Export and External Integration

BMaps offers many options for exporting session data to local storage and via external integrations. Below are summaries of the features available.

Export Session Details

Fragments

Fragment growing results can be exported from the Post Search Fragment menus using the CSV download button in the upper right side of the menu. Additional features under the fragment menu's options provide additional properties that you may want to export.

Save Session

Click the Save button in the upper right hand of the BMaps window. Since BMaps does not currently have cloud storage for user sessions, all session files need to be save to either local or browser storage. Both options are provided in the Save Session menu.

To reload a local storage session, simply open a BMaps browser window and drag the session file onto the window. 

To reload a browser local storage file, click on the Guide button in the upper right of the BMaps window and press "Load saved session". It is VERY IMPORTANT to note that browser storage only saves one session at a time.

Exporting Structure

Exporting structure is available through the right hand actions bar using the Export button. Structures may be exported in the following formats. The output format will be displayed in the window after selecting a format. The file may be downloaded or the text copied.

  • SDF - MDL Structure Data File
  • SMI with Name - SMILES string
  • SMI without Name - SMILES string
  • MOL - MDL MOL File
  • CDXML - ChemDraw XML
  • CML - Chemical Markup Language
  • MOL2 - Tripos Sybyl Molecule
  • PDB - Protein Data Bank
  • XYZ - XYZ File (for QM)
  • InChI - InChI structure definition string
  • CSV - CSV with SMILES and energies

Download Image

Either the 3D Workspace image of the current view or the 2D Workspace image of the ligand can be downloaded. Previews are showing after selecting which to download. 

External Integrations

External integrations are available through the tabs in the Export menu which can be accessed through the right hand bar's Export button.

CDD Vault

CDD Vault is a storage and analysis solution for secure scientific data. CDD Vault's external integration into BMaps is available through their API key system. Please see their knowledge base for additional connection support.

PubChem

PubChem integrations can be used to perform similarity and substructure searches on compounds visualized in the 3D Workspace. Going to the PubChem tab will show the 2D structure of the current compound if found in PubChem. It will also provided additional naming and ID information. To see the full PubChem entry, perform a similarity or a substructure search, then click the associated buttons in the external integrations tab.

Mcule

MCule will display the compound if it is found in their databases. 

Reaxys

The Reaxys search tool enables searching literature, compound properties, and reactions based on your compounds. Clicking the Search Reaxys For Compound will open a new tab where you can log into Reaxys with your account.

Pharmit Screening

Export the currently selected compound to Pharmit for pharmacophore screening. Pharmit will use the selected compound to virtually screen large compound databases to find compounds with matched interactions and shape.

Once in Pharmit, use the left hand controls to set the search features and other criteria, then use the top-left search button to start the database search. Seach databases include MolPort, PubChem, ChEMBL25, Zinc, and others.

Pharmit is maintained by the University of Pittsburgh School of Medicine.

Prolif LID

The Ligand Interaction Diagram that is provided in the Inspector menu, can also be found in the Export Menu so that the diagram can be exported. Clicking and dragging on any label allows it to be moved. Clicking on the molecule allows you to move the entire molecule and all labels. Clicking the different label categories in the lower left corner will show or remove those labels.

The button will return the structure to the default view.

Natural Products Database

The Natural Product Database is an annotated collection of natural products, compiling target activity, biosynthetic information, and other properties. Clicking the Natural Product Substructure Search button will  take you to the database search website.