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Course, academic year 2023/2024
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Chemical Informatics II - MC270P75
Title: Chemická informatika II
Czech title: Chemická informatika II
Guaranteed by: Department of Organic Chemistry (31-270)
Faculty: Faculty of Science
Actual: from 2018
Semester: winter
E-Credits: 2
Examination process: winter s.:
Hours per week, examination: winter s.:1/1, C [HT]
Capacity: unlimited
Min. number of students: 3
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech, English
Note: enabled for web enrollment
Guarantor: doc. RNDr. Jindřich Jindřich, CSc.
Teacher(s): doc. RNDr. Jindřich Jindřich, CSc.
Annotation -
Last update: doc. RNDr. Jindřich Jindřich, CSc. (01.09.2022)
The aim of the course is to explain the basics of programming in scripting languages (Python, Javascript, Povray) in solving chemical problems. Topics discussed: Source code revision control systems (GIT). Python programming language, software processing of data files (.xls, .csv, .txt, .xml, .html), SQL databases, chemical structure formats (SMILES, mol, InChI, cml, ...) an their conversion, substructure searching. Using numpy, matplotlib with Jupyter for statistical calculations and for the graph generation. Using Povray for the preparation of graphics and animations. Using Django framework to create web applications.
Literature -
Last update: doc. RNDr. Jindřich Jindřich, CSc. (01.09.2022)

https://dl2.cuni.cz/course/view.php?id=2161

Git http://progit.org/
Python http://python.org
R http://www.r-project.org, http://www.r-project.cz
SQL http://www.w3schools.com/sql/default.asp, http://www.amazon.com/dp/0980455251/
Povray http://povray.org
Django http://www.djangoproject.org
Jupyter https://jupyter.org/


J.Gasteiger, T. Engel: Chemoinformatics: A Textbook 
http://www.amazon.com/Chemoinformatics-Textbook-Johann-Gasteiger/dp/3527306811
Requirements to the exam -
Last update: doc. RNDr. Jindřich Jindřich, CSc. (24.10.2019)

To pass the course, students have to successfully solve the practical exercises for each lecture.
Syllabus -
Last update: doc. RNDr. Jindřich Jindřich, CSc. (01.09.2022)

1. Source code management
- overview of used systems - CVS, SVN, GIT, MERCURIAL ...
- GIT, practical examples of use

2. Python programming language - introduction
- working with command line 
- object-oriented approach
- basic usage - processing of text files (.txt, .csv, ..)
- testing

3. Working with HTML and XML files in Python
- Python functions for internet communication
- automatic download of pages/files from web pages
- extraction of data from html page
- xml files, structure and usage

4. Python and SQL databases
- overview of used SQL systems
- Python DB API
- Work with data

5. Chemically oriented tasks in Python
- chemical structural formats (SMILES, MOL, InChI, InChIKey, cml, ...)
- Python libraries for working with chemical structures (openbabel, inchi)

6. Using Python for statistical calculations and graph generation
- import data files
- interleaving functions
- visualization - graphs

7. Use of Povray for the preparation of professional quality graphics and animations
- Povray scripts for creating 3D graphics (Ray-tracing)

8. Web applications - introduction
- Python library functions for web server creation
- overview of Python web frameworks (Zope, Pylons, Django, Flask, ...)
- servers providing chemical services

9. Creating web applications with Django
- Introduction to Django framework
- template language
- linking scripts to a web application

10. Web application, JavaScript and jQuery
- creation of user-friendly AJAX applications

11. Testing of web applications
- Selenium
- Django tests
 
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