SDF Reader

This node reads an SDF file and creates several columns with each molecule in a new row. You can select which parts of the molecule should be extracted into columns in the output table. By default only the molecular structure is exported, but in the Property Handling section you can select if and which properties from the SD-file should be extracted into columns of the output table.

Options

Input sources

Select the input source files. These can be local files or URLs. You can add multiple sources and they will be read in order. Empty locations will be ignored.

• File or URL: The file path or URL to read from.

Limit number of read molecules

If enabled, only the specified number of molecules will be read from the input files.

Maximum number of molecules

The maximum number of molecules to read from the input files.

Use molecule name as row ID

Instead of generating row IDs, the molecule's names are taken as row IDs. You have to make sure that the names are unique, otherwise the node will fail.

Extract molecule name

If selected, the molecules' names are put into a column called 'Molecule name' in the output table. This option can be used together with the previous one.

Add column with source location

Enabling this option will add a column showing the source location for each molecule.

Extract SDF blocks

If the complete molecule, starting from the title up to the magic $$$$ should be extracted into a column, select this check box.

Extract Mol blocks

If you are interested in the molecules' Mol blocks (i.e. without the properties) you can select this option in order to extract a column containing the Mol blocks.

Extract Ctab blocks

If you are interested in the molecules' Ctab blocks (i.e. without the header and properties) you can select this option in order to extract a column containing the Ctab blocks.

Extract counts

If you are interested in the molecules' atom and bond counts as they are stored inside the Ctab block you can select this option in order to extract two columns containing the atom and bond counts.

Extract all properties

If this option is enabled, all source locations will be scanned for all existing properties during execution. All found properties will be added to the output table. Please note that this requires two scans over all sources during execution.

Scan for properties

Press this button to perform the action that generates new content for the view.

Cancel

Press this button to cancel the action that is currently being performed.

Properties

Properties found during scanning are displayed here. Select which properties to extract and optionally change their types. You can only change to a more general type (Integer → Double → String).

• Extract: Whether to extract this property.
• Property Name: The name of the property as found in the SDF file.
• Type: The data type of the property. You can change this to a more general type (Integer → Double → String), but changing to a more specific type may cause errors.

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.

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