SimCAL Files

SimCAL is a reaction similarity calculation tool that enables calculation of reaction similarity with multitude of parameters. Specific approach of computing reaction similarity is not efficient to find the most appropriate solution of interest. To enable the user to tune the similarity calculations with different parameters, there by analyzing different solutions will help in finding most appropriate solution.  

SimCAL is built using Java 1.7 and uses the open source libraries CDK and Ambit2.  It is protected under GNU LGPL (Lesser General Public License). 

Getting Started:
----------------

1. Installing latest Java:
--------------------------
a. Install latest version of Java from the following link
http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

b. Set JAVA_HOME and JRE_HOME environment variables appropriately to appropriate installation directories.  The details of setting the variables are available in the link : https://docs.oracle.com/cd/E19182-01/820-7851/inst_cli_jdk_javahome_t/ 
and 
https://docs.oracle.com/cd/E13222_01/wls/docs/techstart/environment.html

Note:
----
Mac OS X users need to download the latest version of JDK. Older version of JDK are not supported by Mac. For details visit: https://java.com/en/download/faq/java_mac.xml

c. Unzip SimCAL.zip file downloaded from the location (https://sourceforge.net/projects/simcal/). 

2. Special instructions for Linux and Mac users:
------------------------------------------------
a. Provide executable writes to SimCAL.sh file using the following command:
	chmod a+x SimCAL.sh
	
3. Special instructions for Mac users:
--------------------------------------
By default, the security settings of Mac Os blocks the execution of the SimCAL.jar file. To enable the execution of the tool, the Gatekeeper settings needs to be updated. The steps are illustrated in the following link (https://kb.wisc.edu/helpdesk/page.php?id=25443).
	a. Open "Apple Menu" -> "System Preferences"
	b. Click on "Security & Privacy"
	c. Select "General" tab. Click the icon labelled "Click the lock to make changes"
	d. Enter username and password into the prompt that appears, and click "Unlock".
	e. Under the section labelled "Allow applications downloaded from" -> Select "Anywhere". On prompt, click "Allow from anywhere".
	f. Exit "System preferences".
	
4. Launching SimCAL Userinterface:
------------------------------------
a. SimCAL user interface system can be launched using one of the following approaches:
	i. For windows system, double click on SimCAL.bat
	ii. For linux and other operating systems, execute the shell script in the terminal 
		./SimCAL.sh
	iii. Alternatively, the following command can be used for launching
		java -Xms1024M -jar SimCAL.jar