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

Example 31 with AminoAcid

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

the class A05_WriteEarlyFoldingContactCsv method handleInteraction.

private static String handleInteraction(PLIPInteraction plipInteraction) {
    AminoAcid aa1 = (AminoAcid) plipInteraction.getPartner1();
    AminoAcid aa2 = (AminoAcid) plipInteraction.getPartner2();
    String pdbId = aa1.getParentStructure().getProteinIdentifier().getPdbId();
    return pdbId + "," + "A" + "," + aa1.getOneLetterCode() + "," + aa1.getFeature(GenericSecondaryStructure.class).getSecondaryStructure().getOneLetterRepresentation() + "," + aa2.getOneLetterCode() + "," + aa2.getFeature(GenericSecondaryStructure.class).getSecondaryStructure().getOneLetterRepresentation() + "," + plipInteraction.getClass().getSimpleName() + "," + (Math.abs(aa1.getResidueIndex() - aa2.getResidueIndex()) > 5 ? "long-range" : "local") + "," + (earlyFoldingResidues.contains(aa1) && earlyFoldingResidues.contains(aa2) ? "efr" : "normal");
}

Example 32 with AminoAcid

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

the class SecondaryStructureAnnotator method calculateHBondEnergy.

/**
     * Calculate HBond energy of two groups in cal/mol see Creighton page 147 f
     * <p>
     * Jeffrey, George A., An introduction to hydrogen bonding, Oxford
     * University Press, 1997. categorizes hbonds with donor-acceptor distances
     * of 2.2-2.5 &aring; as "strong, mostly covalent", 2.5-3.2 &aring; as
     * "moderate, mostly electrostatic", 3.2-4.0 &aring; as "weak,
     * electrostatic". Energies are given as 40-14, 15-4, and <4 kcal/mol
     * respectively.
     * @param residuePair
     * @return the energy of this h-bond
     */
private double calculateHBondEnergy(Pair<AminoAcid, AminoAcid> residuePair) {
    AminoAcid res1 = residuePair.getLeft();
    AminoAcid res2 = residuePair.getRight();
    try {
        Atom nAtom = res1.getN();
        double[] n = nAtom.getCoordinates();
        double[] h = res1.getH().getCoordinates();
        Atom oAtom = res2.getO();
        double[] o = oAtom.getCoordinates();
        double[] c = res2.getC().getCoordinates();
        double dno = LinearAlgebra.on(o).distance(n);
        double dhc = LinearAlgebra.on(c).distance(h);
        double dho = LinearAlgebra.on(o).distance(h);
        double dnc = LinearAlgebra.on(c).distance(n);
        // there seems to be a contact!
        if ((dno < MINDIST) || (dhc < MINDIST) || (dnc < MINDIST) || (dno < MINDIST)) {
            return HBONDLOWENERGY;
        }
        double e1 = Q / dho - Q / dhc;
        double e2 = Q / dnc - Q / dno;
        double energy = e1 + e2;
        // Avoid too strong energy
        if (energy > HBONDLOWENERGY) {
            return energy;
        }
        return HBONDLOWENERGY;
    } catch (NullPointerException e) {
        throw new SelectionException("missing backbone atoms for " + residuePair);
    }
}

Example 33 with AminoAcid

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

the class SecondaryStructureAnnotator method calculateHBonds.

/**
     * Calculate the HBonds between different groups. see Creighton page 147 f
     */
private void calculateHBonds(List<AminoAcid> residues) {
    for (int i = 0; i < residues.size() - 1; i++) {
        for (int j = i + 1; j < residues.size(); j++) {
            AminoAcid res1 = residues.get(i);
            AminoAcid res2 = residues.get(j);
            try {
                double squaredDistance = LinearAlgebra.on(res1.getCa().getCoordinates()).distanceFast(res2.getCa().getCoordinates());
                if (squaredDistance > CA_MIN_DIST_SQUARED) {
                    continue;
                }
                checkAddHBond(res1, res2);
                if (j != (i + 1)) {
                    checkAddHBond(res2, res1);
                }
            } catch (NullPointerException e) {
                throw new SelectionException("missing alpha carbons for " + res1 + " or " + res2);
            }
        }
    }
}

Example 34 with AminoAcid

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

the class SecondaryStructureAnnotator method trackHBondEnergy.

/**
     * Store Hbonds in the Groups. DSSP allows two HBonds per amino acid to
     * allow bifurcated bonds.
     */
private void trackHBondEnergy(Pair<AminoAcid, AminoAcid> residuePair, double energy) {
    AminoAcid res1 = residuePair.getLeft();
    AminoAcid res2 = residuePair.getRight();
    if (isProline(res1)) {
        logger.debug("Ignore: PRO {}", res1.getResidueNumber());
        return;
    }
    // try to findAny entries or create new ones with coil secondary structure
    SecondaryStructure state1 = getState(res1);
    SecondaryStructure state2 = getState(res2);
    double acc1e = state1.getAccept1().getEnergy();
    double acc2e = state1.getAccept2().getEnergy();
    double don1e = state2.getDonor1().getEnergy();
    double don2e = state2.getDonor2().getEnergy();
    // Acceptor: N-H-->O
    if (energy < acc1e) {
        logger.debug("{} < {}", energy, acc1e);
        state1.setAccept2(state1.getAccept1());
        HBond bond = new HBond();
        bond.setEnergy(energy);
        bond.setPartner(res2);
        state1.setAccept1(bond);
    } else if (energy < acc2e) {
        logger.debug("{} < {}", energy, acc2e);
        HBond bond = new HBond();
        bond.setEnergy(energy);
        bond.setPartner(res2);
        state1.setAccept2(bond);
    }
    // The other side of the bond: donor O-->N-H
    if (energy < don1e) {
        logger.debug("{} < {}", energy, don1e);
        state2.setDonor2(state2.getDonor1());
        HBond bond = new HBond();
        bond.setEnergy(energy);
        bond.setPartner(res1);
        state2.setDonor1(bond);
    } else if (energy < don2e) {
        logger.debug("{} < {}", energy, don2e);
        HBond bond = new HBond();
        bond.setEnergy(energy);
        bond.setPartner(res1);
        state2.setDonor2(bond);
    }
}

Example 35 with AminoAcid

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

the class Demo method test.

@Test
public void test() {
    // fetch a structure or load from local PDB if setup
    Structure structure = StructureParser.fromPdbId("1brr").parse();
    // select a chain
    Chain chainB = structure.select().chainId("B").asChain();
    // or a residue
    AminoAcid aminoAcid1 = chainB.select().residueNumber(60).asAminoAcid();
    // and another one
    AminoAcid aminoAcid2 = chainB.select().residueNumber(100).asAminoAcid();
    // compute their distance
    System.out.println("distance of " + aminoAcid1 + " and " + aminoAcid2 + ": " + StandardFormat.format(aminoAcid1.calculate().centroid().distance(aminoAcid2.calculate().centroid())));
    // access amino acid-specific atoms
    chainB.select().aminoAcids().groupName("TRP").asFilteredGroups().map(Tryptophan.class::cast).map(tryptophan -> tryptophan + " CG position: " + Arrays.toString(tryptophan.getCg().getCoordinates())).forEach(System.out::println);
    // compute features on-the-fly and resolve dependencies
    // e.g. assign some random value to each amino acid
    structure.aminoAcids().forEach(aminoAcid -> aminoAcid.getFeatureContainer().addFeature(new Feature(new Random().nextDouble())));
    chainB.aminoAcids().map(aminoAcid -> aminoAcid + " random feature: " + StandardFormat.format(aminoAcid.getFeature(Feature.class).getValue())).forEach(System.out::println);
    System.out.println("averages among chains:");
    structure.chainsWithAminoAcids().map(chain -> chain.getChainIdentifier() + "'s average random feature: " + StandardFormat.format(chain.aminoAcids().map(aminoAcid -> aminoAcid.getFeature(Feature.class)).mapToDouble(Feature::getValue).average().getAsDouble())).forEach(System.out::println);
}