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Python script 1-2

Python Script Node Use-cases

The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between atoms for the conformer generated. It is also illustrated how to use it to run third party tools.

[Requires: Macromodel] [Keywords: Python, scripting]

Find other applications in the following workflow examples:
- In Real world examples, Vendor database preparation, in the descriptor generation metanode: calculate descriptors with Canvas API
- In Pharmacophore modeling, Phase screening 1-2: create a cmd script to pass the hypothesis to Maestro
- In Metanodes, Run PyMOL, Run Maestro 1:1 and Sitemap
- Quantum mechanics - Conformational search and QM optimization 1-2, in the Best conformer and Boltzmann population metanode: measure a dihedral angle

The script "report_cdr.py" is stored in the table creator node and can be edited easily. The python script run is embedded in the workflow. This makes easier to share suchworkflows with colleagues.Create the knime://knime.workflow/Scripts directory to store the "report_cdr.py" script inthe workflow. Run a Python Script in the Chemistry external node:A python script stored in the workflow in run in the Chemistry external tool node. The Python script can also be stored in the Table creatornode to be edited easily. Python Script Node Use-cases:The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between atoms for the conformer generated. It is also illustratedhow to use it to run third party tools.[Requires: Macromodel] [Keywords: Python, scripting]Find other applications in the following workflow examples:- In Real world examples, Vendor database preparation, in the descriptor generation metanode: calculate descriptors with Canvas API- In Pharmacophore modeling, Phase screening 1-2: create a cmd script to pass the hypothesis to Maestro - In Metanodes, Run PyMOL, Run Maestro 1:1 and Sitemap- Quantum mechanics - Conformational search and QM optimization 1-2, in the Best conformer and Boltzmann population metanode: measure a dihedral angleSome properties#ringatoms#nonHatm2D renderer2D view and calculated propertiesRing propertiesAtom numbersRun Maestro commandThis illustrates how to run a third-party tool but there is a dedicated node to run Maestro commands1 ligandMMod conformational searchwith specific parameters that aren't necessarily available in the MMod node configuration panelsDistances between 2 atoms in the conformersLigand titleDistance between 2 atoms1 conformationInspect the conformations%file%Distance %file%Select 2 atomsCDR detection HelpScript nameCDR detection Help report_cdr.py %file% %file% %file%Read a couple of moleculesQikProp Column Filter MAE-to-Smiles Table Viewer Python Script 1:1 Python Script 1:1 Row Filter Python Script 1:1 Table Viewer Extract Properties Python Script 1:1 Row Filter Run Maestro Molecule Writer(from MAE) Set MAE Properties CSV Writer KNIME-MaestroConnector ChemistryExternal Tool Table Viewer Parsing Table Viewer Get PDB Script Script ChemistryExternal Tool Table Viewer Parsing Table Viewer Table Creator Get PDB CSV Writer CSV Writer CSV Writer Molecule Reader(to MAE) The script "report_cdr.py" is stored in the table creator node and can be edited easily. The python script run is embedded in the workflow. This makes easier to share suchworkflows with colleagues.Create the knime://knime.workflow/Scripts directory to store the "report_cdr.py" script inthe workflow. Run a Python Script in the Chemistry external node:A python script stored in the workflow in run in the Chemistry external tool node. The Python script can also be stored in the Table creatornode to be edited easily. Python Script Node Use-cases:The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between atoms for the conformer generated. It is also illustratedhow to use it to run third party tools.[Requires: Macromodel] [Keywords: Python, scripting]Find other applications in the following workflow examples:- In Real world examples, Vendor database preparation, in the descriptor generation metanode: calculate descriptors with Canvas API- In Pharmacophore modeling, Phase screening 1-2: create a cmd script to pass the hypothesis to Maestro - In Metanodes, Run PyMOL, Run Maestro 1:1 and Sitemap- Quantum mechanics - Conformational search and QM optimization 1-2, in the Best conformer and Boltzmann population metanode: measure a dihedral angleSome properties#ringatoms#nonHatm2D renderer2D view and calculated propertiesRing propertiesAtom numbersRun Maestro commandThis illustrates how to run a third-party tool but there is a dedicated node to run Maestro commands1 ligandMMod conformational searchwith specific parameters that aren't necessarily available in the MMod node configuration panelsDistances between 2 atoms in the conformersLigand titleDistance between 2 atoms1 conformationInspect the conformations%file%Distance %file%Select 2 atomsCDR detection HelpScript nameCDR detection Help report_cdr.py %file% %file% %file%Read a couple of moleculesQikProp Column Filter MAE-to-Smiles Table Viewer Python Script 1:1 Python Script 1:1 Row Filter Python Script 1:1 Table Viewer Extract Properties Python Script 1:1 Row Filter Run Maestro Molecule Writer(from MAE) Set MAE Properties CSV Writer KNIME-MaestroConnector ChemistryExternal Tool Table Viewer Parsing Table Viewer Get PDB Script Script ChemistryExternal Tool Table Viewer Parsing Table Viewer Table Creator Get PDB CSV Writer CSV Writer CSV Writer Molecule Reader(to MAE)

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: kuppurar
Created at: 2017-10-16
On NodePit since: 2020-02-17
Last update: 2020-02-26
Created with KNIME version: v4.1.0
Tags: ScriptingMacromodelPython

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