Content from the CDK-Taverna group

QSAR workflow to measure the time used for... (1)

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This workflow loads molecules from a database. Each molecule goes through the atom typing, gets its explecite hydrogens and the detection of the hueckel aromaticity. After that different qsar properties will be calculated. The output of this workflow will be a qsar vector as a csv file and a file which contains the time needed to calculate each qsar property.

Created: 2008-08-29 | Last updated: 2008-08-29

Credits: Thomasku

Reaction Enumeration Workflow (1)

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This workflow performs a reaction enumeration. Therefore it loads a generic reaction rxn file and two educt lists. This SD-Files contains molecules for the enumeration. The products of the enumerated reaction are stored as Mol Files and a PDF will be created which contains the product molecules.

Created: 2008-11-22

Credits: Thomasku

Attributions: Reaction Enumeration Workflow

Reaction Enumeration Workflow (1)

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This workflow performs a reaction enumeration. Therefore it loads a generic reaction rxn file and two educt lists. This SD-Files contains molecules for the enumeration. The products of the enumerated reaction are stored as Mol Files and a PDF will be created which contains the product molecules.

Created: 2008-11-21

Credits: Thomasku

Atom typing of molecules from database (1)

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This workflow loads molecules from a database. For each molecule the atom type gets perceived. The output of this workflow are a couple of text files. The frist text file contains all molecule id's which are loaded from the database. The second text file contains all molecules which had problems with the atom typing. This file contains the molecule id and the atom which caused the problem. The last output file, a pdf, contains all structures of the molecules which caused problems during the a...

Created: 2008-09-06

Credits: Thomasku

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Smiles Search of ChemSpider

Created: 2008-02-27 16:21:30 | Last updated: 2012-01-12 21:12:15

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 533 times | Downloaded: 242 times

Calculation of molecular descriptors for m... (1)

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This workflow loads iteratively molecules from a database. For each molecule the atom typse are perceived before the hydrogens are added and the aromaticity is detected. Than the QSAR worker calculates the selected descriptors. The result of this calculation is stored in database table.

Created: 2008-11-15

Credits: Thomasku

Topological Substructure Search Workflow (1)

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This workflow performs a topological substructure search. The molecules to be searched are loaded from a MDL SD file. The substructure is loaded from a SMILES (workflow input). The matched molecules are converted to CML and for the molecules which do not contain the substructure the InChI is generated.

Created: 2008-11-06

Credits: Thomasku

Insert Molecules into Database (1)

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This workflow reads the molecules form the an MDL SD File and stores them into a database. The database used here is a Postgres SQL database which uses the PGChem::Tigress chemoinformtic extension. To run this workflow you have to install the CDK-Taverna Plug-in for Taverna 1.7.1.0 from http://cdk-taverna.de/plugin

Created: 2008-08-29 | Last updated: 2008-08-29

Credits: Thomasku

CDK Example (1)

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This workflow reads a library from an SD file (change the default value of Read_MDL_SD_File) and identifies those structures that conform to Lipinski's Rule of Five. It then performs a substructure query, represented as SMILES (change the default value on Parse_SMILES), on the structures that pass Lipinski, and creates PNG images of those structures that contain the substructure. The image results will be found in your Taverna Data folder.

Created: 2009-02-26

Credits: Paul Dobson

Get ART2A classification result showing th... (1)

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This workflow load an ART2A classifcation results and creates a diagram showing the origin allocation within the different cluster or classes. This is usable for performing a chemical diversity analysis. The result is stored within an PDF which contains a diagram and a table of the classification result.

Created: 2008-11-17

Credits: Thomasku