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Python script 1

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

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 command[illustrate how to run a third-party tool but there is a dedicated node to run Maestro commands]1 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%Read a couple of molecules%file%Select 2 atoms:eg 13 and 42 for a potential intra-molecular hydrogen bondQikProp 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 Molecule Reader(to MAE) KNIME-MaestroConnector 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 command[illustrate how to run a third-party tool but there is a dedicated node to run Maestro commands]1 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%Read a couple of molecules%file%Select 2 atoms:eg 13 and 42 for a potential intra-molecular hydrogen bondQikProp 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 Molecule Reader(to MAE) KNIME-MaestroConnector

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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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On NodePit since: 2020-02-17
Last update: 2020-02-26
Created with KNIME version: v4.1.0
Tags: ScriptingMacromodelPython

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