Knime To SDF Port

The data on the input port is made available for remote execution via the SDF command line nodes.

Options

Field containing molecule data

Field in input table that contains the molecule data which will be used to generate the molblocks of the sdf file.

Local Exchange Directory

Path from local host to network directory which is accessible from both: the local computer running Knime as well as the remote computer on which the SDF Commands will be executed.

Remote Exchange Directory

Path from remote host to network directory which is accessible from both: the local computer running Knime as well as the remote computer on which the SDF Commands will be executed.

SSH Tab

Options for configuring the remote execution via ssh.

These options will affect all nodes connected via the command line pipe following the first generator node.

Pipe Mode

Decides if environment variables for production or development mode are loaded prior to remote command execution.

Remote Directory

Directory on remote host in which the ssh execution will take place.

Error Log File

If specified the stderr of this command is written to this local file. Specify a full path. Values of flow variable can be inserted using ${varName}. This is especially useful on the server.

Execute in each node

If checked each node directly connected to via a command line pipe will be executed separately on node execution. A copy of the output data and stderror will be available on the output port and the node view. This is slow but ideal for debugging a pipe.

If unchecked no execution takes place on each connected command node. Instead you may use an Executer node (cf. consumer folder) to execute the pipe as a whole. The unix command to execute the pipe is available in each output port view.

Input Ports

Knime port containing molecule field

Output Ports

Data from input port available on remote host

Views

Command Error Output

Error output if single node execution is activated.

Best Friends (Incoming)

• Merge Variables (37 %) Deprecated
• MolConverter (26 %) Streamable
• SDF Reader (26 %) 
• File Reader (5 %) Streamable
• Row Filter (5 %) Streamable

Best Friends (Outgoing)

• SDF Concatenate (86 %) 
• SDF Port To KNIME (10 %) 
• sdf Structure Tagger (5 %) 

Installation

To use this node in KNIME, install Genentech Knime Features from the following update site:

A zipped version of the software site can be downloaded here.

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Developers

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