NodeChemistry External Tool

Source

This node allows users to run a user-specified external program that inputs up to 3 columns and outputs 3 columns.

The allowed input types are: Maestro, Sequence, Alignment, Smiles, Mol2, Sd, Pdb, String, Integer, Double, Text, LogFile, FingerPrint, CanvasMatrix, CanvasPLS, CanvasBayes, GlideGrid, Hypothesis, CMS or Trajectory.

The allowed output types are: Maestro, Sequence, Alignment, Smiles, Mol2, Sd, Pdb, String, Integer, Double, Text, FingerPrint, CanvasMatrix, CanvasPLS, CanvasBayes, GlideGrid, Hypothesis, Surface, CMS, Trajectory or QSARModel.

Return code for the external process needs to be zero or else the node will fail.

Note: For the Hypothesis, Glide Grid and Trajectory types, since each cell represents a group of files, the input and output variables (i.e., %input_1%, %output_1%) represent text files that have a file prefix on each line. Therefore, the underlying script will parse these files to access the inputs and generate a text file with a list of prefixes on each line to send the output back into Knime.
For GlideGrid, apart from mentioning the Grid prefix, user can also specify whether to save grid or not by appending "|save_grid" to the grid prefix in each line.

Input Ports

  1. Port Type: BufferedDataTable
    One column from this input data is used as an argument for the external process
  2. Port Type: BufferedDataTable
    One column from this input data is used as an argument for the external process
  3. Port Type: BufferedDataTable
    One column from this input data is used as an argument for the external process

Output Ports

  1. Port Type: BufferedDataTable
    Output0 data from the external process (can also include the input, if specified)
  2. Port Type: BufferedDataTable
    Output1 data from the external process (can also include the input, if specified)
  3. Port Type: BufferedDataTable
    Output2 data from the external process (can also include the input, if specified)