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java.lang.Objectbelka.mol.Atom
public abstract class Atom
Abstract class describing behavior of an atom.
Constructor Summary | |
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Atom()
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Method Summary | |
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abstract boolean |
addAfter(Atom newAtom)
Adds an atom after the current one. |
abstract boolean |
addBefore(Atom newAtom)
Adds an atom before the current one. |
abstract boolean |
addBond(Bond bond)
Adds a covalent bond to the end of covalent bond array for the current atom. |
abstract Assembly |
assembly()
Returns an assembly the atom belongs to. |
abstract Bond[] |
bondArray()
Returns array of covalent bonds. |
abstract int |
countBonds()
Returns number of bonds for the atom. |
static Atom |
create(String name,
double x,
double y,
double z,
Element element)
Static method to create new atom |
abstract void |
disassemble()
Disassembles atom into null pointers to help garbage collector to free memory. |
abstract double |
distance2To(Atom atom)
Returns squared distance to the given atom. |
abstract double |
distanceTo(Atom atom)
Returns distance to the given atom. |
abstract char |
getAlternative()
Returns atom's alternate location indicator. |
abstract Color |
getColor()
Returns color of the sphere representing the atom on a screen. |
abstract double |
getDerivedX()
Returns derived atom's X coordinate. |
abstract double |
getDerivedY()
Returns derived atom's Y coordinate. |
abstract double |
getDerivedZ()
Returns derived atom's Z coordinate. |
abstract Element |
getElement()
Returns atom's chemical element. |
abstract String |
getName()
Returns atom's name. |
abstract double |
getOccupancy()
Returns atom's occupancy. |
abstract double |
getRadius()
Returns radius of the sphere representing the atom. |
abstract int |
getScreenRadius()
Returns radius of the sphere representing the atom on a screen. |
abstract int |
getScreenX()
Returns atom's X coordinate on a screen. |
abstract int |
getScreenY()
Returns atom's Y coordinate on a screen. |
abstract int |
getScreenZ()
Returns atom's Z coordinate on a screen. |
static int |
getSelectedAttribute()
Returns flag attribute for selected atom. |
abstract int |
getSerialNum()
Returns atom's serial number. |
abstract double |
getTemperature()
Returns atom's temperature factor. |
abstract double |
getX()
Returns atom's X coordinate. |
abstract double |
getY()
Returns atom's Y coordinate. |
abstract double |
getZ()
Returns atom's Z coordinate. |
abstract boolean |
hasAttribute(int att)
Returns true if the provide attribute matches to the attributes of the atom. |
abstract boolean |
isC()
Returns 'true' if atom is carbon of mainchain, 'false' otherwise. |
abstract boolean |
isCA()
Returns 'true' if atom is alpha carbon, 'false' otherwise. |
abstract boolean |
isCB()
Returns 'true' if atom is CB carbon, 'false' otherwise. |
abstract boolean |
isN()
Returns 'true' if atom is nitrogen of mainchain, 'false' otherwise. |
abstract boolean |
isO()
Returns 'true' if atom is oxygen of mainchain, 'false' otherwise. |
abstract boolean |
isSelected()
Returns atom's selection status. |
abstract Atom |
next()
Returns next atom in list. |
abstract Atom |
prev()
Returns previous atom in list. |
static double |
scaleToPixels()
Returns scale used to transform atomic coordinates to pixel coordiantes. |
abstract void |
setAlternative(char altern)
Sets atom's alternate location indicator. |
abstract boolean |
setAssembly(Assembly assembly)
Sets assembly the atom belongs to. |
abstract void |
setColor(Color color)
Sets atom's color on a screen. |
abstract void |
setDerivedX(double x)
Sets derived atom's X coordinate. |
abstract void |
setDerivedY(double y)
Sets derived atom's Y coordinate. |
abstract void |
setDerivedZ(double z)
Sets derived atom's Z coordinate. |
abstract void |
setOccupancy(double occup)
Sets atom's occupancy. |
abstract void |
setRadius(double r)
Sets radius of the sphere representing the atom. |
abstract void |
setScreenRadius(double r)
Sets radius of the sphere representing the atom on a screen. |
abstract void |
setScreenX(double x)
Sets atom's X coordinate on a screen. |
abstract void |
setScreenY(double y)
Sets atom's Y coordinate on a screen. |
abstract void |
setScreenZ(double z)
Sets atom's Z coordinate on a screen. |
abstract void |
setSelected(boolean val)
Sets atom's selection status. |
abstract void |
setSerialNum(int serial)
Sets atom's serial number. |
abstract void |
setTemperature(double temper)
Sets atom's temperature factor. |
String |
toString()
Returns string representation of the atom. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Atom()
Method Detail |
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public static Atom create(String name, double x, double y, double z, Element element)
name
- atom's name.x
- atom's X coordinate.y
- atom's Y coordinate.z
- atom's Z coordinate.element
- atom's chemical element.
public abstract void disassemble()
public abstract Atom next()
public abstract Atom prev()
public abstract boolean addAfter(Atom newAtom)
newAtom
- atom to add.
public abstract boolean addBefore(Atom newAtom)
newAtom
- atom to add.
public abstract Assembly assembly()
public abstract boolean setAssembly(Assembly assembly)
assembly
- assemlby to set.
public abstract int countBonds()
public abstract Bond[] bondArray()
public abstract boolean addBond(Bond bond)
bond
- bond to add.
public abstract double getX()
public abstract double getY()
public abstract double getZ()
public abstract double getDerivedX()
public abstract double getDerivedY()
public abstract double getDerivedZ()
public abstract int getScreenX()
public abstract int getScreenY()
public abstract int getScreenZ()
public abstract void setDerivedX(double x)
x
- atom's derived X coordinate.public abstract void setDerivedY(double y)
y
- atom's derived Y coordinate.public abstract void setDerivedZ(double z)
z
- atom's derived Z coordinate.public abstract void setScreenX(double x)
x
- atom's X coordinate on a screen.public abstract void setScreenY(double y)
y
- atom's Y coordinate on a screen.public abstract void setScreenZ(double z)
z
- atom's Z coordinate on a screen.public abstract double getRadius()
public abstract void setRadius(double r)
r
- of the sphere representing the atom.public abstract int getScreenRadius()
public abstract void setScreenRadius(double r)
r
- radius of the sphere representing the atom on a screen.public abstract Color getColor()
public abstract void setColor(Color color)
color
- atom's color on a screen.public abstract String getName()
public abstract int getSerialNum()
public abstract void setSerialNum(int serial)
serial
- atom's serial number.public abstract char getAlternative()
public abstract void setAlternative(char altern)
altern
- atom's alternate location indicator.public abstract double getOccupancy()
public abstract void setOccupancy(double occup)
occup
- atom's occupancy.public abstract double getTemperature()
public abstract void setTemperature(double temper)
temper
- atom's temperature factor.public abstract Element getElement()
public abstract boolean isSelected()
public abstract void setSelected(boolean val)
val
- atom's selection status.public abstract boolean isCA()
public abstract boolean isC()
public abstract boolean isN()
public abstract boolean isO()
public abstract boolean isCB()
public static int getSelectedAttribute()
public abstract boolean hasAttribute(int att)
public abstract double distanceTo(Atom atom)
public abstract double distance2To(Atom atom)
public String toString()
toString
in class Object
public static double scaleToPixels()
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