Group: CDK-Taverna

Original Uploader

Thomasku

Insert Molecules into Database (v1)

Created: 29/08/08 @ 09:59:06 | Last updated: 29/08/08 @ 10:17:03

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 133 times | Downloaded: 33 times

Original Uploader

Thomasku

QSAR workflow to measure the time used for calculating different qsar properties (v1)

Created: 29/08/08 @ 13:31:12 | Last updated: 29/08/08 @ 13:40:53

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Viewed: 76 times | Downloaded: 43 times

Original Uploader

Thomasku

Atom typing of molecules from database (v1)

Created: 06/09/08 @ 11:08:44

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Viewed: 122 times | Downloaded: 24 times

Original Uploader

Thomasku

Iterative loading of molecules from database with aromaticity detection (v1)

Created: 03/11/08 @ 14:28:32 | Last updated: 03/11/08 @ 14:28:34

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow loads molecules from a database in an iterative manner using the SQL commands LIMIT and OFFSET. After the loading each molecule goes through an atom typing perception before the Hueckel Aromaticity Detector tries to detect the aromaticity. All id of the aromatic molecules will be written wo a text file.

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Viewed: 49 times | Downloaded: 15 times

Original Uploader

Thomasku

InsertMoleculesIntoDatabase (v1)

Created: 05/11/08 @ 10:30:39 | Last updated: 05/11/08 @ 10:30:40

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow load molecules into a database. The molecules originally are stored in a MDL SD file. As workflow input an origin is added to each molecule which gets stored into the database. The output of the workflow shows logs from the database insert process.

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Viewed: 44 times | Downloaded: 16 times

Original Uploader

Thomasku

Load Molecules from a database and create a PDF file showing the structures of the loaded molecules (v1)

Created: 05/11/08 @ 16:15:59 | Last updated: 05/11/08 @ 16:16:00

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow loads molecules from a database. The 2D structure of these molecules are shown within a table of a PDF document.

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Viewed: 25 times | Downloaded: 18 times

Original Uploader

Thomasku

Extraction of atom typing problems after loading of molecules from database (v1)

Created: 05/11/08 @ 17:30:38 | Last updated: 05/11/08 @ 17:30:39

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow load molecules from the database and than checks whether the perception of the atom types works or not. After the extraction of the database identifier from all molecules which caused problems during this process will the identifier be written to a file.

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Viewed: 27 times | Downloaded: 14 times

Original Uploader

Thomasku

Substructure Search On Database (v1)

Created: 06/11/08 @ 12:02:18 | Last updated: 06/11/08 @ 12:02:19

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow takes as input a SMILES. This represents the substructure, for which the database gets searched. The output of this workflow is a PDF showing the 2D structures of the matched structure from the substructure search on the database.

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Viewed: 63 times | Downloaded: 19 times

Original Uploader

Thomasku

Extract ChEBI molecules from TSV file and upload them into a database (v1)

Created: 06/11/08 @ 16:11:54 | Last updated: 06/11/08 @ 16:11:56

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This worklfow load a TSV file from the ChEBI database. (normally structures.tsv) After the extraction of the molecules from the TSV file all non MDL mol files are removed before the valid molecules are inserted into a database.

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Viewed: 31 times | Downloaded: 19 times

Original Uploader

Thomasku

Topological Substructure Search Workflow (v1)

Created: 06/11/08 @ 16:59:02 | Last updated: 06/11/08 @ 16:59:03

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 69 times | Downloaded: 15 times

Original Uploader

Thomasku

Analyse the Atom Typing Result (v1)

Created: 06/11/08 @ 22:25:29 | Last updated: 06/11/08 @ 22:25:30

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow is used to analyse the result of the atom typing workflow. It creates a pdf document contains a diagram to visualise the outcome from the atom typing test to detect the for the cdk unknown atom types.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 13 times

Original Uploader

Thomasku

Molecular Weight Distribution (v1)

Created: 07/11/08 @ 14:18:33 | Last updated: 07/11/08 @ 14:18:34

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow calculates the molecular weight of molecules stored in a postgres sql database with the Pgchem::tigress chemoinformatics cardridge. The cardridge perform the molecular weight calculation. The get a moleculear weight distribution worker creates a chart of the available data.

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Viewed: 38 times | Downloaded: 16 times

Original Uploader

Thomasku

Calculation of molecular descriptors for molecules loaded from database (v1)

Created: 15/11/08 @ 15:12:06 | Last updated: 15/11/08 @ 15:12:08

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Viewed: 68 times | Downloaded: 20 times

Original Uploader

Thomasku

ART2A Classification Workflow (v1)

Created: 17/11/08 @ 13:48:20 | Last updated: 17/11/08 @ 13:48:21

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow loads a vector from a database and performs an ART2A classification. The ART2A classificator contains various options which are changeable within the stored workflow configuration file. There is no UI for these content available.

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Viewed: 26 times | Downloaded: 11 times

Original Uploader

Thomasku

Get ART2A classification result showing the different origins of the vectors (v1)

Created: 17/11/08 @ 14:21:25 | Last updated: 17/11/08 @ 14:21:26

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Viewed: 29 times | Downloaded: 14 times

Original Uploader

Thomasku

Reaction Enumeration Workflow (v1)

Created: 21/11/08 @ 15:25:02 | Last updated: 21/11/08 @ 15:25:03

Credits: Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 34 times | Downloaded: 12 times

Original Uploader

Thomasku

Reaction Enumeration Workflow (v1)

Created: 22/11/08 @ 16:55:35 | Last updated: 22/11/08 @ 16:55:36

Credits: Thomasku

Attributions: Reaction Enumeration Workflow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 40 times | Downloaded: 14 times

Original Uploader

Paul Dobson

CDK Example (v1)

Created: 26/02/09 @ 16:31:22

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Uploader:

Paul Dobson

Smiles Search of ChemSpider

Created: 27/02/08 @ 16:21:30 | Last updated: 04/03/09 @ 10:01:13

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Rating: 4.0 / 5 (1 rating) | Comments: 0 | Viewed: 147 times | Downloaded: 4 times