Examples with SimpleGapPenalty org.biojava.nbio.alignment.SimpleGapPenalty used on opensource projects

Example 6 with SimpleGapPenalty

use of org.biojava.nbio.alignment.SimpleGapPenalty in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method assignValuesForEarly.

private static void assignValuesForEarly(Experiment experiment, Chain chain) {
    String pdbSequence = chain.getAminoAcidSequence();
    String experimentSequence = experiment.getSequence();
    // align sequences to ensure correct mapping
    SequencePair<ProteinSequence, AminoAcidCompound> pair = null;
    try {
        pair = Alignments.getPairwiseAlignment(new ProteinSequence(experimentSequence), new ProteinSequence(pdbSequence), Alignments.PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), SubstitutionMatrixHelper.getBlosum62());
        List<AminoAcid> aminoAcids = chain.aminoAcids().collect(Collectors.toList());
        for (Experiment.Residue residue : experiment.getResidues()) {
            int experimentIndex = residue.getIndex() - 1;
            try {
                int pdbIndex;
                if (residue.getCode().equals("P") && residue.getIndex() == 1) {
                    // super-russian fix for STF0017 where the alignment should match theoretically
                    pdbIndex = 0;
                } else {
                    pdbIndex = pair.getIndexInTargetForQueryAt(experimentIndex);
                }
                AminoAcid aminoAcid = aminoAcids.get(pdbIndex);
                // assign experiment-specific protection level to residue
                aminoAcid.getFeature(Start2FoldResidueAnnotation.class).addProtectionLevelEntry(ProtectionLevel.EARLY);
            } catch (Exception e) {
                // residue not present in structure - e.g. for STF0031 and STF0032
                logger.warn("alignment:{}{}", System.lineSeparator(), pair.toString());
                logger.warn("failed to map residue {}-{}", residue.getCode(), residue.getIndex(), e);
            }
        }
    } catch (CompoundNotFoundException e) {
        throw new IllegalArgumentException(e);
    }
}