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PubChem Search

ChemAxon/Infocom JChem Extensions version 4.3.0.v202000 by Infocom Corporation

Search data by structure, substructure and similarity to PubChem. The node uses the PubChem Power User Gateway (PUG) service. https://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html In the PUG, the node is connecting to the server via HTTPS and FTP protocols during execution process. Therefore, your network has to use both of HTTPS and FTP protocols.

Options

Query structure column
The query structure column.
Search type
Sets different search options according to a predefined search type.
Identity search options
Additional options are provided to return all structures identical to this structure using different notions of chemical structure identity.
Similarity threshold
The degree of similarity is dictated by the Threshold parameter.
Stereochemistry
Sets matching stereochemistry.
Match isotopes
Indicates that the isotopic information within the query is to be used.
Match charges
Indicts that the formal charge information within the query is to be used.
Match tautomers
Indicates that tautomers of the query are allowed to match.
Ringsystems not embedded
Indicates that the results should exactly match the ring systems as they are provided in the query.
Single/double bonds match aromatic bonds
Indicates that singe or double bonds in the query may match aromatic bonds.
Chain bonds match ring bonds
Indicated that chain bonds in the query may match both ring and chain bonds.
Strip hydrogen
Indicates that explicit hydrogen in the query is to be removed prior to searching.
Time Limit
Sets time limit (in CPU seconds).
Result Limit
Sets hit limit count.
Select fields
Selects PubChem System Utilized SD Fields.

Input Ports

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Input table that contains query structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

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Output table that contains search result structure in Marvin format.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install ChemAxon/Infocom JChem Extensions Feature from the following update site:

KNIME 4.3

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Developers

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