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

MAPLE

      

  Maple is a very powerful computer algebra system used by students, educators, mathematicians, statisticians, scientists, and engineers for doing numerical and symbolic computations. Maple is a software package for doing mathematics. Maple can perform both symbolic and numerical computations, and Maple can draw nice pictures.

          Maple is a tool to help you learn, discover, and do mathematics. Maple is a very versatile tool; it is used for teaching math courses all the way from high school algebra and trigonometry up to graduate level math, physics, and engineering courses. Maple is also used extensively for doing research in each of these fields. 

         These worksheets are a tool to help you learn and discover how to use Maple. Each worksheet contains explanations of Maple commands, examples of the use of the commands, and exercises that you are asked to do right in the worksheet. The best way to use these worksheets is to download one of them to your computer, use Maple to open the worksheet, and then "work your way through the worksheet". By this I mean, read the explanations, execute the Maple commands, look carefully at the output of each command and give that output some thought, do the exercises that are in the worksheets, and finally, and most importantly, play around with the content of the worksheet, modify some of the commands and re-execute them, use the help system to look up more information about the commands, enter your own commands into the worksheet, etc. In short, use all the interactive features of the Maple interface to explore Maple. This ability to play around with the content of each worksheet is what makes Maple, and other computer programs like it, a new way to learn mathematics. Maple worksheets are a kind of interactive textbook, something that we will all be seeing much more of in the near future.


What is MAPLE?

• Maple is a procedural programming language. It also includes a number of functional programming constructs. If you have written programs in Basic, Pascal, Algol, C, Lisp, or Fortran, you should be able to write numerical programs in Maple very quickly.
• Maple is not strongly typed like C and Pascal. No declarations are required. Maple is more like Basic and Lisp in this respect. However types exist. Type checking is done at run time and must be programmed explicitly.
• Maple is interactive and the programming language is interpreted. Maple is not suitable for running numerically intensive programs because of the interpreter overhead. Though it is suitable for high-precision numerical calculations and as a tool for generating numerical codes. 

 To learn how to use the maple programming, you can go to maple

Below are the function in four mathematics software:

SOFTWARE	FUNCTION
Mathematica	is the premier all-purpose mathematical software package. It integrates swift and accurate symbolic and numerical calculation, all-purpose graphics, and a powerful programming language. It has a sophisticated ``notebook interface'' which is great for documenting and displaying work.It can save individual graphics in any graphics format. Its functional programming language (as opposed to procedural) makes it possible to do complex programming using very short concise commands; it does, however,allow the use of basic procedural programming constructs like Do and For.
Matlab	Matlab combines efficient computation, visualization and programming for linear-algebraic technical work and other mathematical areas.It is widely used in the Engineering department.
Maple	Maple is powerful analytical and mathematical software which does the same sorts of things that Mathematica does, with similar high quality. Maple's programming language procedural -- like C or Fortran or Basic -- although it has a few functional programming constructs.
IDL	(Interactive Data Language) excels at processing real-world data, especially graphics, and has a reasonably simple syntax, especially for those familiar with Fortran or C.IDL makes it as easy as possible to read in data from files of numerous scientific data formats.IDL is very popular at NASA, universities and research facilities, and especially at C.U. where it was originally developed and is free (see site license).

Finally, don't be afraid to begin using Maple right away in any of your other math or science courses. After you do the first worksheet or two from this course, which shouldn't take more than a week, you will know enough about Maple to be able to use it to help you do calculations in many other courses. Maple also works well for producing lab reports in science courses since Maple can do calculations, plot data, graph functions, and typeset equations, all of which are useful for preparing lab reports (and many other kinds of homework assignments). If you want to use Maple for another course and you feel that you need some extra help or advice on using it, don't hesitate to ask me.