HOWTO: Extract 2D structure from 3D coordinates

The following snippet shows how to extract base pairs from 3D coordinates and what can be done with that information:

    // get chain A only
    final PdbModel model;
    final PdbChain chain =
        model.chains().stream()
            .filter(pdbChain -> "A".equals(pdbChain.identifier()))
            .findFirst()
            .orElseThrow(RuntimeException::new);

    // extract base pairs
    final BpSeq bpSeq = CanonicalStructureExtractor.bpSeq(chain);
    System.out.println("Pairs: " + bpSeq.paired().size());

    // remove isolated base pairs
    final BpSeq withoutIsolatedPairs = bpSeq.withoutIsolatedPairs();
    System.out.println("Non-isolated pairs: " + withoutIsolatedPairs.paired().size());

    // find stems
    final List<Region> regions = Region.createRegions(withoutIsolatedPairs);
    System.out.println("Stems: " + regions.size());
    regions.forEach(
        region ->
            System.out.printf(
                "  %d-%d [length=%d]%n", region.begin(), region.end(), region.length()));

    // convert to CT format
    final Ct ct = Ct.fromBpSeq(bpSeq);
    System.out.println("Strands: " + ct.strandCount());

    // convert to dot-bracket
    final Converter converter = ImmutableDefaultConverter.of();
    final DotBracket dotBracket = converter.convert(bpSeq);
    System.out.println("Pseudoknot order: " + dotBracket.pseudoknotOrder());
    System.out.println("Dot-bracket:\n\n" + dotBracket);

The result:

Pairs: 8
Non-isolated pairs: 5
Stems: 2
  7-22 [length=3]
  12-33 [length=2]
Strands: 1
Pseudoknot order: 2
Dot-bracket:

>strand
gGAACCGGUGCGCAUAACCACCUCAGUGCGAGCAA
......(((.{[[....[[)))...].].}.]]..