Discovery Studio Updates - ProjectKM Migration Tool

The ProjectKM Migration tool allows you to extract data from the ProjectKM as regular files, which can be used in Discovery Studio and other applications.

This tool extracts the following data from the ProjectKM.

  • Data files (including sequences, alignments, etc.)
  • Protocols (as folders, with XML and text files)
  • Molecular data
  • Study Tables
  • CNX X-ray data (as CNX CV files)
  • CHARMm trajectories (as DCD files)

Note. Study Tables are exported as SD files. Note that molecules with more than 999 atoms or bonds are not exportable to this format. Also, only the first column of tables with more than one column of molecular data is exported. Experiment report XML files are exported but are not readable by Discovery Studio 1.5. Dendrograms are not exported but can be regenerated using Discovery Studio 1.5.

Installation

The ProjectKM Migration tool should only be installed on a system that already has at least one of the following DS platform products installed:

  • DS Modeling 1.1
  • DS Modeling 1.2 - SBD
  • DS MedChem Explorer 2.2

To install the ProjectKM Migration tool, do the following.

  • Download setuppkmmig15.exe. (7 Mb)
  • Locate the setuppkmmig15.exe and double-click setuppkmmig15.exe to start the installation program.

The ProjectKM Migration tool will be installed with common components from the DS platform products listed above (the default location is c:\Program Files\Accelrys\shared files\ds platform 1.6 ). The installation program adds a shortcut to the ProjectKM Migration tool on the Start menu of your computer.

Using the ProjectKM Migration tool

Note. Before running the tool, we recommend you back up the Oracle data and not access it during the extraction process. Modifying the database during PKM export may cause the export to fail without warnings.

To use the ProjectKM Migration tool, do the following.

  • Launch the tool by clicking the shortcut:
    Start | Programs | Accelrys DS ProjectKM Migration | DS ProjectKM Export
  • Connect to the ProjectKM with your username and password (see the Discovery Studio ProjectKM documentation for more details). Once logged in, a view of the ProjectKM is displayed.
  • To begin exporting:
    • Select a file or folder in that view
    • Click the Export button to display a dialog
    • On the dialog, select a folder to store the extracted files. Be sure to verify that the output location selected has sufficient disk space for the export process, typically this could be up to twice the size of the database. The tool will stop and will not be able to update the log files if the export process runs out of disk space.
    • Once selected, the exporting process begins

Note. The tool may be run on any folder in the PKM, however folders containing a very large amount of data may cause the tool to exhaust the system resources. We recommend only exporting folders containing less than 2 GB of data.

During the export process, a log file and an error file are created in the selected output folder. A message for each exported file is provided in either the log file or the error file. Note that buffering is performed on these log files and so you may need to close the application after running to see the complete log file. Progress updates are displayed in the dialog, and links in the database are expanded (i.e., copies of the files are extracted).

The file names are based on the names of the files in the database, with the following translation rules:

  • Unique file names are generated by adding a number to the end of the files
  • Forward and backward slashes are replaced by hyphens (-)
  • The non-ASCII characters (|, *, <, >, :, ?, ', ", and `) are replaced by the pound symbol (#)

The hierarchy of the ProjectKM database is preserved through folder creation. All files exported by a Windows user are owned by that user. The ProjectKM username under which the user logs into the database determines which files are visible and which can be exported.

Note. Only the files that the ProjectKM user has permission to read are exported. Note that on Windows very deep hierarchies with long path names (>255 characters) are not exported.