use of de.bioforscher.jstructure.efr.model.Experiment 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);
}
}
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