jlogP: a Hydrophobicity and Molecular Formula Calculator Applet

JlogP is a java applet the calculates two important properties of small molecules:

Molecular Formula: the number of atoms of each element present in the molecule as well as the molecule's overall charge.
Hydrophobicity expressed as logP: this is the calucalted logarithm of the octanol/water partition coefficient of the molecule. The higher the logP, the more hydrophobic the molecule. Note that the logP values calculated by jlogP are very approximate. They are intended for teaching purposes only and not for research or development. See below for other, professional-grade logP calculation programs.

JlogP requres that the molecule's structure be submitted in three different formats simultaneously: SMILES, jme, and MDL molfile. These three input formats are most easily provided by JME: the Java Molecule Editor applet. JME is a very user-friendly molecular drawing applet that can be used in a wide variety of web-based applications. Peter Ertl, the author of JME has generously made the JME applet available for free; see the JME website for details. A sample page using jlogP and JME can be found here.

You can create your own custom jlogp-JME website based on this sample page or use it as is. See below for instructions.

System Requirements
JlogP requires the latest version of the Java Virtual Machine (jvm); this is available for free for most platforms (Windows 98 and above; UNIX/Linux; Mac OS X); it is not possible to run jlogP on Mac Classic (OS 9.2 or lower).

Useful Downloads and Instructions:

A lab exercise that uses jlogP to teach structure-hydrophobicity relationships. For a Microsoft Word version of this file, contact Brian White.
A paper describing the use of jlogP in a teaching lab and a preliminary assessment of learning outcomes from the lab.
A .tar.gz archive of jlogp and a sample website that uses jlogP. Note that you will have to obtain jme separately in order to set up your own jlogP-JME website. Note: if you teach a class using jogP, you are strongly advised to set up your own website for the following reasons:
- You may want to customize the web page to your class.
- I may update my site without warning.
- My server may be down without warning.
To set up your own jlogP-JME website, you should:
1. Obtain JME from Peter Ertl.
2. Download and un-compress the archive described above.
3. Put all three files (jlogp.jar, JME.jar, and test.html) in the same directory on your web server.
4. Make a link to test.html on your course website.
A .tar.gz archive of the JlogP Source Code. This is only useful if you want to modify jlogP and compile it yourself. There are three files in this archive:
- jlogp.java: the jlogp applet itself. This contains the code that determines the hybridization, aromaticity, and neighbors of each atom in the molecule as well as calculating the formula and overall logP.
- Atom.java: an individual atom. This contains the code that categorizes the atom into one of the 90+ types.
- AtomSpec.java: this is a data-carrying object that is passed from Atom to jlogp.
You can build your own version of jlogP as follows (I'd appreciate if you let me know the changes you make so that I might be able to use them myself):
1. Download and un-compress the source files described above into a specific directory. Do all the remaining steps in this directory.
2. Modify them as needed.
3. Compile them (for this, you'll need a java compiler): javac jlogp.java Atom.java AtomSpec.java
4. Put them in a jar-file: jar -cvf jlogp.java *.java
5. Move jlogp.jar into the proper directory on your web server.

Hydrophobicity Calculations: The details:
This software has been developed for use in teaching Introductory Biology at the college level. As a result, it lacks some of the features of similar tools that have been developed for professionals. The important features and limitations of jlogP are listed below:

Allowed structures: Structures using C, N, H, O, P, S, and the halogens are allowed with the following limitations (jlogP will issue a warning if you attempt to calculate the properties of an 'illegal' structure):
- Carbon atoms can make only 4 covalent bonds and cannot be charged.
- Nitrogen atoms can make 3 or 4 covalent bonds (except in the case of NO₂ where they can make 5 covalent bonds); nitrogens can be (+)-charged; (-)-charged N's are not allowed.
- Oxygen atoms can make 1 or 2 covalent bonds; oxygens can be (-)-charged but not (+)-charged.
- Sulfur atoms can make 2 covalent bonds (or 6 as in a SO₂ group); they cannot be charged.
- Phosphorus atoms can make 5 covalent bonds only (as in a PO₄ group).
logP calculation method: jlogP uses a modified version of the atom-additive methods used by Wang et al. (J. Chem. Inf. Comput. Sci. 1997, 37, 615-21 and Perspectives in Drug Discovery and Design 2000: 19, 47-66) in their xlogp software. Briefly, both programs categorize each atom in the molecule into one of 90+ types based on the element, its hybridization, and its neighbors. Each type has a characteristic contribution to the overall logP of the molecule. xlogP sums the individual atom contributions and applies 10 correction factors that take larger scale effects into account. jlogp 1.1 does not apply these correction factors; future versions may.
Charged groups: The only charged groups allowed by jlogP are N+ and O-. Because the logP of charged groups is highly dependent on pH, jlopP's logP estimates for charged molecules are very approximate.

Other software for calculating logP: there are several other programs that can calculate logP values; each has some advantages and disadvantages. The table below summarizes this information:

Program	Input format(s)	Platforms Supported	Cost	Charged Structures?
clogP	SMILES	UNIX/Linux	Yearly License fee	No
xlogp	SYBYL molfile	Any (available as source code).	Free	No.
EPISUITE	SMILES	Windows 98 and above	Free	No
Marvin	Drawing program included	Any (java applet)	Yearly License fee	Yes (also pKa)