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

Output File

The file to write the structures to. Existing files can be overwritten or the node execution can be prevented (see 'If exists' setting below).

If exists

Specifies the action to take if the output file already exists.

• Fail: Will issue an error during the node's execution (to prevent unintentional overwrite).
• Overwrite: Will replace any existing file.

File encoding

Defines the character set used to read a CSV file that contains characters in a different encoding. You can choose from a list of character encodings (UTF-8, UTF-16, etc.), or specify any other encoding supported by your Java Virtual Machine (VM). The default value uses the default encoding of the Java VM, which may depend on the locale or the Java property "file.encoding".

• OS default: Uses the default decoding set by the operating system.
• ISO-8859-1: ISO Latin Alphabet No. 1, a.k.a. ISO-LATIN-1.
• US-ASCII: Seven-bit ASCII, also referred to as US-ASCII.
• UTF-8: Eight-bit UCS Transformation Format.
• UTF-16: Sixteen-bit UCS Transformation Format, byte order identified by an optional byte-order mark in the file.
• UTF-16BE: Sixteen-bit UCS Transformation Format, big-endian byte order.
• UTF-16LE: Sixteen-bit UCS Transformation Format, little-endian byte order.
• Other: Enter a valid charset name supported by the Java Virtual Machine.

Custom encoding

A custom character set used to read a CSV file.

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 title column

Whether a title column should be used for the molecule title or not. Using a title column is mandatory if the structure column is a Ctab column.

Title column

The column to use for the molecule title. Can be the Row ID or any compatible column.

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.

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.

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Workflows

• Convert a string to SMILESKNIME Hub

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