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RNA2DUnifier

A Java library for unifying RNA secondary structure annotations from multiple tools into a single extended BPSEQ format.

RNA2DUnifier reads the output of seven popular RNA structure analysis tools, normalizes their heterogeneous representations, and produces a standardized extended BPSEQ file with full Leontis–Westhof classification of base pairs.

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🚀 Key Features

• Parses 7 different tools: FR3D, RNAview, RNApolis, mc-annotate, Barnaba, bpnet (BPFIND), x3dna-DSSR
• Automatic tool detection – just give it a file, no need to specify the tool
• Leontis–Westhof classification – all 12 geometric families (cWW, tWH, cHS, …)
• Two output formats:
  • Canonical BPSEQ – classic three‑column format (Watson‑Crick pairs only)
  • Extended BPSEQ – one column per LW family, supports multiple partners (e.g., base triples)
• Robust ANTLR4‑based parsers with informative error messages
• Java 21+ – modern language features, easy to integrate into Maven projects

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🔬 Supported Tools

Tool	Format	Detection signature
FR3D	JSON	"annotations" key
RNAview	Plain text	BEGIN_base-pair
RNApolis	FASTA + tabular	> and seq
mc-annotate	Plain text	Residue conformations
Barnaba	Tabular annotations	N_INT_INT N_INT_INT XXc
bpnet (BPFIND)	Tabular annotations	? separator + W:WC tokens
x3dna-DSSR	JSON	"pairs" key

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📦 Quick Example

RnaUnifier unifier = new RnaUnifier();
String result = unifier.process(new File("barnaba_output.out"), true);
System.out.println(result);

The output is an extended BPSEQ file:

Index	Nucleotide	cWW	tWW	cWH	tWH	cWS	tWS	cHH	tHH	cHS	tHS	cSS	tSS
1	G	29	0	0	0	0	0	0	0	0	0	0	0
2	G	28	0	0	0	0	0	0	0	0	0	0	0
5	U	25	0	0	0	0	0	0	0	0	35	0	0