Package jgromacs.data
Class Atom
java.lang.Object
jgromacs.data.Atom
- All Implemented Interfaces:
Cloneable
Objects of this class represent a single atom
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionclone()
Returns an identical Atom objectdouble
Returns the Euclidean distance between this atom and another atomboolean
Returns true if the two atoms are identicalReturns the type of atomdouble
Returns the B-value of atomReturns the coordinates of atomint
getIndex()
Returns the index of atomgetName()
Returns the name of atomdouble
Returns the occupancy of atomdouble
Returns the X coordinate of atomdouble
Returns the Y coordinate of atomdouble
Returns the Z coordinate of atomint
hashCode()
Returns hash codeboolean
Returns true if it is an alpha carbon atomboolean
Returns true if it is a backbone atomboolean
Returns true if it is a beta carbon atomboolean
Returns true if it is a carbonyl oxygen atomboolean
Returns true if it is a C-terminal carbon atomboolean
Returns true if it is a delta carbon atomboolean
Returns true if it is an epsilon carbon atomboolean
Returns true if it is a gamma carbon atomboolean
Returns true if it is a heavy atom (not hydrogen)boolean
Returns true if the atom is a Hydrogenboolean
Returns true if it is a main chain atomboolean
Returns true if it is a main chain hydrogen atomboolean
Returns true if it is a main chain or beta carbon atomboolean
Returns true if it is a main chain or hydrogen atomboolean
Returns true if it is an N-terminal nitrogen atomboolean
Returns true if it is a side chain atomboolean
Returns true if it is a side chain atom but not hydrogenboolean
Returns true if it is a terminal oxygen atomboolean
Returns true if it is a zeta carbon atomvoid
setAtomType
(AtomType atomType) Sets the type of atomvoid
setBvalue
(double bvalue) Sets the B-value of atomvoid
setCoordinates
(Point3D coordinates) Sets the coordinates of atomvoid
setIndex
(int index) Sets the index of atomvoid
Sets the name of atomvoid
setOccupancy
(double occupancy) Sets the occupancy of atomvoid
setXCoordinate
(double x) Sets the X coordinate of atomvoid
setYCoordinate
(double y) Sets the Y coordinate of atomvoid
setZCoordinate
(double z) Sets the Z coordinate of atomtoString()
Returns the String representation of atom
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Constructor Details
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Atom
public Atom()Constructs a new Atom object
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Method Details
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getAtomType
Returns the type of atom- Returns:
- Type of the atom
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getIndex
public int getIndex()Returns the index of atom- Returns:
- Index of the atom
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setIndex
public void setIndex(int index) Sets the index of atom- Parameters:
index
- index of the atom
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getName
Returns the name of atom- Returns:
- Name of the atom
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setName
Sets the name of atom- Parameters:
name
- name of the atom
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setAtomType
Sets the type of atom- Parameters:
atomType
- type of the atom
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getCoordinates
Returns the coordinates of atom- Returns:
- Coordinates of atom
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setCoordinates
Sets the coordinates of atom- Parameters:
coordinates
- coordinates of the atom
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getXCoordinate
public double getXCoordinate()Returns the X coordinate of atom- Returns:
- X coordinate of atom
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setXCoordinate
public void setXCoordinate(double x) Sets the X coordinate of atom- Parameters:
x
- X coordinate of the atom
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getYCoordinate
public double getYCoordinate()Returns the Y coordinate of atom- Returns:
- Y coordinate of atom
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setYCoordinate
public void setYCoordinate(double y) Sets the Y coordinate of atom- Parameters:
y
- Y coordinate of the atom
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getZCoordinate
public double getZCoordinate()Returns the Z coordinate of atom- Returns:
- Z coordinate of atom
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setZCoordinate
public void setZCoordinate(double z) Sets the Z coordinate of atom- Parameters:
z
- Z coordinate of the atom
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getOccupancy
public double getOccupancy()Returns the occupancy of atom- Returns:
- occupancy of atom
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setOccupancy
public void setOccupancy(double occupancy) Sets the occupancy of atom- Parameters:
occupancy
- occupancy of the atom
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getBvalue
public double getBvalue()Returns the B-value of atom- Returns:
- B-value of atom
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setBvalue
public void setBvalue(double bvalue) Sets the B-value of atom- Parameters:
bvalue
- B-value of the atom
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isHydrogenAtom
public boolean isHydrogenAtom()Returns true if the atom is a Hydrogen -
isHeavyAtom
public boolean isHeavyAtom()Returns true if it is a heavy atom (not hydrogen) -
isAlphaCarbon
public boolean isAlphaCarbon()Returns true if it is an alpha carbon atom -
isCTerminalCarbon
public boolean isCTerminalCarbon()Returns true if it is a C-terminal carbon atom -
isBetaCarbon
public boolean isBetaCarbon()Returns true if it is a beta carbon atom -
isGammaCarbon
public boolean isGammaCarbon()Returns true if it is a gamma carbon atom -
isDeltaCarbon
public boolean isDeltaCarbon()Returns true if it is a delta carbon atom -
isEpsilonCarbon
public boolean isEpsilonCarbon()Returns true if it is an epsilon carbon atom -
isZetaCarbon
public boolean isZetaCarbon()Returns true if it is a zeta carbon atom -
isCarbonylOxygen
public boolean isCarbonylOxygen()Returns true if it is a carbonyl oxygen atom -
isTerminalOxygen
public boolean isTerminalOxygen()Returns true if it is a terminal oxygen atom -
isNTerminalNitrogen
public boolean isNTerminalNitrogen()Returns true if it is an N-terminal nitrogen atom -
isBackboneAtom
public boolean isBackboneAtom()Returns true if it is a backbone atom -
isMainChainAtom
public boolean isMainChainAtom()Returns true if it is a main chain atom -
isMainChainHydrogenAtom
public boolean isMainChainHydrogenAtom()Returns true if it is a main chain hydrogen atom -
isMainChainPlusHAtom
public boolean isMainChainPlusHAtom()Returns true if it is a main chain or hydrogen atom -
isMainChainPlusCbAtom
public boolean isMainChainPlusCbAtom()Returns true if it is a main chain or beta carbon atom -
isSideChainAtom
public boolean isSideChainAtom()Returns true if it is a side chain atom -
isSideChainMinusHAtom
public boolean isSideChainMinusHAtom()Returns true if it is a side chain atom but not hydrogen -
distance
Returns the Euclidean distance between this atom and another atom- Parameters:
other
- another atom- Returns:
- distance between atoms
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toString
Returns the String representation of atom -
clone
Returns an identical Atom object -
equals
Returns true if the two atoms are identical -
hashCode
public int hashCode()Returns hash code
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