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java.lang.Object jgromacs.data.Residue
public class Residue
Objects of this class represent a single residue
Constructor Summary | |
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Residue()
Constructs a new Residue object |
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Residue(int index,
java.lang.String name,
ResidueType residueType)
Constructs a new Residue object of given index, name and residue type |
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Residue(int index,
java.lang.String name,
java.lang.String chainID,
ResidueType residueType)
Constructs a new Residue object of given index, name, chainID and residue type |
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Residue(java.lang.String name)
Constructs a new Residue object of given name |
Method Summary | |
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void |
addAtom(Atom atom)
Adds a new atom to the residue |
java.lang.Object |
clone()
Returns an identical Residue object |
double |
distanceAlphaCarbons(Residue other)
Returns the Euclidean distance of alpha-carbon atoms of this amino acid an another |
double |
distanceClosest(Residue other)
Returns the Euclidean distance of the closest atoms of this amino acid and another |
double |
distanceClosestHeavy(Residue other)
Returns the Euclidean distance of the closest heavy atoms of this amino acid and another |
boolean |
equals(java.lang.Object other)
Returns true if the two residues are identical |
java.lang.String |
get1LetterCode()
Returns the 1 letter code of residue type |
java.lang.String |
get3LetterCode()
Returns the 3 letter code of residue type |
PointList |
getAllAtomCoordinates()
Returns the coordinates of all atoms |
Atom |
getAlphaCarbon()
Returns the alpha carbon atom if any (otherwise returns null) |
Point3D |
getAlphaCarbonCoordinates()
Returns the position of alpha-carbon atom |
Atom |
getAtom(int i)
Returns atom #i of the residue |
Atom |
getAtomByIndex(int index)
Returns the atom of given index |
Atom |
getAtomByName(java.lang.String name)
Returns the atom of name |
IndexSet |
getAtomIndices()
Returns the index set of all atoms |
java.util.ArrayList<Atom> |
getAtomsAsArrayList()
Returns the list of atoms as an ArrayList object |
IndexSet |
getBackBoneAtomIndices()
Returns the index set of backbone atoms |
Atom |
getBetaCarbon()
Returns the beta carbon atom if any (otherwise returns null) |
Atom |
getCarbonylOxygen()
Returns the carbonyl oxygen atom of amino acid |
java.lang.String |
getChainID()
Returns the chain ID of residue |
java.lang.String |
getCombinedCode()
Returns residue index and the 3 letter code of residue type |
Atom |
getCTerminalCarbon()
Returns the C-terminal carbon atom of amino acid |
Atom |
getDeltaCarbon()
Returns the delta carbon atom if any (otherwise returns null) |
Atom |
getEpsilonCarbon()
Returns the epsilon carbon atom if any (otherwise returns null) |
Atom |
getGammaCarbon()
Returns the gamma carbon atom if any (otherwise returns null) |
IndexSet |
getHeavyAtomIndices()
Returns the index set of heavy atoms |
IndexSet |
getHydrogenAtomIndices()
Returns the index set of hydrogen atoms |
int |
getIndex()
Returns the index of residue |
IndexSet |
getMainChainAtomIndices()
Returns the index set of main chain atoms |
IndexSet |
getMainChainPlusCbAtomIndices()
Returns the index set of main chain atoms and beta carbon atom |
IndexSet |
getMainChainPlusHAtomIndices()
Returns the index set of main chain atoms and hydrogen atoms |
java.lang.String |
getName()
Returns the name of residue |
Atom |
getNTerminalNitrogen()
Returns the N-terminal nitrogen atom of amino acid |
int |
getNumberOfAtoms()
Returns the number of atoms in the residue |
ResidueType |
getResidueType()
Returns the type of residue |
IndexSet |
getSideChainAtomIndices()
Returns the index set of side chain atoms |
IndexSet |
getSideChainMinusHAtomIndices()
Returns the index set of side chain atoms except of hydrogen atoms |
Atom |
getZetaCarbon()
Returns the zeta carbon atom if any (otherwise returns null) |
int |
hashCode()
Returns hash code |
boolean |
isAminoAcid()
Returns true if it is an amino acid |
boolean |
isAtomIn(Atom atom)
Returns true if the given atom is in the residue |
boolean |
isOther()
Returns true if it is not an amino acid neither a water molecule |
boolean |
isWater()
Returns true if it is a water molecule |
void |
removeAtom(Atom atom)
Removes the given atom from the residue |
void |
removeAtom(int i)
Removes atom #i from the residue |
void |
removeAtomByIndex(int index)
Removes atom of given index from the residue |
void |
setAllAtomCoordinates(PointList pointlist)
Sets the coordinates of all atoms |
void |
setAtom(int i,
Atom atom)
Replaces atom #i of the residue with the given atom |
void |
setAtomCoordinates(int i,
Point3D coordinates)
Sets the coordinates of atom #i |
void |
setAtomOfIndexCoordinates(int index,
Point3D coordinates)
Sets the coordinates of atom of given index |
void |
setChainID(java.lang.String chainID)
Sets the chain ID of residue |
void |
setIndex(int index)
Sets the index of residue |
void |
setName(java.lang.String name)
Sets the name of residue |
void |
setResidueType(ResidueType residueType)
Sets the type of residue |
java.lang.String |
toString()
Returns the String representation of residue |
java.lang.String |
toStringInfo()
Returns summary information about the residue |
Methods inherited from class java.lang.Object |
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getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Residue()
public Residue(java.lang.String name)
public Residue(int index, java.lang.String name, ResidueType residueType)
public Residue(int index, java.lang.String name, java.lang.String chainID, ResidueType residueType)
Method Detail |
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public int getIndex()
public void setIndex(int index)
index
- index of the residuepublic java.lang.String getName()
public void setName(java.lang.String name)
name
- name of the residuepublic ResidueType getResidueType()
public void setResidueType(ResidueType residueType)
residueType
- residue typepublic java.lang.String getChainID()
public void setChainID(java.lang.String chainID)
chainID
- chain IDpublic int getNumberOfAtoms()
public java.util.ArrayList<Atom> getAtomsAsArrayList()
public Atom getAtom(int i)
public Atom getAtomByIndex(int index)
index
- index of atom
public Atom getAtomByName(java.lang.String name)
name
- name of atom
public java.lang.String get1LetterCode()
public java.lang.String get3LetterCode()
public java.lang.String getCombinedCode()
public void addAtom(Atom atom)
atom
- new atompublic void setAtom(int i, Atom atom)
atom
- new atompublic void removeAtom(int i)
public void removeAtom(Atom atom)
atom
- the atom to be removedpublic void removeAtomByIndex(int index)
index
- index of atom to be removedpublic Atom getNTerminalNitrogen()
public Atom getAlphaCarbon()
public Atom getBetaCarbon()
public Atom getGammaCarbon()
public Atom getDeltaCarbon()
public Atom getEpsilonCarbon()
public Atom getZetaCarbon()
public Atom getCTerminalCarbon()
public Atom getCarbonylOxygen()
public IndexSet getAtomIndices()
public IndexSet getHydrogenAtomIndices()
public IndexSet getHeavyAtomIndices()
public IndexSet getBackBoneAtomIndices()
public IndexSet getMainChainAtomIndices()
public IndexSet getMainChainPlusCbAtomIndices()
public IndexSet getMainChainPlusHAtomIndices()
public IndexSet getSideChainAtomIndices()
public IndexSet getSideChainMinusHAtomIndices()
public void setAtomCoordinates(int i, Point3D coordinates)
coordinates
- new atomic coordinatespublic void setAtomOfIndexCoordinates(int index, Point3D coordinates)
coordinates
- new atomic coordinatespublic void setAllAtomCoordinates(PointList pointlist)
pointlist
- list of new atomic coordinatespublic PointList getAllAtomCoordinates()
public Point3D getAlphaCarbonCoordinates()
public double distanceAlphaCarbons(Residue other)
other
- other amino acid
public double distanceClosest(Residue other)
other
- other amino acid
public double distanceClosestHeavy(Residue other)
other
- other amino acid
public boolean isAminoAcid()
public boolean isWater()
public boolean isOther()
public boolean isAtomIn(Atom atom)
atom
- the atom to search forpublic java.lang.Object clone()
clone
in class java.lang.Object
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String toStringInfo()
public boolean equals(java.lang.Object other)
equals
in class java.lang.Object
other
- the other residuepublic int hashCode()
hashCode
in class java.lang.Object
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