Examples with Group de.bioforscher.jstructure.model.structure.Group used on opensource projects

Example 26 with Group

use of de.bioforscher.jstructure.model.structure.Group in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfilerTest method test_ligand_1h2t.

@Test
public void test_ligand_1h2t() {
    Structure structure = StructureParser.fromPdbId("1h2t").parse();
    Group ligand = structure.select().chainId("Z").residueNumber(1151).asGroup();
    InteractionContainer interactions = instance.annotateLigandInteractions(structure).getSubsetOfInteractions(ligand);
    Assert.assertFalse(interactions.getInteractions().isEmpty());
// TODO offset in renumbering of residues
// Group res20 = structure.getGroups().get(21);
// Group res43 = structure.select().residueNumber(43).asGroup();
// Group res112 = structure.select().residueNumber(112).asGroup();
// Group res116 = structure.select().residueNumber(116).asGroup();
// Assert.assertFalse(interactions.getSubsetOfInteractions(res20).getPiStackingInteractions().isEmpty());
// Assert.assertFalse(interactions.getSubsetOfInteractions(res43).getPiStackingInteractions().isEmpty());
// Assert.assertFalse(interactions.getSubsetOfInteractions(res112).getHydrogenBonds().isEmpty());
// Assert.assertFalse(interactions.getSubsetOfInteractions(res116).getSaltBridges().isEmpty());
}

Example 27 with Group

use of de.bioforscher.jstructure.model.structure.Group in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfilerTest method test_ligand_3g1h.

@Test
public void test_ligand_3g1h() {
    Structure structure = StructureParser.fromPdbId("3g1h").parse();
    InteractionContainer interactionContainer = instance.annotateLigandInteractions(structure);
    // there are strange effects regarding how interactions are associated to individual ligands
    Group ligand_H2U_A_229 = structure.select().chainId("A").residueNumber(229).asGroup();
    InteractionContainer ic_H2U_A_229 = interactionContainer.getSubsetOfInteractions(ligand_H2U_A_229);
    Assert.assertEquals("hydrophobic count does not match", 1, ic_H2U_A_229.getHydrophobicInteractions().size());
    Assert.assertEquals("hydrogen bond count does not match", 9, ic_H2U_A_229.getHydrogenBonds().size());
    Assert.assertEquals("water bridge count does not match", // offset between PLIP CLI and web server
    4 + 1, ic_H2U_A_229.getWaterBridges().size());
    Assert.assertEquals("salt bridge count does not match", 1, ic_H2U_A_229.getSaltBridges().size());
}

Example 28 with Group

use of de.bioforscher.jstructure.model.structure.Group in project jstructure by JonStargaryen.

the class PLIPParser method parse.

public static List<PLIPInteraction> parse(Chain chain, Document document) {
    List<PLIPInteraction> plipInteractions = new ArrayList<>();
    for (PLIPInteractionType plipInteractionType : PLIPInteractionType.values()) {
        logger.debug("parsing interactions of type {}", plipInteractionType);
        Elements interactionElements = document.getElementsByTag(plipInteractionType.getInteractionTag());
        for (Element interactionElement : interactionElements) {
            Optional<Group> currentGroup = interactionElement.getElementsByTag("resnr").stream().map(Element::text).filter(string -> string.length() < 10).mapToInt(Integer::valueOf).mapToObj(residueNumber -> chain.select().residueNumber(residueNumber).asOptionalGroup()).findFirst().orElse(Optional.empty());
            if (!currentGroup.isPresent()) {
                // TODO does a partner in another chain actually make sense?
                logger.trace("reference to group in different chain or failed to parse line:{}{}", System.lineSeparator(), interactionElement.text());
                continue;
            }
            try {
                Constructor<? extends PLIPInteraction> constructor = plipInteractionType.getDescribingClass().getDeclaredConstructor(Group.class, Element.class);
                constructor.setAccessible(true);
                PLIPInteraction plipInteraction = constructor.newInstance(currentGroup.get(), interactionElement);
                plipInteractions.add(plipInteraction);
            } catch (Exception e) {
                // move to root cause
                Throwable cause = e;
                while (cause.getCause() != null) {
                    cause = cause.getCause();
                }
                logger.debug("encountered exception during plip parsing: {} - {}", cause.getClass(), cause.getMessage());
            // interactions whose parsing failed are ignore and do not result in a thrown exception
            // TODO strict flag
            // throw new ComputationException(e);
            }
        }
    }
    // merge entries which need merging and remove the merged entries
    logger.debug("merging PLIP entries");
    List<PLIPInteraction> plipInteractionsToRemove = new ArrayList<>();
    for (PLIPInteraction plipInteraction : plipInteractions) {
        Group partner1 = plipInteraction.getPartner1();
        Group partner2 = plipInteraction.getPartner2();
        if (plipInteraction instanceof PiCationInteraction || plipInteraction instanceof PiStacking || plipInteraction instanceof SaltBridge) {
            // keep only those interactions where the first resNum is smaller
            if (partner1.getResidueIdentifier().getResidueNumber() > partner2.getResidueIdentifier().getResidueNumber()) {
                plipInteractionsToRemove.add(plipInteraction);
                continue;
            }
            try {
                if (plipInteraction instanceof PiCationInteraction) {
                    PiCationInteraction otherHalfOfInteraction = plipInteractions.stream().filter(PiCationInteraction.class::isInstance).map(PiCationInteraction.class::cast).filter(piCationInteraction -> piCationInteraction.getPartner1().equals(partner2) && piCationInteraction.getPartner2().equals(partner1)).findFirst().orElseThrow(NoSuchElementException::new);
                    ((PiCationInteraction) plipInteraction).getAtoms1().addAll(otherHalfOfInteraction.getAtoms2());
                } else if (plipInteraction instanceof PiStacking) {
                    PiStacking otherHalfOfInteraction = plipInteractions.stream().filter(PiStacking.class::isInstance).map(PiStacking.class::cast).filter(piStacking -> piStacking.getPartner1().equals(partner2) && piStacking.getPartner2().equals(partner1)).findFirst().orElseThrow(NoSuchElementException::new);
                    ((PiStacking) plipInteraction).getAtoms1().addAll(otherHalfOfInteraction.getAtoms2());
                } else {
                    SaltBridge otherHalfOfInteraction = plipInteractions.stream().filter(SaltBridge.class::isInstance).map(SaltBridge.class::cast).filter(saltBridge -> saltBridge.getPartner1().equals(partner2) && saltBridge.getPartner2().equals(partner1)).findFirst().orElseThrow(NoSuchElementException::new);
                    ((SaltBridge) plipInteraction).getAtoms1().addAll(otherHalfOfInteraction.getAtoms2());
                }
            } catch (NoSuchElementException e) {
                logger.debug("could not find other half of {} {} {}", plipInteraction.getClass().getSimpleName(), plipInteraction.getPartner1().getIdentifier(), plipInteraction.getPartner2().getIdentifier());
            }
        }
    }
    logger.debug("cleaning up PLIP entries");
    for (PLIPInteraction plipInteraction : plipInteractions) {
        // sanity - PLIP does not recognize chain ids correctly, i.e. 'A' and 'a' are assumed to refer to the same chain
        if (plipInteraction.getPartner1().getParentChain() != plipInteraction.getPartner2().getParentChain()) {
            plipInteractionsToRemove.add(plipInteraction);
            continue;
        }
        // ignore interactions with non-amino acids
        if (!plipInteraction.getPartner1().isAminoAcid() || !plipInteraction.getPartner2().isAminoAcid()) {
            plipInteractionsToRemove.add(plipInteraction);
            continue;
        }
        // sometimes, one side of the container will be empty
        if (!plipInteraction.isSane()) {
            plipInteractionsToRemove.add(plipInteraction);
        }
    }
    plipInteractions.removeAll(plipInteractionsToRemove);
    logger.debug("done parsing PLIP data");
    return plipInteractions;
}