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java.lang.Object jgromacs.data.Atom
public class Atom
Objects of this class represent a single atom
Constructor Summary | |
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Atom()
Constructs a new Atom object |
Method Summary | |
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java.lang.Object |
clone()
Returns an identical Atom object |
double |
distance(Atom other)
Returns the Euclidean distance between this atom and another atom |
boolean |
equals(java.lang.Object other)
Returns true if the two atoms are identical |
AtomType |
getAtomType()
Returns the type of atom |
double |
getBvalue()
Returns the B-value of atom |
Point3D |
getCoordinates()
Returns the coordinates of atom |
int |
getIndex()
Returns the index of atom |
java.lang.String |
getName()
Returns the name of atom |
double |
getOccupancy()
Returns the occupancy of atom |
double |
getXCoordinate()
Returns the X coordinate of atom |
double |
getYCoordinate()
Returns the Y coordinate of atom |
double |
getZCoordinate()
Returns the Z coordinate of atom |
int |
hashCode()
Returns hash code |
boolean |
isAlphaCarbon()
Returns true if it is an alpha carbon atom |
boolean |
isBackboneAtom()
Returns true if it is a backbone atom |
boolean |
isBetaCarbon()
Returns true if it is a beta carbon atom |
boolean |
isCarbonylOxygen()
Returns true if it is a carbonyl oxygen atom |
boolean |
isCTerminalCarbon()
Returns true if it is a C-terminal carbon atom |
boolean |
isDeltaCarbon()
Returns true if it is a delta carbon atom |
boolean |
isEpsilonCarbon()
Returns true if it is an epsilon carbon atom |
boolean |
isGammaCarbon()
Returns true if it is a gamma carbon atom |
boolean |
isHeavyAtom()
Returns true if it is a heavy atom (not hydrogen) |
boolean |
isHydrogenAtom()
Returns true if the atom is a Hydrogen |
boolean |
isMainChainAtom()
Returns true if it is a main chain atom |
boolean |
isMainChainHydrogenAtom()
Returns true if it is a main chain hydrogen atom |
boolean |
isMainChainPlusCbAtom()
Returns true if it is a main chain or beta carbon atom |
boolean |
isMainChainPlusHAtom()
Returns true if it is a main chain or hydrogen atom |
boolean |
isNTerminalNitrogen()
Returns true if it is an N-terminal nitrogen atom |
boolean |
isSideChainAtom()
Returns true if it is a side chain atom |
boolean |
isSideChainMinusHAtom()
Returns true if it is a side chain atom but not hydrogen |
boolean |
isTerminalOxygen()
Returns true if it is a terminal oxygen atom |
boolean |
isZetaCarbon()
Returns true if it is a zeta carbon atom |
void |
setAtomType(AtomType atomType)
Sets the type of atom |
void |
setBvalue(double bvalue)
Sets the B-value of atom |
void |
setCoordinates(Point3D coordinates)
Sets the coordinates of atom |
void |
setIndex(int index)
Sets the index of atom |
void |
setName(java.lang.String name)
Sets the name of atom |
void |
setOccupancy(double occupancy)
Sets the occupancy of atom |
void |
setXCoordinate(double x)
Sets the X coordinate of atom |
void |
setYCoordinate(double y)
Sets the Y coordinate of atom |
void |
setZCoordinate(double z)
Sets the Z coordinate of atom |
java.lang.String |
toString()
Returns the String representation of atom |
Methods inherited from class java.lang.Object |
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getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Atom()
Method Detail |
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public AtomType getAtomType()
public int getIndex()
public void setIndex(int index)
index
- index of the atompublic java.lang.String getName()
public void setName(java.lang.String name)
name
- name of the atompublic void setAtomType(AtomType atomType)
atomType
- type of the atompublic Point3D getCoordinates()
public void setCoordinates(Point3D coordinates)
coordinates
- coordinates of the atompublic double getXCoordinate()
public void setXCoordinate(double x)
x
- X coordinate of the atompublic double getYCoordinate()
public void setYCoordinate(double y)
y
- Y coordinate of the atompublic double getZCoordinate()
public void setZCoordinate(double z)
z
- Z coordinate of the atompublic double getOccupancy()
public void setOccupancy(double occupancy)
occupancy
- occupancy of the atompublic double getBvalue()
public void setBvalue(double bvalue)
bvalue
- B-value of the atompublic boolean isHydrogenAtom()
public boolean isHeavyAtom()
public boolean isAlphaCarbon()
public boolean isCTerminalCarbon()
public boolean isBetaCarbon()
public boolean isGammaCarbon()
public boolean isDeltaCarbon()
public boolean isEpsilonCarbon()
public boolean isZetaCarbon()
public boolean isCarbonylOxygen()
public boolean isTerminalOxygen()
public boolean isNTerminalNitrogen()
public boolean isBackboneAtom()
public boolean isMainChainAtom()
public boolean isMainChainHydrogenAtom()
public boolean isMainChainPlusHAtom()
public boolean isMainChainPlusCbAtom()
public boolean isSideChainAtom()
public boolean isSideChainMinusHAtom()
public double distance(Atom other)
other
- another atom
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.Object clone()
clone
in class java.lang.Object
public boolean equals(java.lang.Object other)
equals
in class java.lang.Object
other
- the other atompublic int hashCode()
hashCode
in class java.lang.Object
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