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JChem Update

ChemAxon/Infocom JChem Extensions version 4.0.0.v191500 by Infocom Corporation

Structure updating and inserting in structure tables of relational databases.

Options

Target structure table
Enter the name of the table to which data should be written. Note, if this table exists, the table is dropped before writing.
Append data
Check this to append the input data to an existing table with the same data structure. If the table does not exist a new one will be created. Note, if this box is unchecked an existing table is dropped before execution of this node.
Halt if an error occurs
If an error occurs during import, the error message and the corresponding stack trace information is written to the standard error. Check the Halt if an error occurs box if you would like the system to stop if a molecule can not be imported.
Set chiral flag for MDL formats
If Set chiral flag for MDF formats is checked, will set the chiral flag (absolute stereo flag) for the imported structures.
Allow empty structures
If Allow empty structures is unchecked, will not import empty structures (structures where the atom count is zero).
Compress the structure source during import
Certain file formats are compressed before storing the structure source in the cd_structure field in the database.
Fingerprint length
Specify the number of columns that will contain the chemical hashed fingerprints of the molecules. Higher number provides better screening performance for substructure searching, but too many columns may significantly increase the size of the structure cache.
Bits to be set for patterns
The number of bits to be set for each pattern in the structure. In the case of 16 fingerprint columns, 1 or 2 bits for a pattern are the best choice. Too high or too low value causes too many or too few 1 bits, respectively. The performance of the screening is optimal when the average number of 1 bits is about 50%.
Maximum pattern length
The number of edges in a pattern.
Table Contents
You can select from the following table types according to the desired scope of use: Molecules (default): For the storage of specific structures, like single molecules, mixtures, salts and polymers. Reactions: Table for storing single step reactions. Any structures: All types of structures are allowed, but no structure type-specific searching takes place (e.g. similarity values for reactions will not distinguish reactants, products and reaction centers). Markush libraries: Table for storing markush structures. (this table type is not allowed for Ms Access dbms) Query structures: Table for storing query structures. Typically used for superstructure search. Note: SMILES string imported into this table will be interpreted as SMARTS.
Assume absolute stereo flag
If checked, all query and target structures are treated as absolute stereo.
Filter out duplicate structures
If checked, JChem will filter out the structures which are already imported to the database with the same topology.
Duplicate filtering uses tautomers
If checked tautomers are considered for duplicate filtering during import. Enabling this feature increases import time.
Custom standardization
You may specify a custom standardization for the structure table.
SQL types
Enter the SQL types here to write integer-, double-, or string-valued columns to the database. By default integers are defined as type "integer", doubles as "numeric(10,30)", and all other columns, including strings are written as "varchar(255)". Some databases such as MS Access and Firebird do not allow this numeric precision, therefore you must select "numeric" as the SQL type. If your database allows strings longer than 255 chars, you can change this value in order to write long strings such as SLNs or Smiles.

Input Ports

JChem database connection object
Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) 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 4.0
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