rnalocmin

name	rnalocmin
description	Use when analyzing RNA secondary structure landscapes to find local minima via gradient walks, generate barrier trees, or compute rates for kinetic modeling with treekin.
disable-model-invocation	true
user-invocable	true

rnalocmin

Quick Start

• Command: RNAlocmin [OPTION]... [FILE]...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAlocmin
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Collapse a sampled RNA structure ensemble into local minima by gradient walks.
• Build barrier-tree-like summaries from RNAsubopt output.
• Produce kinetic landscape inputs for treekin.
• Filter minima by basin depth or energy-barrier criteria.

Common Patterns

# 1) Derive local minima from sampled suboptimal structures
RNAsubopt -p 10000 < sequence.txt > suboptp.txt
RNAlocmin -s sequence.txt < suboptp.txt > locmin.txt

# 2) Emit barrier-tree style output
RNAlocmin -s sequence.txt -b < suboptp.txt > barriers.txt

# 3) Keep only minima above a barrier threshold
RNAlocmin -s sequence.txt --minh 1.5 < suboptp.txt > filtered_minima.txt

Recommended Workflow

1. Generate sampled structures using RNAsubopt -p <count> < sequence.txt > suboptp.txt
2. Run RNAlocmin -s sequence.txt < suboptp.txt to compute local minima via gradient descent
3. Add -b for barrier tree output or -r for rates generation if kinetic analysis is needed
4. Filter results with --minh to report only minima exceeding a specified energy barrier threshold

Guardrails

• Requires structure input from stdin (typically from RNAsubopt); sequence file via -s is optional if sequence is first line of input
• Do not combine --noLP with random walk (-w R) or shift move set (-m S)
• Use -p to provide previously found local minima output instead of recomputing from sequence