Downloads

KNIME Workflows for Maestro | or "Click here" for non-Maestro KNIME Workflows

KNIME Workflows for Maestro for Schrödinger Suite 2012 Update 2, Schrödinger Suite 2012 Update 1 and Schrödinger Suite 2012 General Release can be downloaded from this page.

If you require non-Maestro KNIME Workflows for Schrödinger Suite 2012, please click here.

Below are many useful workflows for performing automation, customization, and scientific augmentation to the Schrödinger Suite. The workflows additionally provide a framework for scientists to create custom workflows. Check back regularly, as improvements to existing workflows and new workflows are added frequently. Send requests for improvements or new workflows to help@schrodinger.com.

Downloading and installing workflows: The easiest way to download and install KNIME Workflows for Maestro is from within Maestro. Just click on the "Workflows" menu, choose "KNIME Workflows" then "Update."


Select Workflows

Listed below are example KNIME Workflows for Maestro that utilize many of the Schrödinger KNIME Extensions (Nodes) as well as many other built-in tools.

Check the boxes next to the workflows you wish to download, read the Important Notes, then proceed below to check the Important Notes checkbox and click the Download button.

Select Description Author Updated
Cheminformatics
Nearest neighbor similarity distribution: Report the distribution of the similarities/distances between each molecule and its nearest neighbor.
[Workflow name: Nearest_neighbor_similarity_distribution_install.py (Revision 1.0)] [Workflow type: Maestro/Python] [Requires: Canvas]		 Schrödinger 03/05/2012
Substructure Search: Filter structures by running a substructure query.
[Workflow name: Substructure_search_install.py (Revision 1.0)] [Workflow type: Maestro/Python] [Requires: Canvas]		 Schrödinger 03/05/2012
General Tools
Process PDB codes: Preprocess or prepare a set of structures from a list of PDB codes.
[Workflow name: Process_PDB_codes_install.py (Revision 1.0)] [Workflow type: Maestro/Python] [Requires: Maestro]		 Schrödinger 03/05/2012
Binding site RMSD matrix: Calculate a matrix of RMSDs between protein binding sites.
[Workflow name: Binding_site_RMSD_matrix_install.py (Revision 1.0)] [Workflow type: Maestro/Python] [Requires: Maestro]		 Schrödinger 03/05/2012
Split and align multimers: Split protein multimers by chain ID and align binding sites.
[Workflow name: Split_and_align_multimers_install.py (Revision 1.0)] [Workflow type: Maestro/Python] [Requires: Maestro]		 Schrödinger 03/05/2012


Important Notes

NOTICE: THE WORKFLOWS ON THIS WEB SITE HAVE BEEN GENERATED BY SCHRÖDINGER OR BY USERS OF SCHRÖDINGER SOFTWARE. THE WORKFLOWS ARE PROVIDED FREE OF CHARGE. THE WORKFLOWS ARE PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, AND MAY NOT BE ERROR FREE. SCHRÖDINGER AND THE AUTHORS OF THESE WORKFLOWS DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL SCHRÖDINGER OR THE AUTHORS OF THESE WORKFLOWS BE LIABLE FOR SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND.

I have read the Important Notes above. You must check this box before downloading.

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Installation Instructions
  • Once you have downloaded the .tar file containing the workflows, extract the tar file with the command:

    tar -xvf Schrodinger_MaestroKNIMEWorkflows_Download.tar

    This will create a new directory named Schrodinger_MaestroKNIMEWorkflows_Download containing the workflows grouped into subdirectories, and a README file with additional instructions.

  • The workflows can be installed from the command line or using Maestro. When installing from the command line, you can choose whether to install into just your user area or into a common area for all users. The default common area is the directory $SCHRODINGER/mmshare-vXXXXX/python/workflows
    , but a different common area can be specified by setting the MAESTRO_WORKFLOW_LOCATION environment variable to the desired directory before proceeding with the installation.

    • To install from the command line:

      • Into a common area for all users:

        cd Schrodinger_MaestroKNIMEWorkflows_Download
        $SCHRODINGER/run installscripts.py -k -c -d MaestroWorkflows
        $SCHRODINGER/run installscripts.py -k -c -d PythonScripts

      • Into just your user area for your own use:

        cd Schrodinger_MaestroKNIMEWorkflows_Download
        $SCHRODINGER/run installscripts.py -k -u -d MaestroWorkflows
        $SCHRODINGER/run installscripts.py -k -u -d PythonScripts
    • To install using Maestro:

      • Go to the Workflows menu and choose KNIME, then Install. In the Install Workflows panel, browse to the MaestroWorkflows subdirectory inside your extracted Schrodinger_MaestroKNIMEWorkflows_Download directory and click Choose. Click in the Install column to select workflows for installation, then click OK. Please see the Maestro User Manual for detailed instructions on installing workflows via Maestro.