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Remote ICon

LigandScout Extensions for the KNIME Workbench version 1.8.0 by InteLigand GmbH

The server application running on the remote HPC clusters needs access to the compound libraries that should be used for virtual screening. New compound libaries to be used for remote screening can directly be generated remotely, exploiting the compute capabilities of the underlying HPC cluster.
Use the generated databases as input for new remote screening jobs via the Database List node.

Options

Settings

Conformer Generation Settings
Customizing Conformation Settings allow you to tweak the Inte:Ligand conformer generation algorithm to your needs.
Terminate on cancel
If selected, the node will terminate the remote job when it is canceled. Please note that nodes are automatically canceled when the KNIME workbench is closed. Alternatively, remote conformer generation jobs can be managed via the node view.
(Default: disabled)
Job name
Specifies the name of the new remote job than can later be used to distinguish between remote conformer generation jobs.
Output database name
Name of the new remote screening database.
Decrease priority by
Can be used to decrease the priority of the new jobs in the scheduling queue. A higher value means that the job should have less priority.
Processors per sub-job
Sets the number of processors used by each sub-job.

LigandScout Server

Overview
The LigandScout Server Settings are required for establishing a connection to a LigandScout Server instance used for remote execution on High Performance Computing clusters. See chapter Remote Execution for more details on these features.
IP or hostname
Sets the IP or hostname of the cluster machine that the LigandScout Server is running on.
Port
Sets the port that the LigandScout Server is listening on.
(Default: 8080)
SSH Port
Sets the port used for the SSH protocol on the server host.
(Default: 22)
User
This field should be set to your username on the remote cluster.
Identity File
Sets the path to the secret key file used to authenticate with the remote cluster.
Use Password
If selected, a password can be used instead of the secret key file. Please beware that the password has to be stored on this computer. It is therefore recommended to use an identity file.
Use intermediate Host
If selected, the below settings will be enabled. Usage of an intermediate host allows to tunnel the connection through another host and this way reach otherwise inaccessible clusters. This can be necessary if a firewall restricts access from outside your organizational network or if a gateway host is required to access the remote cluster.
IP or hostname
Sets the IP or hostname of the intermediate host that has access to the remote cluster.
SSH Port
Sets the port used for the SSH protocol on the intermediate host.
(Default: 22)
User
This field should be set to your username on the intermediate host.
Identity File
Sets the path to the secret key file used to authenticate with the intermediate host.
Use Password
If selected, a password can be used instead of the secret key file. Similar to above, please beware that the password has to be stored on this computer. It is therefore recommended to use an identity file.

Input Ports

Icon
Table containing the molecule(s) for which to generate conformations

Views

Manage remote conformer generation jobs
The view allows the monitoring and managing of all past remote conformer generation jobs. Also enables cancellation and deletion of specific remote jobs.

Installation

To use this node in KNIME, install LigandScout Extensions for the KNIME Workbench from the following update site:

KNIME 4.3

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