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GGP2105_​2Dto3D

GGP2105: 2Dto3D Chemical Structures

Merge multiple 2D/3D Mol/SDF file to 1 3D SDF
3D Convertor with CDK or MMFF Geometry Optimizations

Input:
Define a directory or folder containing 2D or 3D chemical structures in MOL format.
You could choose the file names as the ID if you wanted to convert to 1 SDF file.
or
You could load 1 SDF file or multiple SDF files.
And choose which field or property to be considered.
2D SDF or if you want to merge multiple SDF files to 1 SDF you could use this node as a reader.

Output:
SDF, CSV files | 3D and Table Viewer

Options:
You could save in MOL files, consider SMILES and other formats using different freely avaialble KNIME nodes.

Output asSDFCSVView Merge multiple 2D/3D Mol file to 1 3D SDF3D Convertor with CDK or MMFF Geometry Optimizations WorkflowID: NRF18001Name : 2D3DMOLSDFConvertorCreated by: Girinath PillaiCreated on: Jun 26, 18KNIME ver: 3.5.3Citation: KNIME Workflows, ID NRF18001,www.nyrindia.org, Kerala, India.Nodes : RDKit, CDK, KNIME ChemistryDescription:Merge multiple 2D/3D Mol/SDF file to 1 3DSDF3D Convertor with CDK or MMFF GeometryOptimizationsInput:Define a directory or folder containing 2D or 3Dchemical structures in MOL format.You could choose the file names as the ID ifyou wanted to convert to 1 SDF file.orYou could load 1 SDF file or multiple SDF files.And choose which field or property to beconsidered.2D SDF or if you want to merge multiple SDFfiles to 1 SDF you could use this node as areader.Output:SDF, CSV files | 3D and Table ViewerOptions:You could save in MOL files, consider SMILESand other formats using different freelyavaialble KNIME nodes.www.nyroindia.org Mols in directory3D OptimizationMMFF/UFFConvert to RDKitAdd HydrogensSDF File CDK 3D GeneratorView 3DView 3DSave as SDFConvert to SDF/MolSave as SDFView DataSave as CSV Molfile Reader RDKit OptimizeGeometry RDKit From Molecule RDKit Add Hs SDF Reader 3D Coordinates 3D Viewer 3D Viewer SDF Writer CDK to Molecule SDF Writer RDKit InteractiveTable CSV Writer(deprecated) Output asSDFCSVView Merge multiple 2D/3D Mol file to 1 3D SDF3D Convertor with CDK or MMFF Geometry Optimizations WorkflowID: NRF18001Name : 2D3DMOLSDFConvertorCreated by: Girinath PillaiCreated on: Jun 26, 18KNIME ver: 3.5.3Citation: KNIME Workflows, ID NRF18001,www.nyrindia.org, Kerala, India.Nodes : RDKit, CDK, KNIME ChemistryDescription:Merge multiple 2D/3D Mol/SDF file to 1 3DSDF3D Convertor with CDK or MMFF GeometryOptimizationsInput:Define a directory or folder containing 2D or 3Dchemical structures in MOL format.You could choose the file names as the ID ifyou wanted to convert to 1 SDF file.orYou could load 1 SDF file or multiple SDF files.And choose which field or property to beconsidered.2D SDF or if you want to merge multiple SDFfiles to 1 SDF you could use this node as areader.Output:SDF, CSV files | 3D and Table ViewerOptions:You could save in MOL files, consider SMILESand other formats using different freelyavaialble KNIME nodes.www.nyroindia.org Mols in directory3D OptimizationMMFF/UFFConvert to RDKitAdd HydrogensSDF File CDK 3D GeneratorView 3DView 3DSave as SDFConvert to SDF/MolSave as SDFView DataSave as CSV Molfile Reader RDKit OptimizeGeometry RDKit From Molecule RDKit Add Hs SDF Reader 3D Coordinates 3D Viewer 3D Viewer SDF Writer CDK to Molecule SDF Writer RDKit InteractiveTable CSV Writer(deprecated)

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: gpillai
Created at: 2018-06-25
On NodePit since: 2021-10-01
Last update: 2024-04-25
Created with KNIME version: v4.3.2
Tags: giribionyroindia2d3d

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