Skip to content
en English

CDD Vault Update: New import and search capabilities

CDD Vault Update Logo
November 1, 2013

Update structureless molecules en masse (For vaults that use CDD’s molecular registration system)

If you work in a vault with a registration system, you previously had to manually update each structureless molecule when the structure became available. That’s fine for the one-off compound, but a drag for a whole compound library. Now you can bulk update structures just by importing a file! We’ve even built in batch salt and formula weight updating, if you wish to update those, and all you have to do, is include a batch identifier in your import file mapping.

The best part is that any user with sufficient privileges to edit existing molecules can do this!


Here’s how:

  1. Create an import file with the necessary details:
    • To add structures, but not update existing batches, include:
      1. Structure (SMILES, MOL)
      2. Molecule ID
    • To add structures and update existing batch names and salts, include:
      1. Structure (SMILES, MOL)
      2. Unique Batch ID
      3. Molecule ID (optional if unique batch ID is included)
      4. Batch Name (optional if unique batch ID is included)
  2. Import the file to CDD and choose to “Update existing molecules”
  3. Map structure and the molecule and batch IDs just like you would when registering new molecules, and proceed with the import

When the molecule identified in the file record is found to be structureless, we will add the newly imported structure, and update the batch, salt and FW information if present.

Watch out for noteworthy and suspicious events in your QC validation report! You will need to “accept” valid structure updates before they are committed to the vault.


If you start updating mixtures and salts, the details becomes more nuanced, so please read our article on adding structures.

Batch name not required for molecule updates on file import (For vaults that use CDD’s molecular registration system)

When updating molecule fields, such as user-defined fields or synonyms, there’s no reason a batch name should be required. So when making updates to molecules in vaults with chemical registration systems via file import, a batch name doesn’t have to be mapped on step 2.

Simpler ownership of data imports

The user who processes a file will be the effective owner of the data, regardless of who uploads the initial file or who clicks commit. This same user will be the data owner listed on all imported data.

Read-export user role update

We’ve modified the read-export user role to include both the ability to export search results and to download attached files. Read the full user-role descriptions.

Additional options in “Default display” settings

Display Defaults (introduced about a year ago) have been extended to include global results settings: Detail level, Displayed readouts, and dose-response plots scale. You can read all the details, but briefly:

Detail level determines how many rows of data are displayed per each molecule, with the “details” level being the most extended view, and “summary” view showing just one row of data.
Displayed readouts controls what sub-set of protocol results is displayed for each matching molecule.
Dose-Response plots scale controls the y-axis scale, which can be adjusted to a standarized scale across all plots in a single run, or individually for each plot.

Vault administrators may change the defaults on the Settings-> Display Defaults tab, which will apply to all searches performed in the vault. Individual search settings may still be adjusted by any user under “Customize your report”.

This blog is authored by members of the CDD Vault community. CDD Vault is a hosted drug discovery informatics platform that securely manages both private and external biological and chemical data. It provides core functionality including chemical registrationstructure activity relationshipchemical inventory, and electronic lab notebook capabilities.

Collaborative Drug Discovery (CDD) Vault Logo


CDD Support logo

Know that CDD Support is here to help you reference CDD Vault in your talks, posters, or other presentations. Contact us if you want assistance with:

  1. Documenting algorithms used within CDD Vault;
  2. Creating screen shots;
  3. Proofreading slides; or
  4. Any other tasks.

Whatever you need, we're always ready to help!

Scroll To Top