Package io.github.WeronikaJargielo.protein_interaction_finder

Class PdbStructureParser

  • public final class PdbStructureParser
extends java.lang.Object
    Wrapper for BioJava Structure class.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.ArrayList<AromaticRing> getAromaticRings()
      Returns aromatic rings present in parsed PDB structure.
      java.util.ArrayList<org.biojava.nbio.structure.Atom> getAtoms​(java.lang.String[] atomNames)
      Returns atoms of requested atoms' names present in parsed PDB structure.
      java.util.ArrayList<org.biojava.nbio.structure.Atom> getAtoms​(java.lang.String[] atomNames, java.util.List<AminoAcidAbbreviations> allowedAminoAcids)
      Returns atoms of requested atoms' names from allowed amino acids which are present in parsed PDB structure.
      org.biojava.nbio.structure.Structure getProteinStructure()
      Returns parsed protein structure.

      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Method Detail

      • getProteinStructure

        public org.biojava.nbio.structure.Structure getProteinStructure()
        Returns parsed protein structure.
        Returns:
        Parsed BioJava's Structure object.

      • getAtoms

        public java.util.ArrayList<org.biojava.nbio.structure.Atom> getAtoms​(java.lang.String[] atomNames)
        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.
        Parameters:
        atomNames - Array of requested PDB atoms' names (compatible with IUPAC naming convention).
        Returns:
        Atoms of requested names present in parsed PDB structure.

      • getAtoms

        public java.util.ArrayList<org.biojava.nbio.structure.Atom> getAtoms​(java.lang.String[] atomNames,
                                                                     java.util.List<AminoAcidAbbreviations> allowedAminoAcids)
        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.
        Parameters:
        atomNames - Array of requested PDB atoms' names (compatible with IUPAC naming convention).
        allowedAminoAcids - Desired amino acids to look for atoms in.
        Returns:
        Atoms of requested names present in parsed PDB structure belonging to desired allowedAminoAcids.

      • getAromaticRings

        public java.util.ArrayList<AromaticRing> getAromaticRings()
        Returns aromatic rings present in parsed PDB structure.
        Returns:
        Aromatic rings present in parsed PDB structure.
        See Also:
        AromaticRing