ChemAxon Components

Author: Szilard Dorant, Moises Hassan

Version: 1.2

Created: 2006

Modified: 03/2008

Purpose: These components provide a way to access various ChemAxon functionality from Pipeline Pilot.

Requirements: JChem 3.2, PP Server 6.1.1, Chemistry Collection, Integration Collection

O/S: Windows and Linux

Limitations:
If using JChem version 3.2.x an ArrayIndexOutOfBoundsException may arise for BCUT calculations (e.g. in the "Calculating ChemAxon Descriptors" example protocol).
A variant of JChem 3.2.12 is available that addresses this problem.
Please use the jchem.jar from this package:
http://www.chemaxon.com/download.php?dl=&d=/data/downlo...hem_3_2_12patch2.zip
Alternatively use the latest 5.0.x JChem version where there is no such problem.


Keyword: chemaxon jchem marvin chemistry substructure search calculation standardizer canonicalization reaction chemical terms microspecies bcut

Contents:

Components:

ChemAxon Calculator.xml
Chemaxon Chemical Terms Filter.xml
ChemAxon Ionize.xml
ChemAxon Reactor.xml
ChemAxon Standardizer.xml
Connection.xml
Create JChem Base Table.xml
CTAB from DB table.xml
Drop JChem Base Table.xml
Insert.xml
JChemSearch.xml
Chemaxon Ionize Molecule at pH.xml
Chemaxon MicroSpecies.xml
Chemaxon Standardize.xml
Marvin Molecule.xml
ChemAxon Molecular Table Viewer.xml
ChemAxon Reactant Tagger 1.xml
ChemAxon Reactant Tagger 2.xml
ChemAxon Reactant Tagger 3.xml
ChemAxon Reactant Tagger 4.xml
ChemAxon Reactor.xml

Protocols:

Aromatize Molecules.xml
Calculating ChemAxon Descriptors.xml
ChemAxon Microspecies Report.xml
Clustering and Visualization with BCUT Values.xml
CombiChem Reactor Example.xml
Filtering using Chemical terms.xml
JChem Base Insert and Search.xml

Installation:

1. To install, you will need access to the Pipeline Pilot server.
2. Unzip the archive and place the chemaxon folder into the root\apps folder of your Pipeline Pilot Server installation.
3. Follow the installation instructions in the README.txt file in the chemaxon folder.

See also:

Recent presentation on SciTegic UGM:
http://www.chemaxon.com/conf/Scitegic_US_UGM_Mar08.ppt

Access the protocol >