Documentation/Nodes Reference

Node Reference Documentation

Complete documentation for all 100+ nodes available in VERA. Learn about inputs, outputs, properties, and how to use each node in your workflows.

100+
Total Nodes
11
Categories
15+
File Formats
8+
ML Algorithms

Getting Started Guide

Learn the basics of node-based workflows

Example Workflows

Ready-to-use workflow templates

Plugin Development

Create custom nodes for VERA

Browse by Category

Explore nodes organized by their functionality and scientific domain.

8 nodes

Molecular Docking

AutoDock Vina integration for drug discovery

Available Nodes:

  • AutoDock Vina (CPU)
  • AutoDock Vina GPU
  • Receptor Preparation
  • Ligand Preparation
  • Grid Search
  • +3 more...
View Documentation
10 nodes

Molecular Dynamics

GROMACS simulation and trajectory analysis

Available Nodes:

  • GROMACS Preparation
  • GROMACS Minimize
  • GROMACS Equilibrate
  • GROMACS Production
  • MDAnalysis
  • +5 more...
View Documentation
14 nodes

Machine Learning

Scikit-learn algorithms and model management

Available Nodes:

  • Train Test Split
  • Logistic Regression
  • Random Forest Classifier
  • SVM Classifier
  • KNN Classifier
  • +9 more...
View Documentation
23 nodes

Visualization

Molecular viewers and data plotting

Available Nodes:

  • Structure Draw 2D
  • ProLIF Interaction
  • Web 3D Viewer
  • 20+ Plot Types
  • Histogram, Scatter, Line
  • +4 more...
View Documentation
16 nodes

Data Processing

DataFrame operations and data manipulation

Available Nodes:

  • Select Columns
  • Filter Rows
  • Slice Rows
  • Drop Duplicates
  • Sort Rows
  • +5 more...
View Documentation
20 nodes

File I/O

Molecular and data file handling

Available Nodes:

  • SDF Reader
  • MOL/MOL2 Reader
  • PDB/PDBQT Reader
  • XYZ Reader
  • CSV/Excel Reader
  • +5 more...
View Documentation
2 nodes

Database Access

Chemical database connectivity

Available Nodes:

  • PubChem Search
  • RCSB PDB
View Documentation
3 nodes

Cheminformatics

Molecular processing and optimization

Available Nodes:

  • RDKit Minimize
  • OpenBabel Minimize
  • Conformer Generation
View Documentation
6 nodes

Chromatography

Chromatogram analysis and processing

Available Nodes:

  • Chrom Reader
  • Chrom Smoothing
  • Chrom Baseline
  • Chrom Peak Detect
  • Chrom Integrate
  • +1 more...
View Documentation
3 nodes

Response Surface

Response surface methodology

Available Nodes:

  • RSA Prep
  • RSA Fit
  • RSA Surface
View Documentation
3 nodes

Evaluation Metrics

Model evaluation and metrics

Available Nodes:

  • Confusion Matrix
  • Classification Report
  • Regression Metrics
View Documentation

Looking for a specific node?

Use the search function or browse by category to find the nodes you need. Each node page includes detailed information about inputs, outputs, properties, and example workflows.

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