Package org.biojava.nbio.protmod.structure

Class StructureUtil

java.lang.Object
org.biojava.nbio.protmod.structure.StructureUtil
public final class StructureUtil extends Object

  • Method Details

    • getStructureGroup

      public static StructureGroup getStructureGroup(Group group, boolean isAminoAcid)
      Parameters:
      group - a Group in structure.
      isAminoAcid - true if it is an amino acid.
      Returns:
      the StructureGroup of the group.

    • getStructureAtom

      public static StructureAtom getStructureAtom(Atom atom, boolean isParentAminoAcid)
      Parameters:
      atom - a Atom in structure.
      isParentAminoAcid - true if the containing group is an amino acid.
      Returns:
      the StructureAtom of the atom.

    • getStructureAtomLinkage

      public static StructureAtomLinkage getStructureAtomLinkage(Atom atom1, boolean isParentAminoAcid1, Atom atom2, boolean isParentAminoAcid2)
      Parameters:
      atom1 - the first Atom in structure.
      isParentAminoAcid1 - true if the first containing group is an amino acid..
      atom2 - the second Atom in structure.
      isParentAminoAcid2 - true if the second containing group is an amino acid..
      Returns:
      the StructureAtomLinkage of the two atoms.

    • getAtomDistance

      public static double getAtomDistance(Atom atom1, Atom atom2)
      Parameters:
      atom1 - the first Atom in structure.
      atom2 - the second Atom in structure.
      Returns:
      the distance between the two atoms in Angstrom.

    • findNearestAtomLinkage

      public static Atom[] findNearestAtomLinkage(Group group1, Group group2, List<String> potentialNamesOfAtomOnGroup1, List<String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
      Find a linkage between two groups within tolerance of bond length, from potential atoms.
      Parameters:
      group1 - the first Group.
      group2 - the second Group.
      potentialNamesOfAtomOnGroup1 - potential names of the atom on the first group. If null, search all atoms on the first group.
      potentialNamesOfAtomOnGroup2 - potential names of the atom on the second group. If null, search all atoms on the second group.
      ignoreNCLinkage - true to ignore all N-C linkages
      bondLengthTolerance - bond length error tolerance.
      Returns:
      an array of two Atoms that form bond between each other if found; null, otherwise.

    • findAtomLinkages

      public static List<Atom[]> findAtomLinkages(Group group1, Group group2, boolean ignoreNCLinkage, double bondLengthTolerance)
      Find linkages between two groups within tolerance of bond length, from potential atoms.
      Parameters:
      group1 - the first Group.
      group2 - the second Group.
      ignoreNCLinkage - true to ignore all N-C linkages
      bondLengthTolerance - bond length error tolerance.
      Returns:
      a list, each element of which is an array of two Atoms that form bond between each other.

    • findAtomLinkages

      public static List<Atom[]> findAtomLinkages(Group group1, Group group2, List<String> potentialNamesOfAtomOnGroup1, List<String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
      Find linkages between two groups within tolerance of bond length, from potential atoms.
      Parameters:
      group1 - the first Group.
      group2 - the second Group.
      potentialNamesOfAtomOnGroup1 - potential names of the atom on the first group. If null, search all atoms on the first group.
      potentialNamesOfAtomOnGroup2 - potential names of the atom on the second group. If null, search all atoms on the second group.
      ignoreNCLinkage - true to ignore all N-C linkages
      bondLengthTolerance - bond length error tolerance.
      Returns:
      a list, each element of which is an array of two Atoms that form bond between each other.

    • findLinkage

      public static Atom[] findLinkage(Group group1, Group group2, String nameOfAtomOnGroup1, String nameOfAtomOnGroup2, double bondLengthTolerance)
      Find a linkage between two groups within tolerance of bond length.
      Parameters:
      group1 - the first Group.
      group2 - the second Group.
      nameOfAtomOnGroup1 - atom name of the first group.
      nameOfAtomOnGroup2 - atom name of the second group.
      bondLengthTolerance - bond length error tolerance.
      Returns:
      an array of two Atoms that form bond between each other if found; null, otherwise.

    • getAtomNames

      public static List<String> getAtomNames(Group group)
      Parameters:
      group - a Group.
      Returns:
      all atom names of the group.

    • getAminoAcids

      public static List<Group> getAminoAcids(Chain chain)
      Get all amino acids in a chain.
      Parameters:
      chain -
      Returns: