io.github.WeronikaJargielo.protein_interaction_finder.PdbStructureParser Maven / Gradle / Ivy

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Library for finding possible interactions in proteins.
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package io.github.WeronikaJargielo.protein_interaction_finder;

import com.google.common.collect.Lists;
import org.biojava.nbio.structure.*;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.Stream;

/**
 * Wrapper for BioJava Structure class.
 */
public final class PdbStructureParser {
    private final Structure proteinStructure;

    /**
     * Instantiates new PdbStructureParser by parsing given PDB file to BioJava Structure object.
     *
     * @param pdbFilename Path to PDB file to parse.
     * @throws IOException        Probably given PDB file does not exist.
     * @throws StructureException Probably given PDB file is incorrectly formatted.
     */
    PdbStructureParser(String pdbFilename) throws IOException, StructureException {
        proteinStructure = readProteinStructure(pdbFilename);
    }

    /**
     * Returns parsed protein structure.
     *
     * @return Parsed BioJava's Structure object.
     */
    public Structure getProteinStructure() {
        return proteinStructure;
    }

    private Structure readProteinStructure(String pdbFilename) throws IOException, StructureException {
        return StructureIO.getStructure(pdbFilename);
    }

    /**
     * Returns atoms of requested atoms' names present in parsed PDB structure.
     *
     * Note: for each amino acid atoms are added to returned list only if all requested atoms are present in particular amino acid.
     *
     * @param atomNames Array of requested PDB atoms' names (compatible with IUPAC naming convention).
     * @return Atoms of requested names present in parsed PDB structure.
     */
    public ArrayList getAtoms(String[] atomNames) {
        ArrayList atoms = new ArrayList<>(Arrays.asList(StructureTools.getAtomArray(proteinStructure, atomNames)));

        // Filter unrecognizable amino acid abbreviations.
        atoms.removeIf((a) -> {
            final String aminoAcidName = a.getGroup().getPDBName();
            try {
                final AminoAcidAbbreviations aminoAcidAbbr = AminoAcidAbbreviations.valueOf(aminoAcidName);
            } catch (java.lang.IllegalArgumentException e) {
                return true;
            }
            return false;
        });

        return atoms;
    }

    /**
     * Returns atoms of requested atoms' names from allowed amino acids which are present in parsed PDB structure.
     *
     * Note: For each amino acid atoms are added to returned list only if all requested atoms are present in particular amino acid.
     *
     * @param atomNames         Array of requested PDB atoms' names (compatible with IUPAC naming convention).
     * @param allowedAminoAcids Desired amino acids to look for atoms in.
     * @return Atoms of requested names present in parsed PDB structure belonging to desired allowedAminoAcids.
     */
    public ArrayList getAtoms(String[] atomNames, List allowedAminoAcids) {
        ArrayList atoms = this.getAtoms(atomNames);

        atoms.removeIf((a) -> {
            final String aminoAcidName = a.getGroup().getPDBName();
            final AminoAcidAbbreviations aminoAcidAbbr = AminoAcidAbbreviations.valueOf(aminoAcidName);
            return ( ! allowedAminoAcids.contains(aminoAcidAbbr));
        });

        return atoms;
    }

    /**
     * Returns aromatic rings present in parsed PDB structure.
     * @see io.github.WeronikaJargielo.protein_interaction_finder.AromaticRing
     *
     * @return Aromatic rings present in parsed PDB structure.
     */
    public ArrayList getAromaticRings() {

        final List phenylalanineAtoms = getAtoms(new String[]{"CG", "CD1", "CD2", "CE1", "CE2", "CZ"}, Arrays.asList(AminoAcidAbbreviations.PHE));
        final List tyrosineAtoms = getAtoms(new String[]{"CG", "CD1", "CD2", "CE1", "CE2", "CZ"}, Arrays.asList(AminoAcidAbbreviations.TYR));

        final List tryptophanPyrroleRingAtoms = getAtoms(new String[]{"CG", "CD1", "CD2", "NE1", "CE2"}, Arrays.asList(AminoAcidAbbreviations.TRP));
        final List tryptophanBenzeneRingAtoms = getAtoms(new String[]{"CD2", "CE2", "CE3", "CZ2", "CZ3", "CH2"}, Arrays.asList(AminoAcidAbbreviations.TRP));

        final int pyrroleRingLen = 5;
        final int benzeneRingLen = 6;

        final List> phes = Lists.partition(phenylalanineAtoms, benzeneRingLen);
        final List> tyrs = Lists.partition(tyrosineAtoms, benzeneRingLen);
        final List> phesAndTyrs = Stream.concat(phes.stream(), tyrs.stream()).collect(Collectors.toList());

        final List> tryPyrroles = Lists.partition(tryptophanPyrroleRingAtoms, pyrroleRingLen);
        final List> tryBenzenes = Lists.partition(tryptophanBenzeneRingAtoms, benzeneRingLen);

        ArrayList  aromaticRings = new ArrayList<>();

        phesAndTyrs.forEach(aromaticRingAtoms -> aromaticRings.add(new AromaticRing(aromaticRingAtoms)));
        tryPyrroles.forEach(aromaticRingAtoms -> aromaticRings.add(new AromaticRing(aromaticRingAtoms)));
        tryBenzenes.forEach(aromaticRingAtoms -> aromaticRings.add(new AromaticRing(aromaticRingAtoms)));

        return aromaticRings;
    }

}