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Is it possible to add structures to structureless molecules?

You can manually update a structureless molecule when the structure becomes available. Since this is not practical for updating a large library of molecules, it is also possible to update via a file import, which is the subject of this article.

Here are the two main use-cases for updating structureless molecules:


Here are also two less common scenarios that you may encounter:
Adding structures to structureless molecule records is very similar to registering new molecules, so if you are not familiar with the process, start with this article.

 

Add structure, do not update any batch information

Use this option if you wish to add a core structure to the molecule record, but do not want to change the existing batch name or salt information.

The chemical registration system strips salt and hydrate data on import and captures this information under batch name, salt code, and formula weight of each batch. Since batch information is not updated in this instance, any salt information will be stripped and discarded. If you wish to capture the salt information, go directly to the next section.

Import step 1: Choose file

The following information needs to be present in the import file:

  • Molecule name- primary identifier or synonym that is registered in the CDD vault.
  • Structure- as SMILES or MOL. Structure may contain salt and hydrate information which will be discarded.

 

Import step 2: Mapping

Set the import to "update existing molecules", map molecule name and structure, leave batch name unmapped, and process the import.

update_structureless.png

Notice that the batch ID, though present in the file, is not mapped, since we do not wish to update batch information.

 

Import step 3: Validation

Review the QC validation report. The event types you see on the report depend on whether or not there are salts and hydrates present in the structures.

  • Structure does NOT contain salts or hydrates 

If the imported structureless molecule was found in your vault, there will be 1 noteworthy and 1 suspicious event for each  molecule to be updated.   

If you wish to complete the structure update of the molecule, you MUST click the accept button on the "Molecule Structure Modification" event type. Recall that by default all suspicious events are set to be rejected, with an option to override and accept all entries under each event type. When this is done, you can finalize the import by clicking "Commit Data Import".

Screen_Shot_2013-11-02_at_12.31.42_AM.png

 

  • Salts or hydrates are found and will be discarded

Since batch information is not updated under this data mapping, any salt information will be stripped and discarded. You will see 3 validation events for each such molecule. Don't forget to click "accept" on each suspicious event type if you wish to import the data. If you do not want to discard any salt data, you may reject the event type and import the rejected structures separately, following the steps in the next section.

 Screen_Shot_2013-11-02_at_12.58.21_AM.png

 

Add structure and update associated batch name, salt and formula weight

Use this option if you wish to add a core structure to the molecule record, and to capture and update salt and hydrate information under batch fields of an existing batch.  If your vault uses prefixed batch names (i.e. AA-001 or AQ-001),  the updated batch name may change as a result.

The chemical registration system strips salt and hydrate data on import, and captures this information under batch name, salt code, and formula weight of a batch. In order to preserve this information while updating a structureless molecule, you will need to supply an existing batch name in your import file.

Import step 1: Choose file

The following information needs to be present in the import file:

  • Unique batch ID- any registered unique batch identifier is sufficient to identify both the molecule and batch.
  • Molecule name- optional if unique batch identifier is mapped. This is the primary name or synonym that is registered in the CDD vault.
  • Batch name- optional if unique batch identifier is mapped. This is the primary name of the batch that was registered in the CDD vault.
  • Structure- as SMILES or MOL. Structure may contain salt and hydrate information which will be saved as batch fields.

 

Import step 2: Mapping

Set the import to "update existing molecules", map molecule structure, batch, and molecule identifiers, and process the import.

Screen_Shot_2013-11-02_at_1.42.25_AM.png

Notice that the batch ID is mapped to batch name, since we wish to capture and update batch information.

 

Import step 3: Validation

Review the QC validation report. The number and types of validation events in this scenario will depend on the batch naming convention in your vault. 

In vaults with prefixed batch naming convention (e.g. ZZ-001, AA-002) there will be 2 noteworthy and 2 suspicious event for each updated molecule.

You will see a "Batch Salt Modification" event regardless of whether salt data was found, since you are changing the batch salt from unknown (ZZ prefix) to known, whether the known salt is 'no salt, free base or acid' (AA prefix), or another salt form. The formula weight of this batch will also change as a result of salt update. 

You may  see fewer events in your report if your vault uses the numeric batch naming convention (e.g. 001, 002) in place of the prefixed naming convention. 

Recall that by default all suspicious events are set to be rejected, with an option to override and accept all entries under a given event type. If you wish to complete the structure update of the molecule, you MUST click the accept button on the "Molecule Structure Modification" and "Batch name modification" event types.  When this is done, you can finalize the import by clicking "Commit Data Import".

Screen_Shot_2013-11-02_at_1.54.57_AM.png

 

Add a "mixture" (several components) structure

When you register a mixture, you need to map the "Batch salt" field on import, which will prevent salt stripping, and thus register all structure components as a mixture. Since salt stripping is skipped entirely by doing this, a structure will be registered with all of it's components, even if one of those components is a salt (or hydrate).

When you are updating an exiting structureless molecule with a mixture structure, the steps will be a combination of registering a new mixture, and updating an existing batch: you must map the batch salt field in order to register a mixture, and you must map a batch name in order to update it's salt field.

Let's break that down:

 

Import step 1: Choose file

The following information needs to be present in the import file:

  • Unique batch ID- any registered unique batch identifier is sufficient to identify both the molecule and batch.
  • Molecule name- optional if unique batch identifier is mapped. This is the primary name or synonym that is registered in the CDD vault.
  • Batch name- optional if unique batch identifier is mapped. This is the primary name of the batch that was registered in the CDD vault.
  • Structure- as SMILES or MOL. Structure may contain salt and hydrate information which will be saved as batch fields.
  • Salt data- a separate field that contains a text value (CDD salt code or full name) to describe salt data. See this article for supported salt nomenclature, and mixture registration.

 

Import step 2: Mapping

Set the import to "update existing molecules", map molecule structure, batch identifiers, molecule identifiers,  batch salt, and process the import.

Screen_Shot_2013-11-04_at_10.09.24_AM.png

 

Import step 3: Validation

Review the QC validation report carefully. The number and types of validation events in this scenario will depend on the batch naming convention in your vault. 

In vaults with prefixed batch naming convention (e.g. ZZ-001, AA-002) there will be 2 noteworthy and 2 suspicious event for each updated molecule.

You will see a "Batch Salt Modification" event regardless of whether salt data was found, because you are changing an existing batch with unknown salt (ZZ prefix) to a known salt which may be "no salt" (AA prefix) or another salt form. The formula weight of this batch will also change as a result of salt update. 

You may  see fewer events in your report if your vault uses the numeric batch naming convention (e.g. 001, 002). 

Recall that by default all suspicious events are set to be rejected, with an option to override and accept all entries under a given event type. If you wish to complete the structure update of the molecule, you MUST click the accept button on the "Molecule Structure Modification" and "Batch name modification" event types.  When this is done, you can finalize the import by clicking "Commit Data Import".

Screen Shot 2013-11-02 at 1.54.57 AM.png

 

 

Do not update structure, update batch information including name, salt form and formula weight

This is a rare case where you may want to update the batch information, but keep the molecule structureless. As you may have guessed, in this case you will need to map the batch fields and the molecule name, but omit the structure. In order to update the salt data, you will need to map the "batch salt" field in addition to batch name.

 

Import step 1: Choose file

The following information needs to be present in the import file:

  • Unique batch ID- any registered unique batch identifier is sufficient to identify both the molecule and batch.
  • Molecule name- optional if unique batch identifier is mapped. This is the primary name or synonym that is registered in the CDD vault.
  • Batch name- optional if unique batch identifier is mapped. This is the primary name of the batch that was registered in the CDD vault.

 

Import step 2: Mapping

Set the import to "update existing molecules", map molecule name, batch identifiers, batch salt, and process the import.

Screen_Shot_2013-11-04_at_10.22.01_AM.png

 

Import step 3: Validation

Review the QC validation report carefully. You should see 2 validation events- one "noteworthy" event to indicate a batch update, and one "suspicious" event to indicate batch salt modification, since you are changing the batch salt from unknown (ZZ prefix) to known, whether the known salt is 'no salt, free base or acid' (AA prefix), or another salt form. There should be NO molecule modification events for this record, since none of the molecule fields (structure, user-defined fields or names) are affected by the update.

Recall that by default all suspicious events are set to be rejected, with an option to override and accept all entries under a given event type. If you wish to complete the structure update of the molecule, you MUST click the accept button on the  "Batch salt modification" event types.  When this is done, you can finalize the import by clicking "Commit Data Import".

Screen_Shot_2013-11-04_at_10.32.05_AM.png

 

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