Preparing and Running JChem's Batch Files and Shell Scripts

Version 5.0.3

Software Requirements

In order to run the applications in the JChem package Java Virtual Machine version 1.4.2 or later has to be installed.

JChemManager (jcman) has more requirements. See the Administration Guide for details.

Setting Environmental Variables

Some environmental variables should be set manually.

How to set environment variables ?

Windows:

Under Windows these variables can be set from the Control Panel. For example in the case of Windows XP:
Start menu -> Control panel -> System-> Advanced -> Environment variables
After changing the environment variables a new console (Command Prompt) should be opened so the changes can take effect.

To check the current setting of an environment variables, type "set" in the console. To print a specific variable type "echo %VARIABLE_NAME%".

Linux / UNIX:

The variables are usually set in a profile file for the used shell (e.g. ".bash_profile").

To check the current setting of an environment variables, type "set" in the console. To print a specific variable type "echo $VARIABLE_NAME".

PATH

Including the <JChem home>\bin directory of your JChem installation in the PATH variable allows you to start these programs from other directories of your system.
Under Windows you also have to set JCHEMHOME for this functionality (see below).

CLASSPATH / JDBC driver

To allow database access for JChem applications, the appropriate JDBC driver should be included in the CLASSPATH environment variable (create this variable if not already present). This is usually a .jar file, which is either distributed with the database, or can be downloaded from the vendor's site. Please note, that the actual file should be listed in the CLASSPATH, not the directory that contains it.

JCHEMHOME (Windows only)

In the case of Windows, if you would like to call the batch files from directories other than <JChem home>\bin, you should inform these files about the location of JChem by setting the JCHEMHOME environment variable. The variable should point to the JChem installation directory, e.g.: "C:\jchem". Warning! If the name of a directory contains spaces, use the short form in the definition of JCHEMHOME (e.g Progra~1 for Program Files).

UNIX Shell Scripts and Windows Batch Files in JChem

Since running Java classes directly from command line might be difficult because of the long class names and the necessary setting of the classpath, JChem is supplied with batch files and shell scripts that simplify this task. These files can be found in the <JChem home>/bin directory.

Command Name Function

compr Compr Diversity/dissimilarity calculations for comparing compound libraries and individual compounds in a set.

crview CreateView Composing a new SDfile from an SDfile and a data table. It is useful for viewing the results of clustering.

cxcalc Calculator Performs chemical calculations by invoking calculator plugins.

evaluate Chemical Term Evaluator Evaluates chemical terms.

fragment Fragmenter Creates molecule fragments by applying predefined cleavage rules.

fragstat Fragment Statistics Creates fragment statistics from the output of Fragmenter.

generatemd GenerateMD Generates molecular descriptor for molecular stuctures.

hitstatistics HitStatistics Statistics about the performance of parametrized dissimilarity metrics when used for screening.

jarp Jarp Clustering by a modified Jarvis-Patrick method.

jcman JChemManager Administration of structure tables

jcsearch Search Substructure searching in structure files from command line.

libmcs LibMCS Maximum Common Substructure based hierarchical clustering.

molconvert MolConverter Interconverting various file formats

msketch MarvinSketch Drawing molecules

mspace MarvinSpace High performance 3D visualization

mview MarinView Displaying structure files

nneib NNeib Nearest neighbor search for creating input for Jarp.

optimizemetrics OptimizeMetrics Optimization of molecular descriptor dissimilarity metrics for enhancing screening selectivity.

pmapper PMapper Perceives pharmacophoric point types and maps them to atoms.

react Reactor Simulates chemical reactions.

screeningoptimizer ScreeningOptimizer Virtual screening optimizer (combination of optimizemetrics and hitstatistics).

screenmd ScreenMD Performs virtual screening of large compound libraries using various molecular descriptors.

standardize Standardizer Brings molecules to standardized form based on XML configuration.

ward Ward Clustering by Ward's hierarchic clustering method using the RNN approach.

Command	Name	Function
`compr`	Compr	Diversity/dissimilarity calculations for comparing compound libraries and individual compounds in a set.
`crview`	CreateView	Composing a new SDfile from an SDfile and a data table. It is useful for viewing the results of clustering.
`cxcalc`	Calculator	Performs chemical calculations by invoking calculator plugins.
`evaluate`	Chemical Term Evaluator	Evaluates chemical terms.
`fragment`	Fragmenter	Creates molecule fragments by applying predefined cleavage rules.
`fragstat`	Fragment Statistics	Creates fragment statistics from the output of Fragmenter.
`generatemd`	GenerateMD	Generates molecular descriptor for molecular stuctures.
`hitstatistics`	HitStatistics	Statistics about the performance of parametrized dissimilarity metrics when used for screening.
`jarp`	Jarp	Clustering by a modified Jarvis-Patrick method.
`jcman`	JChemManager	Administration of structure tables
`jcsearch`	Search	Substructure searching in structure files from command line.
`libmcs`	LibMCS	Maximum Common Substructure based hierarchical clustering.
`molconvert`	MolConverter	Interconverting various file formats
`msketch`	MarvinSketch	Drawing molecules
`mspace`	MarvinSpace	High performance 3D visualization
`mview`	MarinView	Displaying structure files
`nneib`	NNeib	Nearest neighbor search for creating input for Jarp.
`optimizemetrics`	OptimizeMetrics	Optimization of molecular descriptor dissimilarity metrics for enhancing screening selectivity.
`pmapper`	PMapper	Perceives pharmacophoric point types and maps them to atoms.
`react`	Reactor	Simulates chemical reactions.
`screeningoptimizer`	ScreeningOptimizer	Virtual screening optimizer (combination of `optimizemetrics` and `hitstatistics`).
`screenmd`	ScreenMD	Performs virtual screening of large compound libraries using various molecular descriptors.
`standardize`	Standardizer	Brings molecules to standardized form based on XML configuration.
`ward`	Ward	Clustering by Ward's hierarchic clustering method using the RNN approach.

Setting Options in the batch files and scripts

At the beginning of each startup file there are some editable variables with some explanation text.

The following two options are present in every script:

HEAP_LIMIT: specifies the maximum amount of memory that can be allocated by the application in megabytes. (This corresponds to the "-Xmx" JVM option.)
SERVER_MODE: if set to "true", the application startup and initial speed will be slower, but long calculations will perform better due to more extensive runtime optimization. (This corresponds to the "-server" JVM option.)

The shell scripts (under Linux-like command prompts) can also accept JVM options beginning with "-X" and the "-server" / "-client" options as an argument. Example:

    jcman -Xmx200m -server [additional arguments]

This overrides the default settings in the script.