use of de.bioforscher.jstructure.model.structure.Structure in project jstructure by JonStargaryen.
the class A05_WriteEarlyFoldingContactCsv method handleLineLocally.
private static Optional<String> handleLineLocally(String line) {
try {
System.out.println(line);
String[] split = line.split(";");
String entryId = split[0];
String pdbId = split[1];
List<Integer> experimentIds = Pattern.compile(",").splitAsStream(split[2].replaceAll("\\[", "").replaceAll("]", "")).map(Integer::valueOf).collect(Collectors.toList());
Structure structure = StructureParser.fromPdbId(pdbId).parse();
Chain chain = structure.chains().findFirst().get();
Start2FoldXmlParser.parseSpecificExperiment(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"), experimentIds);
earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).collect(Collectors.toList());
// filter for contacts of EFR
PLIPInteractionContainer plipInteractionContainer = chain.getFeature(PLIPInteractionContainer.class);
System.out.println(pdbId + "\t" + earlyFoldingResidues.size() + "\t" + StandardFormat.format(plipInteractionContainer.getInteractions().size() / (double) earlyFoldingResidues.size()) + "\t" + plipInteractionContainer.getInteractions().size());
// ignore really small or non-interacting groups of EFR
if (plipInteractionContainer.getInteractions().size() < 2) {
return Optional.empty();
}
return Optional.of(plipInteractionContainer.getInteractions().stream().map(A05_WriteEarlyFoldingContactCsv::handleInteraction).collect(Collectors.joining(System.lineSeparator())));
} catch (Exception e) {
e.printStackTrace();
logger.info("calculation failed for {}", line, e);
return Optional.empty();
}
}
use of de.bioforscher.jstructure.model.structure.Structure in project jstructure by JonStargaryen.
the class A01_ReportGeneralStatistics method handleStrongFile.
private static void handleStrongFile(Path path) {
try {
String pdbId = Jsoup.parse(path.toFile(), "UTF-8").getElementsByTag("protein").attr("pdb_id");
Structure structure = StructureParser.fromPdbId(pdbId).parse();
Chain chain = structure.chains().findFirst().get();
Start2FoldXmlParser.parse(chain, path);
boolean hasStabilityData = chain.aminoAcids().map(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class)).anyMatch(Start2FoldResidueAnnotation::isStrong);
if (!hasStabilityData) {
return;
}
long count = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isStrong()).count();
strong.add((int) count);
weak.add((int) (chain.aminoAcids().count() - count));
} catch (IOException e) {
throw new UncheckedIOException(e);
}
}
use of de.bioforscher.jstructure.model.structure.Structure in project jstructure by JonStargaryen.
the class A03_WriteFunctionalClassificationArff method handleLine.
private static Optional<String> handleLine(String line) {
try {
logger.info("handling {}", line);
String[] split = line.split(";");
String pdbId = split[1];
Structure structure = StructureParser.fromPdbId(pdbId).parse();
Chain chain = structure.getFirstChain();
List<AminoAcid> aminoAcids = chain.aminoAcids().collect(Collectors.toList());
aminoAcids.forEach(RawFeatureVector::assignRawFeatureVector);
List<Integer> functionalResidueNumbers = Start2FoldConstants.extractFunctioanlResidueNumbers(split);
List<AminoAcid> functionalResidues = new ArrayList<>();
// do nothing if no annotation of functional residues exists
if (!functionalResidueNumbers.isEmpty()) {
FunctionalResidueParser.parse(chain, functionalResidueNumbers);
chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(FunctionalResidueAnnotation.class).isFunctional()).forEach(functionalResidues::add);
}
// ignore proteins lacking annotation of functional residues
if (functionalResidues.isEmpty()) {
return Optional.empty();
}
// smooth features
aminoAcids.forEach(aminoAcid -> SmoothedFeatureVector.assignSmoothedFeatureVector(aminoAcids, aminoAcid));
return Optional.of(aminoAcids.stream().filter(aminoAcid -> !(aminoAcid instanceof Proline)).map(aminoAcid -> {
SmoothedFeatureVector smoothedFeatureVector = aminoAcid.getFeature(SmoothedFeatureVector.class);
return StandardFormat.format(smoothedFeatureVector.getEnergy()) + "," + StandardFormat.format(smoothedFeatureVector.getEgor()) + "," + StandardFormat.format(smoothedFeatureVector.getSecondaryStructureElementSize()) + "," + StandardFormat.format(aminoAcid.getFeature(LoopFraction.class).getLoopFraction()) + // already smoothed
"," + StandardFormat.format(smoothedFeatureVector.getRasa()) + "," + StandardFormat.format(smoothedFeatureVector.getLocalInteractions()) + "," + StandardFormat.format(smoothedFeatureVector.getLocalHydrogen()) + "," + StandardFormat.format(smoothedFeatureVector.getLocalHydrophobic()) + "," + StandardFormat.format(smoothedFeatureVector.getLocalBackbone()) + "," + StandardFormat.format(smoothedFeatureVector.getNonLocalInteractions()) + "," + StandardFormat.format(smoothedFeatureVector.getNonLocalHydrogen()) + "," + StandardFormat.format(smoothedFeatureVector.getNonLocalHydrophobic()) + "," + StandardFormat.format(smoothedFeatureVector.getNonLocalBackbone()) + "," + StandardFormat.format(smoothedFeatureVector.getBetweenness()) + "," + StandardFormat.format(smoothedFeatureVector.getCloseness()) + "," + StandardFormat.format(smoothedFeatureVector.getClusteringCoefficient()) + "," + StandardFormat.format(smoothedFeatureVector.getHydrogenBetweenness()) + "," + StandardFormat.format(smoothedFeatureVector.getHydrogenCloseness()) + "," + StandardFormat.format(smoothedFeatureVector.getHydrogenClusteringCoefficient()) + "," + StandardFormat.format(smoothedFeatureVector.getHydrophobicBetweenness()) + "," + StandardFormat.format(smoothedFeatureVector.getHydrophobicCloseness()) + "," + StandardFormat.format(smoothedFeatureVector.getHydrophobicClusteringCoefficient()) + "," + StandardFormat.format(smoothedFeatureVector.getConvBetweenness()) + "," + StandardFormat.format(smoothedFeatureVector.getConvCloseness()) + "," + StandardFormat.format(smoothedFeatureVector.getConvClusteringCoefficient()) + "," + StandardFormat.format(smoothedFeatureVector.getDistinctNeighborhoods()) + "," + StandardFormat.format(smoothedFeatureVector.getConvDistinctNeighborhoods()) + "," + (functionalResidues.contains(aminoAcid) ? "functional" : "non-functional");
}).collect(Collectors.joining(System.lineSeparator())));
} catch (Exception e) {
logger.warn("computation for {} failed", line, e);
return Optional.empty();
}
}
use of de.bioforscher.jstructure.model.structure.Structure in project jstructure by JonStargaryen.
the class A06_EarlyFoldingFrequencies method handleLine.
private static void handleLine(String line) {
System.out.println(line);
String[] split = line.split(";");
String entryId = split[0];
String pdbId = split[1];
List<Integer> experimentIds = Pattern.compile(",").splitAsStream(split[2].replaceAll("\\[", "").replaceAll("]", "")).map(Integer::valueOf).collect(Collectors.toList());
Structure structure = StructureParser.fromPdbId(pdbId).parse();
Chain chain = structure.chains().findFirst().get();
Start2FoldXmlParser.parseSpecificExperiment(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"), experimentIds);
List<AminoAcid> earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).collect(Collectors.toList());
chain.aminoAcids().forEach(aminoAcid -> {
int ordinal = AminoAcid.Family.resolveOneLetterCode(aminoAcid.getOneLetterCode()).ordinal();
aminoAcidFrequencies[ordinal]++;
});
earlyFoldingResidues.forEach(aminoAcid -> {
int ordinal = AminoAcid.Family.resolveOneLetterCode(aminoAcid.getOneLetterCode()).ordinal();
earlyFoldingFrequencies[ordinal]++;
});
}
use of de.bioforscher.jstructure.model.structure.Structure in project jstructure by JonStargaryen.
the class A02_CreatePyMolRenderJobsForStrongResidues method composePyMolCommand.
private static Optional<String> composePyMolCommand(Path path) {
try {
String entryId = path.toFile().getName().split("\\.")[0];
String pdbId = Jsoup.parse(path.toFile(), "UTF-8").getElementsByTag("protein").attr("pdb_id");
Structure structure = StructureParser.fromPdbId(pdbId).parse();
Chain chain = structure.chains().findFirst().get();
Start2FoldXmlParser.parse(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"));
List<Integer> strongResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isStrong()).map(AminoAcid::getResidueIdentifier).map(ResidueIdentifier::getResidueNumber).collect(Collectors.toList());
if (strongResidues.isEmpty()) {
return Optional.empty();
}
return Optional.of("delete all" + System.lineSeparator() + "fetch " + pdbId + ", async=0" + System.lineSeparator() + // hide non-relevant stuff
"hide everything" + System.lineSeparator() + "show cartoon, chain A" + System.lineSeparator() + // decolor everything
"color grey80" + System.lineSeparator() + "zoom (chain A)" + System.lineSeparator() + strongResidues.stream().map(res -> "color efr, resi " + res).collect(Collectors.joining(System.lineSeparator())) + System.lineSeparator() + "ray" + System.lineSeparator() + "png " + Start2FoldConstants.PYMOL_DIRECTORY.resolve(entryId + "-strong.png") + System.lineSeparator());
} catch (IOException e) {
return Optional.empty();
}
}
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