myExperiment.org - Workflows - Retrieve Single Molecule from ZINC - structure and figure (Steffen Möller) [Taverna 1 Workflow]

Workflow Entry: Retrieve Single Molecule from ZINC - structure and figure

Created at: 24/08/08 @ 22:52:26 Last updated: 25/08/08 @ 21:57:16

Version 1 (of 1)

Version created on: 24/08/08 @ 22:52:25 by: Steffen Möller | Revision comments Expand

Last edited on: 25/08/08 @ 21:57:16 by: Steffen Möller

Title: Retrieve Single Molecule from ZINC - structure and figure

Type: Taverna 1

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Description

The ZINC database (http;//zinc.docking.org) is a collection of substances with known structures and some chemical characterisation that are commercially available. It is freely available and a much respected resource for computational screening for functional compounds.

With the ZINC ID at hand, the ZINC web site is contacted and from there the URL parsed the refence to the real data. This workflow does not scale for regular docking applications. One would retrieve a collection of data instead. However, this workflow might find its audience for some experimental workflows towards docking experiments and their interpretation.

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Workflow Components

Inputs (1)

Name	Description
ZINC_ID	A ZINC ID like '3395872' .

Processors (20)

Name	Type	Description
Form_URL_Image	local
Retrieve_ZINC_Molecule_Figure	local
Retrieve_ZINC_Molecular_Summary_Page	local
Form_URL_Summary	local
ZINC_URL_Single_Molecule_Figure	stringconstant
Regex_for_internal_id	stringconstant
Split_string_into_string_list_by_regular_expression	local
LineBreak	stringconstant
Filter_list_of_strings_by_regex	local
ZINC_URL_Fetch	stringconstant
ZINC_Fetch_Param_SMILE	stringconstant
ZINC_Fetch_Param_MOL2	stringconstant
Retrieve_Internal_ID	local
ZINC_URL_Single_Molecule	stringconstant
ZINC_URL_Fetch_Prefix	local
ZINC_URL_SMILES	local
ZINC_URL_MOL2	local
Regex_for_internal_id_with_group	stringconstant
Fetch_MOL2_Data_from_URL	local
Fetch_SMILES_Data_from_URL	local

Outputs (6)

Name	Description
ZINC_Molecule_Figure	2D graphics that is shown on the summary page of a molecule.
ZINC_Data_SMILES_String	The structural representation of a 3D molecule as a 1D string.
ZINC_Data_MOL2
InternalID	A numeric ID representing the molecule in datasets.
ZINC_URL_SMILES	The URL at which to retrieve the SMILE string.
ZINC_URL_MOL2	The URL at which to retrieve the MOL2-formatted structural representation.

Links (26)

Sink	Source
Form_URL_Summary:string2	ZINC_ID
Split_string_into_string_list_by_regular_expression:string	Retrieve_ZINC_Molecular_Summary_Page:contents
Filter_list_of_strings_by_regex:stringlist	Split_string_into_string_list_by_regular_expression:split
Fetch_SMILES_Data_from_URL:url	ZINC_URL_SMILES:output
ZINC_Data_MOL2	Fetch_MOL2_Data_from_URL:contents
ZINC_Data_SMILES_String	Fetch_SMILES_Data_from_URL:contents
Retrieve_Internal_ID:stringlist	Filter_list_of_strings_by_regex:filteredlist
Retrieve_ZINC_Molecular_Summary_Page:url	Form_URL_Summary:output
Form_URL_Image:string2	ZINC_ID
Retrieve_ZINC_Molecule_Figure:url	Form_URL_Image:output
Split_string_into_string_list_by_regular_expression:regex	LineBreak:value
Filter_list_of_strings_by_regex:regex	Regex_for_internal_id:value
Retrieve_Internal_ID:regex	Regex_for_internal_id_with_group:value
InternalID	Retrieve_Internal_ID:filteredlist
ZINC_URL_Fetch_Prefix:string2	Retrieve_Internal_ID:filteredlist
ZINC_Molecule_Figure	Retrieve_ZINC_Molecule_Figure:image
ZINC_URL_MOL2:string2	ZINC_Fetch_Param_MOL2:value
ZINC_URL_SMILES:string2	ZINC_Fetch_Param_SMILE:value
ZINC_URL_Fetch_Prefix:string1	ZINC_URL_Fetch:value
ZINC_URL_MOL2:string1	ZINC_URL_Fetch_Prefix:output
ZINC_URL_SMILES:string1	ZINC_URL_Fetch_Prefix:output
Fetch_MOL2_Data_from_URL:url	ZINC_URL_MOL2:output
Form_URL_Summary:string1	ZINC_URL_Single_Molecule:value
Form_URL_Image:string1	ZINC_URL_Single_Molecule_Figure:value
ZINC_URL_MOL2	ZINC_URL_MOL2:output
ZINC_URL_SMILES	ZINC_URL_SMILES:output

Coordinations (0)

Taverna 1 workflow

Information Original Uploader

Steffen Möller

Information License

All versions of this Workflow are licensed under the Creative Commons Attribution-Share Alike 3.0 License.

Information Credits (1)

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Steffen Möller

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Information Tags (4)

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Information Shared with Groups (1)

Taverna 2 beta tester programme

Information Featured In Packs (1)

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Statistics

199 viewings

126 downloads

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Version History

Earliest Version:
[1] - Retrieve Single Molecule from ZINC - structure and figure

Created on: Sunday 24 August 2008 @ 22:52:25 (BST)

Created by: Steffen Möller

Last edited on: Monday 25 August 2008 @ 21:57:16 (BST)

Last edited by: Steffen Möller

Revision comments:

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This Workflow only has one version.

Comments (1)

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Stian Soiland-Reyes	Monday 15 September 2008 @ 10:28:44 (BST)
	Hi! Could you unshare this item from the t2 beta tester group and only share it through the "Don't run properly" pack..? We'll look at your workflow shortly.