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

Example 1 with SimpleGapPenalty

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

the class Start2FoldXmlParser method assignValues.

private static void assignValues(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());
        // logger.info("alignment:{}{}",
        // System.lineSeparator(),
        // pair.toString());
        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);
                // logger.debug("mapped experiment {}-{} onto PDB {}-{}",
                // residue.getCode(),
                // residue.getIndex(),
                // aminoAcid.getOneLetterCode(),
                // aminoAcid.getResidueIdentifier());
                // if(!residue.getCode().equals(aminoAcid.getOneLetterCode())) {
                // logger.warn("alignment:{}{}",
                // System.lineSeparator(),
                // pair.toString());
                // logger.warn("could not map data correctly for {}-{} and {}-{}",
                // residue.getCode(),
                // residue.getIndex(),
                // aminoAcid.getOneLetterCode(),
                // aminoAcid.getResidueIdentifier());
                // }
                // ignore: STF0034 (cannot align)
                // assign experiment-specific protection level to residue
                aminoAcid.getFeature(Start2FoldResidueAnnotation.class).addProtectionLevelEntry(Stream.of(ProtectionLevel.values()).filter(pl -> pl == experiment.getProtectionLevel()).findFirst().get());
            } 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);
    }
}

Example 2 with SimpleGapPenalty

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

the class A01_SingleLinkageClusterer method computeNeedlemanWunschSimilarity.

/**
 * Compute the Needleman-Wunsch alignment between 2 sequence and report the sequence identity.
 *
 * @param entry1 the reference sequence
 * @param entry2 the query sequence
 * @return the fraction of identically aligned positions
 */
private double computeNeedlemanWunschSimilarity(Chain entry1, Chain entry2) {
    try {
        ProteinSequence sequence1 = new ProteinSequence(entry1.getAminoAcidSequence());
        ProteinSequence sequence2 = new ProteinSequence(entry2.getAminoAcidSequence());
        SequencePair<ProteinSequence, AminoAcidCompound> pair = Alignments.getPairwiseAlignment(sequence1, sequence2, Alignments.PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), SubstitutionMatrixHelper.getBlosum62());
        System.out.println(pair.getPercentageOfIdentity());
        return pair.getPercentageOfIdentity();
    } catch (CompoundNotFoundException e) {
        throw new IllegalArgumentException(e);
    }
}

Example 3 with SimpleGapPenalty

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

the class Start2FoldXmlParser method assignValues.

private static void assignValues(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());
        logger.debug("alignment:{}{}", System.lineSeparator(), pair.toString());
        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);
                logger.debug("mapped experiment {}-{} onto PDB {}-{}", residue.getCode(), residue.getIndex(), aminoAcid.getOneLetterCode(), aminoAcid.getResidueIdentifier());
                // if(!residue.getCode().equals(aminoAcid.getOneLetterCode())) {
                // logger.warn("alignment:{}{}",
                // System.lineSeparator(),
                // pair.toString());
                // logger.warn("could not map data correctly for {}-{} and {}-{}",
                // residue.getCode(),
                // residue.getIndex(),
                // aminoAcid.getOneLetterCode(),
                // aminoAcid.getResidueIdentifier());
                // }
                // ignore: STF0034 (cannot align)
                // assign experiment-specific protection level to residue
                aminoAcid.getFeature(Start2FoldResidueAnnotation.class).addProtectionLevelEntry(Stream.of(ProtectionLevel.values()).filter(pl -> pl == experiment.getProtectionLevel()).findFirst().get());
            } 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);
    }
}

Example 4 with SimpleGapPenalty

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

the class Start2FoldXmlParser method assignValuesForStrong.

private static void assignValuesForStrong(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.STRONG);
            } 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);
    }
}

Example 5 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);
    }
}