RDKit Structure Normalizer

Checks structures and tries to normalize them, if necessary. Structures that are normalized already will appear in the first output table. Structures, which need to be normalized will be corrected and also put in the first output table. Information about the normalization is made available as bit mask (flags) as well as warning messages. Structures, which cannot be normalized or have been normalized causing a certain warning flag that the user wants to treat as error are put in the second table ("Failed Molecules").

The following flags and messages are currently used:

• 1 - BAD_MOLECULE, Unable to recognize a molecule (ERROR)
• 2 - ALIAS_CONVERSION_FAILED, The atom alias conversion failed (ERROR)
• 4 - TRANSFORMED, Structure has been transformed
• 8 - FRAGMENTS_FOUND, Multiple fragments have been found
• 16 - EITHER_WARNING, A wiggly bond has been removed
• 32 - STEREO_ERROR, Stereo chemistry is ambiguously defined (ERROR)
• 64 - DUBIOUS_STEREO_REMOVED, A stereo bond has been removed
• 128 - ATOM_CLASH, There are two atoms or bonds are too close to each other (ERROR)
• 256 - ATOM_CHECK_FAILED, The atom environment is not correct(ERROR)
• 512 - SIZE_CHECK_FAILED, The molecule is too big (ERROR)
• 1024 - RECHARGED, Structure has been recharged
• 2048 - STEREO_FORCED_BAD, Structure has failed: Bad stereo chemistry (ERROR)
• 4096 - STEREO_TRANSFORMED, Stereo chemistry has been modified
• 8192 - TEMPLATE_TRANSFORMED, Structure has been modified using a template

Options

Mol column

The input column with SDF, SMILES or RDKit Molecules. The latter ones are treated as SDF values. SMILES input will be converted internally into mol blocks before the normalization is done.

Corrected structure column name

The name of the column that will contain the original or corrected structure, in case that any normalization has been applied.

Flags column name

The name of the column that will contain the warning flags. This is a bit mask where each bit has a certain meaning as described in the node description.

Warning messages column name

The name of the column that will contain the warning messages associated with the flags. The "Passed Molecules" table contains only warnings, which are not classified as errors.

Flags column name

The name of the column that will contain the error flags. This is a bit mask where each bit has a certain meaning as described in the node description.

Error messages column name

The name of the column that will contain the error messages associated with the flags. The "Failed Molecules" table contains only errors that prevented successful normalization.

Logfile output (optional)

A logfile can be specified here which logs additional output in case of normalizations of structures. It can be used for informal purposes only. There is no need to define a logfile for the node to work correctly. Leave this field empty to disable logging.

• Disable logging: No log file will be created and no log output will be produced.
• Enable logging: A log file will be created and log output will be produced according to the selected options.

Selected log file

Select the file to which the log output of the node will be written. If the file already exists, the behavior depends on the selected overwrite policy. If no file is selected, no log output will be produced.

Create missing folders

Select if the folders of the selected output location should be created if they do not already exist. If this option is unchecked, the node will fail if a folder does not exist.

If exists

Specify the behavior of the node in case 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.

Warning codes to treat as failures

Define here which warning flags should be treated as errors. If defined as an error, the rows will appear in the second output table ("Failed Molecules" table). Hover over a code to see its description and value.

Transformation configuration file (.trn) (optional)

Lets the user define a customized transformation configuration file. The default built-in configuration file will be used when no file is specified. The file must have the .trn extension.

• Default configuration: Loads the default configuration file.
• File selection: Specify a configuration file.

Selected transformation config file

Specify a custom transformation configuration file to use. The file must have the .trn extension.

Augmented atoms configuration file (.chk) (optional)

Lets the user define a customized augmented atoms configuration file. The default built-in configuration file will be used when no file is specified. The file must have the .chk extension.

• Default configuration: Loads the default configuration file.
• File selection: Specify a configuration file.

Selected augmented atoms config file

Specify a custom augmented atoms configuration file to use. The file must have the .chk extension.

Advanced switches (optional)

Configure here certain switches that influence how the Structure Normalizer performs its work:

Additional options

Normally, there is no need to change these settings. However, if you are familiar with the underlying StruChk tool, you may define here manually options to be passed to it. These options come in addition to the switches defined above.

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