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262 lines (226 loc) · 5.45 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on 28.04.2004
* @author Andreas Prlic
*
*/
package org.biojava.nbio.structure;
import java.util.List;
import javax.vecmath.Point3d;
/**
* A simple interface for an Atom.
* The coordinates can be accessed via the
* {@link #getCoords()}, or the
* {@link #getX()}, {@link #getY()}, {@link #getZ()} methods.
* There are a few additional methods here to provide some PDB specific information.
*
* @author Andreas Prlic
* @author Horvath Tamas
* @version %I% %G%
* @since 1.4
*
*/
public interface Atom extends Cloneable, PDBRecord {
/**
* Set atom name, e.g. "CA".
* @param s a trimmed String specifying the name value
* @see #getName
*/
public void setName(String s);
/**
* Get atom name, e.g. "CA".
* Beware that some PDB atom names are ambiguous (e.g. CA, which means C-alpha or Calcium),
* the ambiguity can simply be resolved by also checking the element with {@link #getElement()}
* @return a trimmed String representing the name value
* @see #setName
*/
public String getName();
/**
* Set element of the atom name, e.g. {@link Element#Fe}
* @param e an Element enumeration
* @see #getElement
*/
public void setElement(Element e);
/**
* Get element of the atom, e.g. {@link Element#Ca}
* @return an Element enumeration
* @see #setElement
*/
public Element getElement();
/**
* Set PDB atom number.
* @param i an int specifying the PDBserial value
* @see #getPDBserial
*/
public void setPDBserial(int i) ;
/**
* Get PDB atom number.
* @return an int representing the PDBserial value
* @see #setPDBserial
*/
public int getPDBserial() ;
/**
* Set the coordinates.
* @param c an array of doubles specifying the coords value
* @see #getCoords
*/
public void setCoords(double[] c);
/**
* Get the coordinates.
* @return a new array of doubles representing the coords value
* @see #setCoords
* @see #getCoordsAsPoint3d()
*/
public double[] getCoords() ;
/**
* Get the coordinates.
* <p>
* Internally the coordinates are represented as Point3d so this
* is recommended over {@link #getCoords()}
* @return a reference to the Point3d coordinates
* @see #getCoords()
*/
public Point3d getCoordsAsPoint3d();
/**
* Set the X coordinate.
* @param x a double
* @see #getX()
*/
public void setX(double x);
/**
* Set the Y coordinate.
* @param y a double
* @see #getY()
*/
public void setY(double y);
/**
* Set the Z coordinate.
* @param z a double
* @see #getZ()
*/
public void setZ(double z);
/**
* Get coordinate X.
* @return a double
* @see #setX(double)
*/
public double getX() ;
/**
* Get coordinate Y.
* @return a double
* @see #setY(double)
*/
public double getY() ;
/**
* Get coordinate Z.
* @return a double
* @see #setZ(double)
*/
public double getZ() ;
/**
* Set alternate Location.
* @param c a Character object specifying the alt loc value
* @see #getAltLoc
*/
public void setAltLoc(Character c);
/**
* Get alternate Location.
* @return a Character object representing the alt loc value
* @see #setAltLoc
*/
public Character getAltLoc();
/**
* Set occupancy.
* @param occupancy a float specifying the occupancy value
* @see #getOccupancy
*/
public void setOccupancy(float occupancy) ;
/**
* Get occupancy.
* @return a float representing the occupancy value
* @see #setOccupancy
*/
public float getOccupancy();
/**
* Set temp factor .
* @param temp a float specifying the temp factor value
* @see #getTempFactor
*/
public void setTempFactor(float temp) ;
/**
* Get temp factor.
* @return a float representing the temp factor value
* @see #setTempFactor
*/
public float getTempFactor() ;
/**
* Return an identical copy of this object .
* @return an identical copy of this object
*/
public Object clone();
/**
* Set the back-reference to its parent Group.
* @param parent the parent Group
* @see #getGroup()
*/
public void setGroup(Group parent);
/**
* Return the parent Group of the Atom.
* returns null if the referenced object is not Group
* @return Group the parent Group of the Atom, or null
* @see #setGroup(Group)
*/
public Group getGroup();
/**
* Add a bond
* @param bond to be added
* @see #getBonds()
*/
public void addBond(Bond bond);
/**
* Get all {@link Bond}s this atom is part of.
*
* @return a list of {@link Bond}s or null if no bonds exist for this Atom
*/
public List<Bond> getBonds();
/**
* Sets the bonds
* @param bonds
*/
public void setBonds(List<Bond> bonds);
/** Test if another atom has a bond to this atom
*
* @param other
* @return
*/
public boolean hasBond(Atom other);
/**
* Get the charge of this atom
*
* @return a the integer charge.
*/
public short getCharge();
/**
* Set the charge of this atom
*
* @return void.
*/
public void setCharge(short charge);
}