Some useful features are available only as additional Webservices, such as the 2D structure cleanup. For this, unfortunately a separate Tomcat server has to be set up, which is fairly heavy weight, but instructions for this are provided further below, as well.
The Marvin JS distribution is available in the .zip
archive format.
unzip marvinjs-16.1.11.1-all.zipNext, define a shell environment variable called
MARVIN_JS_PATH and set
it to the absolute path of the directory containing editor.html file. It is best to do this in one
of the user's shell init scripts such as .cshrc or .login. For
example, in csh syntax:
setenv MARVIN_JS_PATH /example/of/full/marvinjs/pathFor Mac OS X, you have
bash as your default shell, so you'd want to add the following to your .bashrc file:
export MARVIN_JS_PATH=/example/of/full/marvinjs/pathThe license file has to be placed in the directory indicated by MARVIN_JS_PATH , according to the instructions that ChemAxon supplies.
C:\Program Files\ChemAxon\Marvin).
Next, you need to create an environment variable called
MARVIN_JS_PATH, and set it to the absolute directory path, in
which the file editor.html was installed. To do so:
right-click on the "My Computer" icon (on the desktop), and choose
"Properties". In the window that opens click on the "Advanced" tab,
then click on the "Environment Variables" button. A window like the
one depicted in the Figure below will open.
Under "System Variables", click the "New" button and type
MARVIN_JS_PATH for the Variable name, and the absolute
path of the editor.html file for the Variable value, as
seen in the Figure below.
The license file has to be placed in the directory indicated by MARVIN_JS_PATH , according to the instructions that ChemAxon supplies.
.zip archive format. Unzip the downloaded file into a
newly created local directory.
The license file has to be placed into a directory under the home directory of the user's account. This is very likely the same license as used above for Marvin JS, but it is another copy (and with a different name, according to the instructions that ChemAxon supplies). As an example for UNIX and Mac OS X, the appropriate directory can be created at a terminal like this:
mkdir -p ~/.chemaxon/licenses/
.zip archive format. Unzip the downloaded file.
JRE_HOME has to refer to the absolute path of the directory of the Java Runtime installation.
CATALINA_HOME has to refer to the absolute path of the directory of the Tomcat installation.
CATALINA_OPTS should contain a string of options
recommended by the Webservices installation instructions.
MARVIN_JS_PATH above,
these additional 3 definitions should go into one of the init shell scripts
of the user. The following are examples of what this should look
like:
In csh syntax:
setenv JRE_HOME /usr/lib/jvm/jre1.8.0_101 setenv CATALINA_HOME /homedir/brg/bio/software/apache-tomcat/apache-tomcat-8.5.4 setenv CATALINA_OPTS "-Xmx1500m -Djava.awt.headless=true"In bash syntax (for Mac OS X):
JRE_HOME=/usr/lib/jvm/jre1.8.0_101 export JRE_HOME CATALINA_HOME=/homedir/brg/bio/software/apache-tomcat/apache-tomcat-8.5.4 export CATALINA_HOME CATALINA_OPTS="-Xmx1500m -Djava.awt.headless=true" export CATALINA_OPTSThen, copy the file
webservices.war from the installation directory of
the Webservices to the directory $CATALINA_HOME/webapps/
, to make the Webservices code available to Tomcat, when the server
starts up.
By default, Tomcat exposes its server on port 8080 . However, if this
would cause a collision with another existing service on the same
port, then the port should be changed to a different number. To do
this, search for 8080 in the file
$CATALINA_HOME/conf/server.xml and edit this file. When
invoking Marvin JS from Pathway Tools, this file will serve as the
authoritative source of the port number needed to interact with the
Webservices.
JRE_HOME and CATALINA_HOME environment
variables, then the Tomcat server will be launched. This server will
thereafter stay up and running, to avoid having to repeat the heavy
weight launching.