SeeSAR Interactive GUI

Use SeeSAR interactively, taking advantage of all its features, namely Inspirator, Molecule Editor, Docking and Analyzer. You can use the node for starting a new project as well by simply executing the node.

After having finished (and saved) your work in the SeeSAR graphical interface, you will be able to access all SeeSAR molecules of all (small) molecule related modes in subsequent KNIME nodes. For details see output port "SeeSAR Molecules".

SeeSAR has to be licensed separately, see http://www.biosolveit.de/SeeSAR/ for more details.

Options

Library column
The molecules provided in this column are shown in SeeSAR. If the input table contains more than one column with a compatible type, you can choose here which column should be taken. The molecules have to be in sdf or mol2 format with 3D coordinates.
Keep debug files and show the log after the run
This setting keeps all temporary files and opens an editor to show the output of SeeSAR. This setting is useful for debugging.

Input Ports

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Library: Input table with a molecule column in sdf or mol2 format.
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SeeSAR Project

Output Ports

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SeeSAR Project: The SeeSAR project file storing the status of SeeSAR as saved upon exit.
After having run this node, a tooltip on this port will indicate, whether a docking is defined or not. If a docking is present, it will show "(with defined docking)", which is necessary to use it as input for the FlexX docking node.
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SeeSAR Molecules: The SeeSAR molecules of all (small) molecule related modes. If there are two tables in one mode, e.g. docking, only the result molecules will be exported.
The molecule names are used as row keys, together with a row index to avoid ambiguities. The original molecule name is exported in a separate column.
In order to map the molecules to the mode in SeeSAR, there is also a mode column, which indicates in plain text the mode source, e.g. "analyzer".

Note: You have to save the project in SeeSAR to retrieve the molecules at this output port.

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