Evaluate Diversity

Runs diversity evaluation pipeline on the provided batch of proteins. Clusters structures based on TM-score and outputs a CSV table with cluster indices for each input.

Quick Start

1. Connect a batch of PDB structures to the node.
2. Set the maximum TM-score threshold for clustering (e.g., 0.6).
3. Specify the number of processes for parallel evaluation (default: 8).
4. Run the node to obtain a CSV with cluster assignments.

Setup Guide

1. Prepare Input Structures

1. Generate or collect a batch of PDB structures to evaluate.
2. Ensure each structure has a unique identifier.

2. Configure Diversity Evaluation

1. Set max_ctm_threshold to control cluster separation (lower = stricter clustering).
2. Adjust num_processes for available compute resources.

Basic Usage

Batch Diversity Assessment

• Cluster a set of generated or designed proteins to assess structural diversity.
• Identify representative structures from each cluster for downstream analysis.

Configuration

Required Inputs

Field	Description	Type	Example
pdb	Structures to evaluate.	PDB	{"design_1": "...", "design_2": "..."}
max_ctm_threshold	Maximum TM score threshold between clusters.	FLOAT	0.6
num_processes	Number of processes for parallel evaluation.	INT	8

Optional Inputs

None

Outputs

Field	Description	Example
score.csv	Scores of the pdbs (cluster indices).	CSV file with cluster assignments

Best Practices

Diversity Parameter Tuning

• Use a lower max_ctm_threshold for stricter clustering (more clusters, higher diversity sensitivity).
• Increase num_processes to speed up evaluation on large batches if hardware allows.

Workflow Integration

• Use after protein generation to select diverse candidates for further analysis.
• Combine with functional evaluation nodes for comprehensive assessment.

Troubleshooting

Common Issues

• All structures assigned to one cluster: Try lowering max_ctm_threshold to increase sensitivity.
• Node runs slowly on large batches: Increase num_processes if possible, or reduce batch size.

Need Help?

• Contact support for further assistance.