Installing desktop applications

Installation of Cresset desktop applications Flare™ and Spark™ is straightforward. They involve a similar set of steps as detailed below, however, Spark requires additional steps to install the databases.

On first execution, some operating systems will warn that the applications are requesting access to the internet. If run locally, internet access is not required so they could be blocked by the firewall. However, to access remote resources, database updates or a remote Cresset Engine Broker™ service, internet access will be required.

Installing the main applications

Windows®

Standard installation

If you have a previous version of the application installed, is it recommended to remove it using the standard Windows tools before installing a new version.

1. Browse to the Windows folder of the distribution media or locate the installer in your Downloads folder.
2. Double-click the .msi installer file. Installers are named according to the application and version that you are installing.
3. Follow the on-screen instructions.

Silent installation

Flare and Spark can be installed silently using one of the following commands.

1. To install in the default folder:

    msiexec.exe /I Appnameinstaller_64bit_<vers>.msi /q

2. To install in a specified folder:

   msiexec.exe /I Appnameinstaller_64bit_<vers>.msi /q  INSTALLDIR="C:/Program Files/Appname"

Note that this may require administrator access to the directory chosen for the installation.

The install process places an entry in the ‘Start menu’ and a shortcut on your desktop. To start the application, double click the application shortcut.

Alternatively, type the application name in the search box on the taskbar (the search panel opens automatically as you type): in the search results, click the application name to start it.

Linux®

1. Install the packages required for running the application.

   RHEL 8 and CentOS Stream 8
   dnf install mesa-libGLU libXScrnSaver libnsl xcb-util-keysyms xcb-util-renderutil xcb-util-image xcb-util-wm nss libglvnd libatomic xcb-util-cursor libglvnd-opengl
   Debian and Ubuntu
   apt-get install libglu1-mesa libxss1 libxcb-xinerama0 libjpeg-turbo8 libatomic1 libxcb-cursor0
   

2. Browse to the Linux directory of the distribution media or locate the installer in your Downloads directory.
3. Applications can be installed using a relocatable rpm or from a tar.xz file.
4. To install from a re-locatable rpm package use the following command:

   yum install cresset-<appname>-<vers>-1.<arch>.rpm
   

   or

   rpm -U [--prefix <path>] cresset-<appname>-<vers>-1.<arch>.rpm
   

   where <appname> and <vers> are respectively the name and the version number of the application that you are installing; <arch> is the architecture of your system; <path> is a custom install location (/opt by default).

5. Alternatively, unpack the supplied tar.xz file to a suitable location (e.g.  or /usr/local or /opt). Note that the location directory in which the tar.xz file will be unpacked must be empty.

To start the newly installed application either use the shortcut in the Applications menu (only if installation was from rpm) or call the application at:

/path/to/install/cresset/<appname>/bin/<appname>

e.g.

/opt/cresset/Spark/bin/Spark

macOS

1. Open the supplied disc image.
2. Read and agree to the license agreement.
3. Drag the application icon onto the ‘Applications’ icon to install the application in the Applications folder.

To start the application, navigate to the Applications folder and double click the application icon.

Installing Spark databases

Cresset supply a range of fragment and reagent databases for use in Spark, derived from commercially available compounds and reagents, literature reports, patent data, linkers, small molecule crystal structures, and theoretical ring systems. See the currently available databases.

Spark fragment databases can be installed as follows:

1. By copying the databases from a network location, or a USB key, to one of the default database locations. Note that administrator privileges will be required to copy them to a system location.
2. Using the built-in Spark Database Updater (available from the Spark GUI).
3. Using the command line ‘sparkdbupdate’.

Databases can be installed to any location including network disks but please note that Spark will run slower if accessing the databases via a network. If multiple Spark processes are running at the same time with databases located on a shared drive, then significant load is likely be placed on the network infrastructure.

Fragment databases

We recommend installing at least the ‘VeryCommon’ and ‘Common’ databases from commercial compounds (requiring a total of 885MB of disk space) as these cover most fragments that are convenient to synthesize. The ‘ChEMBL_common’ database (additional 1.7GB) would be a good secondary install as there is only a modest overlap with the recommended Commercial databases.

Reagent databases

The 23 reagent databases require a total of approximately 2.5GB of disk space (however, these databases are updated on a monthly basis, so the required disk space may change slightly). Alternatively, if you are interested only in specific R-group chemistries, you can install just the corresponding reagent databases.

Additional databases

Additional databases available for download from Cresset:

1. Agrochemical ‘PubChem’ (56MB)
2. Commercial ‘LessCommon’ (1.2GB), ‘Rare’ (1.6GB), ‘VeryRare’ (3.1 GB), ‘ExtremelyRare’ (3.3GB) and ‘UltraRare’ (4.9GB)
3. ‘ChEMBL_rare’ (2.4GB), ‘ChEMBL_veryrare’ (3.2GB)
4. ‘SureChEMBL_verycommon’ (4.1 GB), ‘SureChEMBL_common’ (6.9 GB) and ‘SureChEMBL_uncommon’ (7.1 GB)
5. ‘COD’ database (799MB) from small molecule crystal structures
6. ‘VEHICLe’ database (205MB) from theoretical ring systems.
7. ‘PROTAC-DB_Linkers’ (1.1GB), ‘Enamine_Stock_Linkers’ (154MB), ‘Enamine_MADE_Aromatic_Linkers’ (174MB), ‘Enamine_MADE_Aliphatic’ (520MB)

Additional optional databases (Commercial ‘Doubleton’ and ‘Singleton’, ‘ChEMBL_extremelyrare’, ‘SureChEMBL_rare’, ‘SureChEMBL_veryrare’, ‘SureChEMBL_extremelyrare’, ‘SureChEMBL_doubleton’ and ‘SureChEMBL_singleton’) are also available. Please contact Cresset support to download these databases.

See details of the currently released Spark fragment databases.

Installing databases using the Spark Database Updater

The Database Updater (available from the Spark or Flare GUI) can be used to download and/or install and update databases from the internet. The updater will install or update system-wide databases if the user has permission to write to these locations, otherwise it will write to a user location or a custom location set in the Flare or Spark preferences. Please refer to the Spark (‘Database Updater’) or Flare (‘Update Databases’) manual sections, or contact Cresset support, for a detailed explanation. To update system-wide databases either run the application as an administrator and set the database download location in the Preferences, or download the databases to a user directory then move them to the system location.

Installing databases using ‘sparkdbupdate’

Spark application

The ‘sparkdbupdate’ binary can be used to install and update all or selected Spark fragment databases from the command line. Please refer to the command line manual (or run ‘sparkdbupdate -H’) for details.

Flare application

The ‘sparkdbupdate.py’ python script can be used to install and update all or selected Spark fragment databases from the command line via the dedicated Python binary (pyflare). Please refer to the ‘Spark pyflare scripts’ section in the Flare manual (or run ‘pyflare sparkdbupdate.py -h’) for details. Note an additional license might be required for accessing the Database Update functionality via pyflare.

Spark database locations

Spark application

Below the details for the database location for the native Spark standalone application.

Flare application

Below the details for the Spark database location in Flare.

Licensing

Cresset applications require will require a valid license file (Flare and Spark) or activation key (Flare only) which will be supplied by Cresset. If you are a customer and cannot locate your license file, then please contact the Cresset support team. Alternatively, request an evaluation license.

Activation Key

In the ‘License Manager’ panel that appears as the application starts, select the ‘Activation Key’ tab, then paste or enter the activation key provided by Cresset. Press the ‘Activate’ button to activate your license.

Single User License

Flare

In the ‘License Manager’ panel that appears as the application starts, select the ‘License Files’ tab, click on the ‘Install a License’ button, browse to the location where you have saved the license file, select the license file and press ‘Open’.

Alternatively, the license file can be manually placed in one of the directories listed in ‘License Search Directories’.

Spark

If you have a single-user license, either place it in one of the license file locations or click the ‘Install license’ button that appears when the application starts and browse for the license file supplied by Cresset.

Site, Node-locked or Counted License

If you have been issued with a node-locked or counted license from Cresset, then we will also supply you with a license server. Please contact Cresset support for details.