatter plot in excel:

        scatter plot in excel

      The scatter plot will be like shown below:

 The difference between scatter chart and line chart in excel are as follow:

TYPE	SCATTER CHART	LINE CHART
Axis Value Variable Type	Continuously Variable Numeric Values	Non-Numeric Attributes (even if numbers are used)
Axis Scale Limits	Adjustable	Fixed
Stacked Series	Not Supported	Supported

Below is one of the picture of exercise that i have done in class in scatter plot:

 

 exercise 1