SDF Writer

This node writes SDF or Mol cells into a continuous SDF file. You may also add additional properties from columns to the SDF molecules while they are written out.

Options

Default Settings

Filename

The path to the output file.

Overwrite OK

If unchecked, the node refuses to execute when the output file exists (prevent unintentional overwrite).

Structure column

Select the column containing the structures that should be written to the output file here. You can select SDF, Mol or Ctab columns. For Ctab column it is mandatory to also select a title column, see below.

Use column as molecule title

If selected, the molecules' titles will be exchanged by the values in the selected column or the row ID.

Omit properties with missing values

If selected, columns that contain missing values are not inserted into the molecule as properties but rather they are omitted. Otherwise they will be inserted but with an empty value.

Add 'no structure' molecules for missing values

If selected, rows with missing molecule entries are written as molecules with no structure into the file. Otherwise missing molecules are simply ignored and not written into the file.

Insert Properties

Select the columns that should be used as properties in the output file. If the structure column is a SDF column and a property already exists in the SDF block, it will be overwritten by the values in the selected column.

Encoding

File Encoding

To write an SDF file with a different encoding, you can select a character set in this tab (UTF-8, UTF-16, etc.) or specify any other encoding supported by your Java VM. By default, the node uses US-ASCII (7 bit encoding).

Views

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Workflows

• _01_ChemicalLibraryEnumerationKNIME Hub
• 01_Chemistry external toolKNIME Hub
• 01_Chemistry external toolKNIME Hub
• 01_Chemistry_basicsKNIME Hub
• 01_Chemistry_basicsKNIME Hub
• Show all 104 workflows

Links

• .xlsx to .sdf conversionby izaychik63 on 2020-07-15

  forum.knime.com/p/97045
• Erlwood Chemical File Writer SDF Compound Namesby elsamuel on 2020-07-27

  forum.knime.com/p/98088

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