JChemExtensions

About KNIME

KNIME, pronounced [naim], is a modular data exploration platform that enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models. KNIME was developed (and will continue to be expanded) by the Chair for Bioinformatics and Information Mining at the University of Konstanz, Germany. The group headed by Michael Berthold is also using KNIME for teaching and research at the University.

Nodes of JChem Extensions

JChem Extensions: Base
Extension	Node
Converter	MrvConverter
	MrvToMol2Converter
	MrvToPdbConverter
	MrvToSdfConverter
	MrvToSmilesConverter
	MrvToStringConverter
IO	MarvinSketch
	MolExporter
	MolImporter
	PdbImporter
Visualizer	MarvinSpace
	MarvinTable
	MarvinView
JChem Extensions :Option
Extension	Node
Database	JChemCartridge
	JChemManager
	JChemSearch
	JChemUpdata
Manipulator	Calculator Plug-ins	Partitioning	LogD
			LogP
		Protonation	IsoelectricPoint
			MajorMicrospecies
			pKa
		Elemental Analysis
		IUPAC Name
	ChemicalTerms
	LibraryMCS
	MolSearch
	RGroupDecomposition
	Standardizer

* These nodes may not include all function of original tools. Please contact us or refer brochure.
* In using JChem Extensions, user needs formal license of ChemAxon separately.
　

Details of JChem Extensions Nodes

Base
Converter Extension
These nodes convert "Molecule Data Type" between JChemExtensions and the third parties (e.g. Schrodinger, CDK, etc).It’s necessary to convert to “Molecule Data Type" which the third parties can recognize when user pass the structure information to the nodes of third party from JChemExtensions. And vice versa. Each third party defines its "Molecule Data Type” which recognizes the structure information on the KNIME platform. The "Molecule Data Type" of JChemExtensions is "MrvCell"
	MrvConverter Convert "Molecule Data Type" of the third parties to "MrvCell" which JChemExtensions recognize.
	MrvToMol2Converter Convert "Molecule Data Type" of JChemExtensions to "Mol2Cell" for the third parties which recognize "mol2" format.;
	MrvToPdbConverter Convert "Molecule Data Type" of JChemExtensions to "PdbCell" for the third parties which recognize "PDB" format.
	MrvToSdfConverter Convert "Molecule Data Type" of JChemExtensions to "SdfCell" for the third parties which recognize "SD" or "SDF" format.
	MrvToSmilesConverter Convert "Molecule Data Type" of JChemExtensions to "SmilesCell" for the third parties which recognize "SMILES" format.
	MrvToStringConverter Convert "Molecule Data Type" of JChemExtensions to "StringCell" for the third parties which recognize "string" format.

IO Extension
These nodes are for input and output of the structures on the KNIME platform. Whereas the nodes in Converter convert "Molecule Data Type" between the third parties and JChem Extensions, the MolImporter and MolExporter in IO can import/export the structure file (SDF, SMILES.etc..) directly. It is also possible to sketch structures on the Knime even if you have no structure file.
	MarvinSketch Chemical editor for drawing chemical structures, queries and reactions. Allow to sketch molecular structure in the dialog. Upon execute, the structure is available in the output table. "Molecule Data Type" defines "MrvCell".
	MolExporter The output file format can be specified as an argument with this node. Many different output file formats are supported "mol", "sdf", "smiles", "png", "jpeg", etc.
	MolImporter The input file format is guessed automatically. Many different formats are supported like "mol", "rgf", "sdf", "rdf", ", "mrv", "smiles", "pdb", "xyz". MolImporter can also import gzip compressed and base64 encoded structures.
	PdbImporter Imports biochemical data from PDB file. Complex information defined by the PDB file is maintained. MolImporter can also import PDB file, but it does not recognize complex information.
Visualizer Extension
These nodes achieve high-quality structural visualization by using ChemAxon's tool on the Knime platform.
	MarvinSpace Using MarvinSpace you can visualize small molecules, proteins, nucleic acids, crystals, various molecular surfaces, molecular orbitals as well as volumetric data such as electrostatic potential, hydrophobicity. Manual overlay of structures and manual change of internal coordinates are also available.
	MarvinTable Load multiple molecules from a data and displays them in a regular two-dimensional tables of cells.
	MarvinView Load multiple molecules from a data and displays them in a scrollable viewer.

Option
Database Extension
These nodes connect to the relational database from the Knime platform
	JChemCartridge Connecting to JChemCartridge for Oracle, it is available for the structure search (substructure, exact match and similarity). Searching is carried out in Oracle.
	JChemManager It is possible to connect to relational database by JDBC from Knime. (MS Access, MySQL, etc.)
	JChemSearch The structure search can be carried out through the relational database with JChemManager. The searching is on Knime.
	JChemUpdata It is possible to upload structures into relational database (MySQL, MS Access, etc.)
Manipulator Extension
A variety of ChemAxon's tools can be executed on the Knime platform.
	LogD Calculate "logD" using ChemAxon Plugins
	LogP Calculate "logP" using ChemAxon Plugins
	IsoelectricPoint Calculate "IsoelectricPoint" using ChemAxon Plugins
	MajorMicrospecies Calculate "MajorMicrospecies" using ChemAxon Plugins.
	pKa Calculate "pKa" using ChemAxon Plugins
	Elemental Analysis Calculate elemental properties using ChemAxon Plugins （Mass, Exact Mass, Formula, Isotope formula, Dot-disconnect formula, Composition, Isotope compositionAtomCount）
	IUPAC Name Generate "IUPAC Name" using ChemAxon Plugins
	ChemicalTerms Calculate some properties using ChemAxon Plugins. The combination of two or more expressions is possible.
	Fragmenter Fragmenter cleaves single bonds to generate molecular fragments. The cleavage rules correspond to chemical reactions in order to enhance synthetic accessibility. The cleavage points on the fragments are labeled with the cleavage rules.
	LibraryMCS LibraryMCS computes the maximum common substructure (MCS) of a set of compounds.
	MolSearch The substructure search on Knime platform
	RGroup Decomposition R-group decomposition is a special kind of substructure search that aims at finding a central structure - scaffold - and identify its ligands at certain attachment positions. The query molecule consists of the scaffold and ligand attachment points represented by R-groups.
	Standardizer Standardizer is a structure canonicalization tool in JChem for converting molecules from different sources into standard representational forms. Standardizer can automate the identification of mesomers and tautomers and can be used for counter-ion removal.

System requirement

KNIME 1.3.1or later.
ChemAxon's License and products.
Other resources.

The 'knime_chemistry_types_feature' plug-in is at least necessary to run the JChem extension.
KNIME Downloads
KNIME Chemistry Extension

Evaluation version and free academic package

Evaluation version
Academic package (JChem Extensions: Base)

How to get

Download : Evaluation version

We are ready for the evaluation version for customer's considering the purchase of it.
After downloading the program, you need to inquire the evaluation license code by e-mail. Please send us the following information. After confirmation of those information, we will send you the evaluation license which you can use JChem Extensions for two months maximally.

Download (Evaluation Version) Order Evaluation License

[Contact info]

info-science@infocom.co.jp
Chem & Bio Informatics Department
Infocom Corporation

[Necessary information for license]

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