use of de.bioforscher.start2fold.model.Experiment 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);
}
}
use of de.bioforscher.start2fold.model.Experiment in project jstructure by JonStargaryen.
the class Start2FoldXmlParser method parse.
public static void parse(Chain chain, InputStream inputStream) {
try {
// assign baseline resp. entry container for each residue
chain.aminoAcids().forEach(aminoAcid -> aminoAcid.getFeatureContainer().addFeature(new Start2FoldResidueAnnotation()));
Document document = Jsoup.parse(inputStream, "UTF-8", "/");
Elements experimentElements = document.getElementsByTag("experiment");
// logger.info("found {} experiments",
// experimentElements.size());
List<Experiment> experiments = experimentElements.stream().map(Experiment::parse).collect(Collectors.toList());
for (Experiment experiment : experiments) {
assignValues(experiment, chain);
}
} catch (IOException e) {
throw new UncheckedIOException(e);
}
}
use of de.bioforscher.start2fold.model.Experiment in project jstructure by JonStargaryen.
the class Start2FoldXmlParser method parseSpecificExperiment.
public static void parseSpecificExperiment(Chain chain, InputStream inputStream, List<Integer> experimentIds) {
// experimentIds);
try {
// assign baseline resp. entry container for each residue
chain.aminoAcids().forEach(aminoAcid -> aminoAcid.getFeatureContainer().addFeature(new Start2FoldResidueAnnotation()));
Document document = Jsoup.parse(inputStream, "UTF-8", "/");
Elements experimentElements = document.getElementsByTag("experiment");
List<Experiment> experiments = experimentElements.stream().map(Experiment::parse).filter(experiment -> experimentIds.contains(experiment.getExperimentId())).collect(Collectors.toList());
if (experimentIds.size() != experiments.size()) {
throw new IllegalArgumentException("did not find all referenced experiments");
}
for (Experiment experiment : experiments) {
assignValuesForEarly(experiment, chain);
}
} catch (IOException e) {
throw new UncheckedIOException(e);
}
}
use of de.bioforscher.start2fold.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);
}
}
Aggregations