0 ×

Upload as LiveDesign Model

Schrödinger extension for KNIME Workbench version 21.2.117.202105180045 by Schrödinger

Upload this workflow as LiveDesign Model
Requires Workflow Credentials or 'Credentials Input' Quick Form node with name: ld_credentials
Backend implementation
upload_to_ld.py from KNIME scripts

Options

LiveDesign host
Specify a LiveDesign host url which has the required protocol to upload this KNIME workflow as Model. If "From the Preferences" is selected, then the value set in Preferences is taken. Once a host is modified, the protocols and projects are fetched from the new host and the dropdown lists are updated automatically. The refresh button can also be used to manually update the protocols and projects.
LiveDesign protocol
Select a protocol under which the Model has to be added. This dropdown will list all the protocols from the host which has the text 'KNIME'. Clicking on the "Refresh" button will reload the protocols from the current host.
LiveDesign project
Select a project to which this model will be available. Clicking on the "Refresh" button will reload the projects from the current host.
Schordinger Suite
Specify the Schrodinger Suite (on LiveDesign host) to be used for this Model. This will be the value of the 'SCHRODINGER' MODEL DATA in the Model. The format could be an absolute path of the SCHRODINGER on the LiveDesign host or simply the release year like '2019-3'. If "From the Preferences" is selected, then the value set in Preferences is taken. If "Same as current" is selected, the current Schroinger release version will be used. If left empty, the value in Preferences will be taken. If it is empty in Preferences too, then current Schrodinger release version will be used.
Folder
Specify the destination folder (under 'Computational Models') to upload the Model
Choose a Corporate ID column
Choose a column as Corporate ID column. For most cases, it will be title (s_m_title) column.
3D column type
Choose the entry type for the 3D column if there in one. Default is 'Ligands'.
Command type
Choose the LiveDesign Model command type.
Overwrite Model
If ON and if exactly one Model already exists with the current workflow name, then it will be overwritten instead of creating another Model with same name. If multiple Models exist with same name, then a new Model with same name will be created.
PyMOL script
PyMOL script commands entered in this field will be executed while generating the pse file for ligand surfaces.

Surfaces will be loaded into the pymol session with their column name as object name. So to control any surface setting, use the column name of the surface (spaces must be replaced with underscores).
Flow variables can be used in the script. Flow variable prefix keyword: Upload_
Ex: If "Command script" has a variable "%var1%" and if there exists a flow variable "Upload_var1", then its value will get substituted in the command script.

Input Ports

Icon
Table of columns

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.3

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.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.