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Tag: bioclipse

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Bioclipse Scripting Language

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Egon Willighagen

Search OpenTox data sets by title. (1)

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Use of an OpenTox ontology server to find data sets with a particular string in the title, such as 'EPA' as in this case.

Created: 2010-11-14 | Last updated: 2010-11-14

Credits: Egon Willighagen

Bioclipse Scripting Language

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Egon Willighagen

Calculate molecular descriptors with OpenT... (1)

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Queries an OpenTox ontology server for available molecular descriptor, picks one, and calculates the descriptor value for a few molecules.

Created: 2010-10-30 | Last updated: 2010-10-30

Credits: Egon Willighagen

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De maas

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filter a sdfile by a list of ids, keep in memory

Created: 2010-10-05 14:40:24 | Last updated: 2010-10-05 14:40:26

Credits: De maas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

In order to speedup a second run keep the sd-file in memory. So use a list in stead of a iterator which reads from disk.

File type: JavaScript

Comments: 0 | Viewed: 25 times | Downloaded: 19 times

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De maas

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filter a sdfile by a list of ids

Created: 2010-10-05 11:17:35 | Last updated: 2010-10-05 11:18:37

Credits: De maas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Used an array to hold the ids but I'm curious if there is a better way like a (sorted) list or an index file.

File type: JavaScript

Comments: 0 | Viewed: 29 times | Downloaded: 20 times

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Bioclipse Scripting Language

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Egon Willighagen

Visualize the boiling point data from the ... (1)

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Downloads the RDF data from a HTML page, extracts the boiling point data, calculates atom counts from SMILES representations, and opens the data in a matrix editor, ready to be visualized in a scatter plot.

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: Egon Willighagen

Bioclipse Scripting Language

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Egon Willighagen

Count the number of MetaPrint2D predicted ... (1)

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MetaPrint2D (doi: 10.1186/1471-2105-11-362) is used to calculate the number of red, orange, and green markers that indicate how likely an atom in the drug is metabolized (read the paper for the fine prints). It counts them for each molecule and reports them, as a set of three molecular descriptors that could potentially correlate with how well the molecule is metabolized (hypothesis).