Upload as LiveDesign Model

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.

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.

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.

Folder

Specify the destination folder (under 'Computational Models') to upload the Model

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. If "Same as current" is selected, one of the KNIME generic protocols ('Compound structure input' or 'column input') for the current Schrodinger release version will be used. The exact protocol will be chosen based on the flowvariable 'protocol_type' with possible values: 'compound_structure' or 'column_input'. If no such flow variable is available, then by default 'Compound structure input' will be considered. If the protocol for the current release is not available in the LD host, the same will be first created in LD host.

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.

Preserve Model data

If ON, then the MODEL DATA in the LiveDesign model will be preserved else the value in the current workflow will be overwritten.

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.

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Workflows

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