Structure

java.lang.Object
- jgromacs.data.Structure

All Implemented Interfaces:

java.lang.Cloneable
```
public class Structure
extends java.lang.Object
implements java.lang.Cloneable
```
Objects of this class represent a single structure

Constructor Summary

Constructors
Constructor and Description

Structure()
Constructs a new Structure object

Structure(java.lang.String name)
Constructs a new Structure object of given name

Constructors
Constructor and Description
`Structure()` Constructs a new Structure object
`Structure(java.lang.String name)` Constructs a new Structure object of given name

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAtomToResidue(int i, Atom atom)` Adds the given atom to residue #i
`void`	`addAtomToResidueOfIndex(int index, Atom atom)` Adds the given atom to the residue of given index
`void`	`addResidue(Residue residue)` Adds a new residue to the structure
`java.lang.Object`	`clone()` Returns an identical Structure object
`java.util.ArrayList<java.lang.Integer>`	`convertIndicesToArrayListIndices(IndexSet indices)` Converts atomic indices into list indices
`boolean`	`equals(java.lang.Object other)` Returns true if the two structures are identical
`PointList`	`getAllAtomCoordinates()` Returns the coordinates of all atoms
`IndexSet`	`getAlphaCarbonIndexSet()` Returns the index set of alpha carbon atoms
`Atom`	`getAtom(int i)` Returns atom #i of the structure
`Atom`	`getAtomByIndex(int index)` Returns the atom of given index
`Atom`	`getAtomInResidueOfIndex(int residueindex, int i)` Returns atom #i of the residue of given index
`Atom`	`getAtomInResidueOfIndex(int residueindex, java.lang.String chainID, int i)` Returns atom #i of the residue of given index and chain ID
`IndexSet`	`getBackboneIndexSet()` Returns the index set of backbone atoms
`java.util.ArrayList<java.lang.String>`	`getChainIDs()` Returns the list of chain IDs in the structure
`Structure[]`	`getChains()` Returns all chains in an array of Structure objects
`IndexSetList`	`getDefaultIndexSetList()` Returns the list of default index sets
`IndexSet`	`getHeavyProteinIndexSet()` Returns the index set of protein atoms except of hydrogen atoms
`IndexSet`	`getIndexSetOfChainID(java.lang.String chainID)` Returns the index set of atoms of a given chain ID
`IndexSet`	`getMainChainIndexSet()` Returns the index set of main chain atoms
`IndexSet`	`getMainChainPlusCbIndexSet()` Returns the index set of main chain plus beta carbon atoms
`IndexSet`	`getMainChainPlusHIndexSet()` Returns the index set of main chain plus hydrogen atoms
`java.lang.String`	`getName()` Returns the name of structure
`IndexSet`	`getNonProteinIndexSet()` Returns the index set of non-protein atoms
`int`	`getNumberOfAtoms()` Returns the number of atoms in the structure
`int`	`getNumberOfChains()` Returns the number of chains in the structure
`int`	`getNumberOfResidues()` Returns the number of residues in the structure
`IndexSet`	`getProteinIndexSet()` Returns the index set of protein atoms
`Residue`	`getResidue(int i)` Returns residue #i of the structure
`Residue`	`getResidueByIndex(int index)` Returns the residue of given index
`Residue`	`getResidueByIndex(int index, java.lang.String chainID)` Returns the residue of given index and given chain ID
`java.util.ArrayList<Residue>`	`getResiduesAsArrayList()` Returns residues as an ArrayList object
`Sequence`	`getSequence()` Returns the amino acid sequence of the structure
`IndexSet`	`getSideChainIndexSet()` Returns the index set of side chain atoms
`IndexSet`	`getSideChainMinusHIndexSet()` Returns the index set of side chain atoms except of hydrogen atoms
`Structure`	`getSubStructure(IndexSet indices)` Returns the substructure defined by the given index set
`IndexSet`	`getSystemIndexSet()` Returns the index set of all atoms in the system
`IndexSet`	`getWaterIndexSet()` Returns the index set of water atoms
`int`	`hashCode()` Returns hash code
`java.util.ArrayList<java.lang.Integer>`	`mapAtomIndicesToResidueIndices(IndexSet indices)` Maps atomic indices to residue indices (i.e.
`IndexSet`	`mapResidueIndicesToAtomIndices(java.util.ArrayList<java.lang.Integer> indices)` Maps residue indices to atomic indices (i.e.
`void`	`removeAtom(Atom atom)` Removes the given atom from the structure
`void`	`removeAtom(int i)` Removes atom #i from the structure
`void`	`removeAtomByIndex(int index)` Removes the atom of given index from the structure
`void`	`removeResidue(int i)` Removes residue #i from the structure
`void`	`removeResidue(Residue residue)` Removes a residue from the structure
`void`	`setAllAtomCoordinates(PointList pointlist)` Sets the coordinates of all atoms
`void`	`setAtomCoordinates(int i, Point3D coordinates)` Sets the coordinates of atom #i
`void`	`setAtomInResidue(int i, int j, Atom atom)` Replaces atom #j of residue #i with a new atom
`void`	`setAtomInResidueOfIndex(int index, int i, Atom atom)` Replaces atom #i of the residue of given index with a new atom
`void`	`setAtomOfIndexCoordinates(int index, Point3D coordinates)` Sets the coordinates of atom of given index
`void`	`setName(java.lang.String name)` Sets the name of structure
`void`	`setResidue(int i, Residue residue)` Replaces residue #i with a new residue
`java.lang.String`	`toString()` Returns the String representation of structure
`java.lang.String`	`toStringAsGRO()` Returns the String representation of structure in GRO format
`java.lang.String`	`toStringAsPDB()` Returns the String representation of structure in PDB format
`java.lang.String`	`toStringInfo()` Returns summary information about the structure

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Structure
```
public Structure()
```
    Constructs a new Structure object
  - Structure
```
public Structure(java.lang.String name)
```
    Constructs a new Structure object of given name
- Method Detail
  - getName
```
public java.lang.String getName()
```
    Returns the name of structure
    
    Returns:
    
    name of structure
  - setName
```
public void setName(java.lang.String name)
```
    Sets the name of structure
    
    Parameters:
    
    name - of structure
  - getResiduesAsArrayList
```
public java.util.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 java.util.ArrayList<java.lang.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,
                                 java.lang.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,
                                    java.lang.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(java.lang.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 java.util.ArrayList<java.lang.Integer> convertIndicesToArrayListIndices(IndexSet indices)
```
    Converts atomic indices into list indices
    
    Parameters:
    
    indices - set of atomic indices
    
    Returns:
    
    list indices
  - mapAtomIndicesToResidueIndices
```
public java.util.ArrayList<java.lang.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(java.util.ArrayList<java.lang.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 java.lang.String toString()
```
    Returns the String representation of structure
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    String representation
  - toStringAsGRO
```
public java.lang.String toStringAsGRO()
```
    Returns the String representation of structure in GRO format
    
    Returns:
    
    String representation in GRO format
  - toStringAsPDB
```
public java.lang.String toStringAsPDB()
```
    Returns the String representation of structure in PDB format
    
    Returns:
    
    String representation in PDB format
  - toStringInfo
```
public java.lang.String toStringInfo()
```
    Returns summary information about the structure
    
    Returns:
    
    summary information
  - clone
```
public java.lang.Object clone()
```
    Returns an identical Structure object
    
    Overrides:
    
    clone in class java.lang.Object
    
    Returns:
    
    clone of the structure
  - equals
```
public boolean equals(java.lang.Object other)
```
    Returns true if the two structures are identical
    
    Overrides:
    
    equals in class java.lang.Object
    
    Parameters:
    
    other - the other structure
  - hashCode
```
public int hashCode()
```
    Returns hash code
    
    Overrides:
    
    hashCode in class java.lang.Object

Class Structure

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Structure

Structure

Method Detail

getName

setName

getResiduesAsArrayList

getNumberOfResidues

getNumberOfAtoms

getNumberOfChains

getChainIDs

getResidue

getResidueByIndex

getResidueByIndex

getAtom

getAtomByIndex

getAtomInResidueOfIndex

getAtomInResidueOfIndex

addResidue

removeResidue

removeResidue

setResidue

removeAtom

removeAtomByIndex

removeAtom

addAtomToResidue

addAtomToResidueOfIndex

setAtomInResidue

setAtomInResidueOfIndex

getSystemIndexSet

getProteinIndexSet

getHeavyProteinIndexSet

getAlphaCarbonIndexSet

getBackboneIndexSet

getMainChainIndexSet

getMainChainPlusCbIndexSet

getMainChainPlusHIndexSet

getSideChainIndexSet

getSideChainMinusHIndexSet

getNonProteinIndexSet

getWaterIndexSet

getDefaultIndexSetList

getIndexSetOfChainID

setAtomCoordinates

setAtomOfIndexCoordinates

setAllAtomCoordinates

getAllAtomCoordinates

getSequence

getChains

getSubStructure

convertIndicesToArrayListIndices

mapAtomIndicesToResidueIndices

mapResidueIndicesToAtomIndices

toString

toStringAsGRO

toStringAsPDB

toStringInfo

clone

equals

hashCode