Roozbeh Sanaei Blog

The ChemNomParse project is an open source project to create a chemical nomenclature parser. The project aims to build molecules from an IUPAC chemical name and comes in two parts:

• The ChemNomParse library - which contains the core of the project and is now part of the CDK.
• Nomen - A complete program which demonstrates the library's abilities.

The project is released under the LGPL Licence by the University of Manchester.

The program currently supports:

• Carbon chains upto 99 atoms long as main chains or substituents.
• Cyclic main carbon chains.
• Limited set of organometalics.
• Following organic functional groups occuring 1,2 or 3 times:
  • Ketones
  • Amides
  • Amines
  • Aminos
  • Oxo
  • Nitrile
  • Nitro
  • 4 Halogens
  • Carboxylic Acid Chloride
  • Carboxylic Acid
  • Aldehydes
  • Alcohols
• Limited benzene rings
• Support for bond orders upto 3

At its most fundamental level, CHEMKIN software enables the simulation of complex chemical reactions. With the advanced capabilities now available, sophisticated Design-of-Ssimulations (DoSs) can be created to parametrically explore potential design solutions well before costly hardware is built.CHEMKIN evolved from its origin as a Ssandia National Laboratory combustion
code (Chemkin II) into today’s commercial-quality software suite with a user-friendly interface, best-in-class simulation speed, and unparalleled accuracy. No other chemistry simulation product is more widely validated or cited in technical peer-reviewed journals.Reaction Design offers multiple CHEMKIN products to satisfy unique requirements.
CHEMKIN-PRO™ is specifically designed for large chemical simulation applications requiring complex mechanisms. CHEMKIN-PRO’s advanced solvers and full feature set support the quick and accurate development
of models for specific applications. CHEMKIN 4 provides industry-leading simulation technology for the simulation of less complex systems at an affordable price. CHEMKIN-CFD™ extends the power of CHEMKIN into Computational Fluid Dynamics (CFD) and enables the introduction of more accurate chemistry into reacting, fluid flow simulations.

The Chemistry Development Kit (CDK) is a Java library for structural chemo- and bioinformatics. It is now developed by more than 50 developers all over the world and used in more than 10 different academic as well as industrial projects world wide.

The CDK originated in the lab of Christoph Steinbeck as a successor of his older CompChem libraries, which urgently needed a rewrite. In autumn 2000, Christoph Steinbeck, Egon Willighagen and Dan Gezelter met at Notre Dame University, South Bend, USA, to discuss the architecture of the package. On the flight back to Europe, a first draft of the data classes were written.

In the following years, the CDK library evolved into a fully blown open source and open development chemoinformatics package with code reaching from QSAR descriptor calculations to 2D and 3D model building. Programs like the 2D structure editor JChemPaint, NMRShiftDB, a database of organic molecules and their NMR spectra, and Bioclipse are based on or use the CDK. You can learn about these and others on the page Software using CDK. A full list of features is available.

Chemistry 4-D Draw is a next-generation chemistry program combining the most advanced technologies in structure drawing.

Chemistry 4-D Draw Modules

• NamExpert that understands IUPAC nomenclature rules.
• Nomenclator
• Chem4D Database
  manages databases of molecular structures, graphics and information associated with the data. It helps you to search and reuse graphics you have created.

Chem4D Graph module that creates multi-line graphs of different styles. It supports non-linear and linear curve fitting, response curve fitting and data analysis

The program allows you to create high-quality structures simply by entering molecular names. It assigns systematic names to structures. It includes a full set of tools for drawing, text and structure editing, and labeling.

Features include:

• interactive 3-D rotation
• syntax checking
• hot-key labeling
• multi-step undo
• and creating structure templates with user-defined trivial names.

Next-generation Drawing Program:

• Advanced Drawing Tools, Easy to Use!
• Chem4D Database Organizes structures and graphics
• Nomenclator Assigns IUPAC Names to Structures
• NamExpert Interprets Chemical Names
• NEW Chem4D Graph creates multi-line graphs of different styles
• NEW Assign Chirality
• OLE-2 Technology Saves You Time!
• Full Color and All Fonts!
• Object Transformations-rotate, move, scale, flip, align!
• Multipage Document!
• Export MDL MOL Files, Graphic Files!
• Internet-Ready Send/Receive Graphics via Regular E-mail!

Cross Platforms:
Windows 95/98/NT/2000/Me/XP OS/2 Macintosh Java*

Chemicalinventory is a web application that manage the chemical stock in a laboratory-, production- or other facilities, where chemicals must be safely stored, easily found and tracked. This inventory solution is currently productive at The University Of Copenhagen

The goal of our research project is to develop a versatile chemical database engine based on MySQL, servlets and JDBC. In order to test those technologies we made a molecular formula calculator.
It calculates the molecular formula, molecular mass, exact mass, elemental analysis and plots the isotopic distribution graph. Just enter a formula in the box, click the button and see the results! You can enter atoms, isotopes as well as groups. The goal is to store everything in a MySQL database and allow the users add their own groups (not implemented yet).
Some examples of syntax:

• CH3CH2Cl
• C1000H1000
• Ru2(CO)8
• RuClH(CO)(PPh3)3
• PhSiMe3
• Ph(CO)C(CH3)3
• HGlyGluTyrOH - note that aminoacids are treated as biradicals!
• HCysTyrIleGlnAsnCysProLeuGlyNH2
• HCysp(Trt)Tyrp(Tbu)IleGlnp(Trt)Asnp(Trt)ProLeuGlyNH2
• CDCl3
• [13C]Cl4
• C5(PhBu(EtCHBr)2)3
• PhNH2.HCl
• NH3.BF3
• CuSO4.5H2O
• CaSO4.1/2H2O
• CaSO4.nH2O
• RuCl3.XH2O
• {Ph,Me}Me - ie. 0.5PhMe+0.5MeMe
  

This program is the result of a collaboration between the Faculty of Chemistry of the Silesian University of Technology (Poland) and the University of Lausanne (Switzerland). ChemCalc has been presented on 5th International Electronic Conference on Synthetic Organic Chemistry.

Written by: Michal Krompiec in collaboration with Dr Luc Patiny.