Package jgromacs.data

Class Structure

java.lang.Object
jgromacs.data.Structure
All Implemented Interfaces:
Cloneable

public class Structure extends Object implements Cloneable
Objects of this class represent a single structure
  • Constructor Details

    • Structure

      public Structure()
      Constructs a new Structure object
    • Structure

      public Structure(String name)
      Constructs a new Structure object of given name
  • Method Details

    • getName

      public String getName()
      Returns the name of structure
      Returns:
      name of structure
    • setName

      public void setName(String name)
      Sets the name of structure
      Parameters:
      name - of structure
    • getResiduesAsArrayList

      public ArrayList<Residue> getResiduesAsArrayList()
      Returns residues as an ArrayList object
      Returns:
      residues as an ArrayList
    • getNumberOfResidues

      public int getNumberOfResidues()
      Returns the number of residues in the structure
      Returns:
      number of residues
    • getNumberOfAtoms

      public int getNumberOfAtoms()
      Returns the number of atoms in the structure
      Returns:
      number of atoms
    • getNumberOfChains

      public int getNumberOfChains()
      Returns the number of chains in the structure
      Returns:
      number of chains
    • getChainIDs

      public ArrayList<String> getChainIDs()
      Returns the list of chain IDs in the structure
      Returns:
      list of chain IDs
    • getResidue

      public Residue getResidue(int i)
      Returns residue #i of the structure
      Returns:
      residue #i
    • getResidueByIndex

      public Residue getResidueByIndex(int index, String chainID)
      Returns the residue of given index and given chain ID
      Parameters:
      index - index of residue
      chainID - chain ID of residue
      Returns:
      residue of given index and chain ID
    • getResidueByIndex

      public Residue getResidueByIndex(int index)
      Returns the residue of given index
      Parameters:
      index - index of residue
      Returns:
      residue of given index
    • getAtom

      public Atom getAtom(int i)
      Returns atom #i of the structure
      Returns:
      atom #i
    • getAtomByIndex

      public Atom getAtomByIndex(int index)
      Returns the atom of given index
      Parameters:
      index - index of atom
      Returns:
      atom of given index
    • getAtomInResidueOfIndex

      public Atom getAtomInResidueOfIndex(int residueindex, String chainID, int i)
      Returns atom #i of the residue of given index and chain ID
      Parameters:
      residueindex - index of residue
      chainID - chain ID of residue
      Returns:
      atom #i in residue of given index and chain ID
    • getAtomInResidueOfIndex

      public Atom getAtomInResidueOfIndex(int residueindex, int i)
      Returns atom #i of the residue of given index
      Parameters:
      residueindex - index of residue
      Returns:
      atom #i in residue of given index
    • addResidue

      public void addResidue(Residue residue)
      Adds a new residue to the structure
      Parameters:
      residue - new residue
    • removeResidue

      public void removeResidue(Residue residue)
      Removes a residue from the structure
      Parameters:
      residue - the residue to be removed
    • removeResidue

      public void removeResidue(int i)
      Removes residue #i from the structure
    • setResidue

      public void setResidue(int i, Residue residue)
      Replaces residue #i with a new residue
      Parameters:
      residue - new residue
    • removeAtom

      public void removeAtom(int i)
      Removes atom #i from the structure
    • removeAtomByIndex

      public void removeAtomByIndex(int index)
      Removes the atom of given index from the structure
      Parameters:
      index - index of atom
    • removeAtom

      public void removeAtom(Atom atom)
      Removes the given atom from the structure
      Parameters:
      atom - the atom to be removed
    • addAtomToResidue

      public void addAtomToResidue(int i, Atom atom)
      Adds the given atom to residue #i
      Parameters:
      atom - new atom
    • addAtomToResidueOfIndex

      public void addAtomToResidueOfIndex(int index, Atom atom)
      Adds the given atom to the residue of given index
      Parameters:
      index - index of residue
      atom - new atom
    • setAtomInResidue

      public void setAtomInResidue(int i, int j, Atom atom)
      Replaces atom #j of residue #i with a new atom
      Parameters:
      atom - new atom
    • setAtomInResidueOfIndex

      public void setAtomInResidueOfIndex(int index, int i, Atom atom)
      Replaces atom #i of the residue of given index with a new atom
      Parameters:
      index - index of residue
      atom - new atom
    • getSystemIndexSet

      public IndexSet getSystemIndexSet()
      Returns the index set of all atoms in the system
      Returns:
      index set of all atoms
    • getProteinIndexSet

      public IndexSet getProteinIndexSet()
      Returns the index set of protein atoms
      Returns:
      index set of protein atoms
    • getHeavyProteinIndexSet

      public IndexSet getHeavyProteinIndexSet()
      Returns the index set of protein atoms except of hydrogen atoms
      Returns:
      index set of protein atoms except of hydrogen atoms
    • getAlphaCarbonIndexSet

      public IndexSet getAlphaCarbonIndexSet()
      Returns the index set of alpha carbon atoms
      Returns:
      index set of alpha carbon atoms
    • getBackboneIndexSet

      public IndexSet getBackboneIndexSet()
      Returns the index set of backbone atoms
      Returns:
      index set of backbone atoms
    • getMainChainIndexSet

      public IndexSet getMainChainIndexSet()
      Returns the index set of main chain atoms
      Returns:
      index set of main chain atoms
    • getMainChainPlusCbIndexSet

      public IndexSet getMainChainPlusCbIndexSet()
      Returns the index set of main chain plus beta carbon atoms
      Returns:
      index set of main chain plus beta carbon atoms
    • getMainChainPlusHIndexSet

      public IndexSet getMainChainPlusHIndexSet()
      Returns the index set of main chain plus hydrogen atoms
      Returns:
      index set of main chain plus hydrogen atoms
    • getSideChainIndexSet

      public IndexSet getSideChainIndexSet()
      Returns the index set of side chain atoms
      Returns:
      index set of side chain atoms
    • getSideChainMinusHIndexSet

      public IndexSet getSideChainMinusHIndexSet()
      Returns the index set of side chain atoms except of hydrogen atoms
      Returns:
      index set of side chain atoms except of hydrogen atoms
    • getNonProteinIndexSet

      public IndexSet getNonProteinIndexSet()
      Returns the index set of non-protein atoms
      Returns:
      index set of non-protein atoms
    • getWaterIndexSet

      public IndexSet getWaterIndexSet()
      Returns the index set of water atoms
      Returns:
      index set of water atoms
    • getDefaultIndexSetList

      public IndexSetList getDefaultIndexSetList()
      Returns the list of default index sets
      Returns:
      list of default index sets
    • getIndexSetOfChainID

      public IndexSet getIndexSetOfChainID(String chainID)
      Returns the index set of atoms of a given chain ID
      Parameters:
      chainID - selected chain ID
      Returns:
      index set defined by chain ID
    • setAtomCoordinates

      public void setAtomCoordinates(int i, Point3D coordinates)
      Sets the coordinates of atom #i
      Parameters:
      coordinates - new atomic coordinates
    • setAtomOfIndexCoordinates

      public void setAtomOfIndexCoordinates(int index, Point3D coordinates)
      Sets the coordinates of atom of given index
      Parameters:
      coordinates - new atomic coordinates
    • setAllAtomCoordinates

      public void setAllAtomCoordinates(PointList pointlist)
      Sets the coordinates of all atoms
      Parameters:
      pointlist - list of new atomic coordinates
    • getAllAtomCoordinates

      public PointList getAllAtomCoordinates()
      Returns the coordinates of all atoms
      Returns:
      list of atomic coordinates
    • getSequence

      public Sequence getSequence()
      Returns the amino acid sequence of the structure
      Returns:
      amino acid sequence
    • getChains

      public Structure[] getChains()
      Returns all chains in an array of Structure objects
      Returns:
      array of chains
    • getSubStructure

      public Structure getSubStructure(IndexSet indices)
      Returns the substructure defined by the given index set
      Parameters:
      indices - index set of substructure
      Returns:
      substructure
    • convertIndicesToArrayListIndices

      public ArrayList<Integer> convertIndicesToArrayListIndices(IndexSet indices)
      Converts atomic indices into list indices
      Parameters:
      indices - set of atomic indices
      Returns:
      list indices
    • mapAtomIndicesToResidueIndices

      public ArrayList<Integer> mapAtomIndicesToResidueIndices(IndexSet indices)
      Maps atomic indices to residue indices (i.e. returns which residues contain the given atoms). If an atom is not present in any residue it is mapped to residue index -1
      Parameters:
      indices - set of atomic indices
      Returns:
      residue indices
    • mapResidueIndicesToAtomIndices

      public IndexSet mapResidueIndicesToAtomIndices(ArrayList<Integer> indices)
      Maps residue indices to atomic indices (i.e. returns which atoms are present in the given residues).
      Parameters:
      indices - ArrayList of residue indices
      Returns:
      IndexSet of atomic indices
    • toString

      public String toString()
      Returns the String representation of structure
      Overrides:
      toString in class Object
      Returns:
      String representation
    • toStringAsGRO

      public String toStringAsGRO()
      Returns the String representation of structure in GRO format
      Returns:
      String representation in GRO format
    • toStringAsPDB

      public String toStringAsPDB()
      Returns the String representation of structure in PDB format
      Returns:
      String representation in PDB format
    • toStringInfo

      public String toStringInfo()
      Returns summary information about the structure
      Returns:
      summary information
    • clone

      public Object clone()
      Returns an identical Structure object
      Overrides:
      clone in class Object
      Returns:
      clone of the structure
    • equals

      public boolean equals(Object other)
      Returns true if the two structures are identical
      Overrides:
      equals in class Object
      Parameters:
      other - the other structure
    • hashCode

      public int hashCode()
      Returns hash code
      Overrides:
      hashCode in class Object