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01 CCDC CSD Text-Numeric Searches

CCDC CSD Text-Numeric Searches

CCDC CSD Text-Numeric Searches

This example workflow illustrates the use of the CCDC CSD Text/Numeric Search components. Currently available are CCDC CSD Chemical Name Search and CCDC CSD Author Search.

CCDC CSD Text/Numeric SearchingThis example workflow illustrates the use of the CCDC CSD Text/Numeric Search components. Currently available are CCDC CSD Chemical Name Search and CCDC CSD Author Search. Note that example values are supplied for the searches here and that options are not necesasarily set to the defaults. No extra files are required.As with all of the CSD Search components, the hits here can be viewed using the CCDC Run Mercury component (which allows visualisation of the experimentally-determined 3Dstructures), via a KNIME Table View or simply by using a component's built-in viewer.Note that the experimentally-determined 3D coordinates from the CSD are returned in MOL2 format in the column mol2_mol. As KNIME does not have a 3D viewer, the 3D coordinates aredepicted in 2D in the built-in viewer, which is not particularly useful. The Table View node doesn't have any molecular depiction capability at all, so can only show the text of the molfiles; thiscolumn is thus removed before the Table View node is used.Search filters are constraints on CSD search results that are independent of the search type. They include, for example, applying an R-factor threshold, disallowing the presence of disorderetc. These filters cannot currently be applied as part of a search in KNIME as they can in e.g. ConQuest. However, all the required properties are returned by the various CSD Searchcomponents, so the filtering may be applied as a post-processing step. A commonly-used (but reasonably rigorous) set of filters is applied by the CSD Search Filters metanode in theexample below. The filters applied can easily be modified if required: simply double-click on the metanode to inspect or alter the filters. Some example author names are supplied.Note that, if multiple author names are pecified, they will be AND'edtogether ( i.e. all must be present). An example chemical name is supplied, and the option to ignore non-alphabeticcharacters in names is checked (the default is unchecked). Try the search for this name with the 'ignore non-alphabetc charcters' optionchecked and unchecked. Here, we subset the columns just tohighlight the publication details. Execute to run Mercury Right-click > Interactive View: JavaScript Table View The Table View node cannot 3Dmolfiles so we remove this column. Double-click to accessthe individual filters.Remove molfileView hitsPublication columns CCDC CSDAuthor Search CSD Search Filters Column Filter Table View Column Filter CCDC Run Mercury CCDC CSD ChemicalName Search CCDC CSD Text/Numeric SearchingThis example workflow illustrates the use of the CCDC CSD Text/Numeric Search components. Currently available are CCDC CSD Chemical Name Search and CCDC CSD Author Search. Note that example values are supplied for the searches here and that options are not necesasarily set to the defaults. No extra files are required.As with all of the CSD Search components, the hits here can be viewed using the CCDC Run Mercury component (which allows visualisation of the experimentally-determined 3Dstructures), via a KNIME Table View or simply by using a component's built-in viewer.Note that the experimentally-determined 3D coordinates from the CSD are returned in MOL2 format in the column mol2_mol. As KNIME does not have a 3D viewer, the 3D coordinates aredepicted in 2D in the built-in viewer, which is not particularly useful. The Table View node doesn't have any molecular depiction capability at all, so can only show the text of the molfiles; thiscolumn is thus removed before the Table View node is used.Search filters are constraints on CSD search results that are independent of the search type. They include, for example, applying an R-factor threshold, disallowing the presence of disorderetc. These filters cannot currently be applied as part of a search in KNIME as they can in e.g. ConQuest. However, all the required properties are returned by the various CSD Searchcomponents, so the filtering may be applied as a post-processing step. A commonly-used (but reasonably rigorous) set of filters is applied by the CSD Search Filters metanode in theexample below. The filters applied can easily be modified if required: simply double-click on the metanode to inspect or alter the filters. Some example author names are supplied.Note that, if multiple author names are pecified, they will be AND'edtogether ( i.e. all must be present). An example chemical name is supplied, and the option to ignore non-alphabeticcharacters in names is checked (the default is unchecked). Try the search for this name with the 'ignore non-alphabetc charcters' optionchecked and unchecked. Here, we subset the columns just tohighlight the publication details. Execute to run Mercury Right-click > Interactive View: JavaScript Table View The Table View node cannot 3Dmolfiles so we remove this column. Double-click to accessthe individual filters.Remove molfileView hitsPublication columns CCDC CSDAuthor Search CSD Search Filters Column Filter Table View Column Filter CCDC Run Mercury CCDC CSD ChemicalName Search

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Created by: flatk
Created at: 2020-07-22
On NodePit since: 2020-09-10
Last update: 2024-04-18
Created with KNIME version: v4.1.3

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