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Example 6 with Experiment

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);
    }
}
Also used : CompoundNotFoundException(org.biojava.nbio.core.exceptions.CompoundNotFoundException) AminoAcid(de.bioforscher.jstructure.model.structure.aminoacid.AminoAcid) Experiment(de.bioforscher.jstructure.efr.model.Experiment) Start2FoldResidueAnnotation(de.bioforscher.jstructure.efr.model.Start2FoldResidueAnnotation) SimpleGapPenalty(org.biojava.nbio.alignment.SimpleGapPenalty) CompoundNotFoundException(org.biojava.nbio.core.exceptions.CompoundNotFoundException) IOException(java.io.IOException) UncheckedIOException(java.io.UncheckedIOException) ProteinSequence(org.biojava.nbio.core.sequence.ProteinSequence) AminoAcidCompound(org.biojava.nbio.core.sequence.compound.AminoAcidCompound)

Aggregations

Experiment (de.bioforscher.jstructure.efr.model.Experiment)6 Start2FoldResidueAnnotation (de.bioforscher.jstructure.efr.model.Start2FoldResidueAnnotation)6 IOException (java.io.IOException)6 UncheckedIOException (java.io.UncheckedIOException)6 AminoAcid (de.bioforscher.jstructure.model.structure.aminoacid.AminoAcid)5 SimpleGapPenalty (org.biojava.nbio.alignment.SimpleGapPenalty)5 CompoundNotFoundException (org.biojava.nbio.core.exceptions.CompoundNotFoundException)5 ProteinSequence (org.biojava.nbio.core.sequence.ProteinSequence)5 AminoAcidCompound (org.biojava.nbio.core.sequence.compound.AminoAcidCompound)5 Document (org.jsoup.nodes.Document)4 Elements (org.jsoup.select.Elements)4 Method (de.bioforscher.jstructure.efr.model.Method)3 ProtectionLevel (de.bioforscher.jstructure.efr.model.ProtectionLevel)3 Chain (de.bioforscher.jstructure.model.structure.Chain)3 InputStream (java.io.InputStream)3 Files (java.nio.file.Files)3 Path (java.nio.file.Path)3 List (java.util.List)3 Collectors (java.util.stream.Collectors)3 Stream (java.util.stream.Stream)3