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Retrieve Single Molecule from ZINC - structure and figure

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

Created at: 24/08/08 @ 22:52:25 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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Option 1:

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Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/380/download?version=1
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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

Beanshells (0)

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)

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

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Steffen Möller

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Steffen Möller

Information Attributions (0)

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None

Information Tags (4)

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Information Featured In Packs (1)

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Information Attributed By (0)

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Information Favourited By (1)

Pharaxe

Information Statistics

734 viewings

796 downloads

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Citations (0)

None

Version History

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

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

Created by: Steffen Möller

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

Last edited by: Steffen Möller

Revision comments:

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This Workflow only has one version.

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Comments (1)

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Stian Soiland-Reyes	Monday 15 September 2008 @ 10:28:44 (GMT)
	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.