Package org.openscience.cdk.protein.data

Class PDBAtom

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.Element

org.openscience.cdk.Isotope

org.openscience.cdk.AtomType

org.openscience.cdk.Atom

org.openscience.cdk.protein.data.PDBAtom

All Implemented Interfaces:

Serializable, Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IIsotope, IPDBAtom

Direct Known Subclasses:

DebugPDBAtom

public class PDBAtom
extends Atom
implements Cloneable, IPDBAtom

Represents the idea of an atom as used in PDB files. It contains extra fields normally associated with atoms in such files.

See Also:

• Atom
• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType

IAtomType.Hybridization

Field Summary

Fields inherited from class org.openscience.cdk.Atom

charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity

Fields inherited from class org.openscience.cdk.AtomType

electronValency, formalCharge, formalNeighbourCount, hybridization

Fields inherited from class org.openscience.cdk.Isotope

exactMass, naturalAbundance

Fields inherited from class org.openscience.cdk.Element

atomicNumber

Fields inherited from interface org.openscience.cdk.interfaces.IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Fields inherited from interface org.openscience.cdk.interfaces.IElement

Ac, Ag, Al, Am, Ar, As, At, Au, B, Ba, Be, Bh, Bi, Bk, Br, C, Ca, Cd, Ce, Cf, Cl, Cm, Cn, Co, Cr, Cs, Cu, Db, Ds, Dy, Er, Es, Eu, F, Fe, Fl, Fm, Fr, Ga, Gd, Ge, H, He, Hf, Hg, Ho, Hs, I, In, Ir, K, Kr, La, Li, Lr, Lu, Lv, Mc, Md, Mg, Mn, Mo, Mt, N, Na, Nb, Nd, Ne, Nh, Ni, No, Np, O, Og, Os, P, Pa, Pb, Pd, Pm, Po, Pr, Pt, Pu, Ra, Rb, Re, Rf, Rg, Rh, Rn, Ru, S, Sb, Sc, Se, Sg, Si, Sm, Sn, Sr, Ta, Tb, Tc, Te, Th, Ti, Tl, Tm, Ts, U, V, W, Wildcard, Xe, Y, Yb, Zn, Zr

Constructor Summary

Constructors

Constructor	Description
PDBAtom(String symbol)	Constructs an IPDBAtom from a String containing an element symbol.
PDBAtom(String symbol, javax.vecmath.Point3d coordinate)	Constructs an IPDBAtom from an Element and a Point3d.
PDBAtom(IElement element)	Constructs an IPDBAtom from a Element.

Method Summary

Modifier and Type	Method	Description
String	getAltLoc()	get the Alternate location indicator of this atom.
String	getChainID()	get the Chain identifier of this atom.
Boolean	getHetAtom()	Determine whether this is a heteroatom or not.
String	getICode()	get Code for insertion of residues of this atom.
String	getName()	get the Atom name of this atom.
Double	getOccupancy()	get the Occupancy of this atom.
Boolean	getOxt()	Returns true of this atom is a PDB OXT atom.
String	getRecord()	get one entire line from the PDB entry file which describe the IPDBAtom.
String	getResName()	get the Residue name of this atom.
String	getResSeq()	get the Residue sequence number of this atom.
String	getSegID()	get the Segment identifier, left-justified of this atom.
Integer	getSerial()	get the Atom serial number of this atom.
Double	getTempFactor()	get the Temperature factor of this atom.
void	setAltLoc(String newAltLoc)	set the Alternate location indicator of this atom.
void	setChainID(String newChainID)	set the Chain identifier of this atom.
void	setHetAtom(Boolean newHetAtom)	Mark the atom as a heteroatom.
void	setICode(String newICode)	set the Code for insertion of residues of this atom.
void	setName(String newName)	set the Atom name of this atom.
void	setOccupancy(Double newOccupancy)	set the Occupancy of this atom.
void	setOxt(Boolean newOxt)	Change the state of this atom in being the PDB OXT atom.
void	setRecord(String newRecord)	set one entire line from the PDB entry file which describe the IPDBAtom.
void	setResName(String newResName)	set the Residue name of this atom.
void	setResSeq(String newResSeq)	set the Residue sequence number of this atom.
void	setSegID(String newSegID)	set the Segment identifier, left-justified of this atom.
void	setSerial(Integer newSerial)	set the Atom serial number of this atom.
void	setTempFactor(Double newTempFactor)	set the Temperature factor of this atom.
String	toString()	Returns a one line string representation of this Atom.

Methods inherited from class org.openscience.cdk.Atom

bonds, clone, compare, equals, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, hashCode, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setMapIdx, setPoint2d, setPoint3d, setStereoParity

Methods inherited from class org.openscience.cdk.AtomType

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency

Methods inherited from class org.openscience.cdk.Isotope

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

Methods inherited from class org.openscience.cdk.Element

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, clear, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.IAtom

bonds, clone, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, getTotalHydrogenCount, isAromatic, isInRing, neighbors, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d, setStereoParity

Methods inherited from interface org.openscience.cdk.interfaces.IAtomType

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from interface org.openscience.cdk.interfaces.IElement

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from interface org.openscience.cdk.interfaces.IIsotope

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

Constructor Details

PDBAtom

public PDBAtom(IElement element)

Constructs an IPDBAtom from a Element.

Parameters:

element - IElement to copy information from

PDBAtom

public PDBAtom(String symbol)

Constructs an IPDBAtom from a String containing an element symbol.

Parameters:

symbol - The String describing the element for the PDBAtom

PDBAtom

public PDBAtom(String symbol,
 javax.vecmath.Point3d coordinate)

Constructs an IPDBAtom from an Element and a Point3d.

Parameters:

symbol - The symbol of the atom

coordinate - The 3D coordinates of the atom

Method Details

getRecord

public String getRecord()

get one entire line from the PDB entry file which describe the IPDBAtom. It consists of 80 columns.

Specified by:

getRecord in interface IPDBAtom

Returns:

a String with all information

setRecord

public void setRecord(String newRecord)

set one entire line from the PDB entry file which describe the IPDBAtom. It consists of 80 columns.

Specified by:

setRecord in interface IPDBAtom

Parameters:

newRecord - A String with all information

getTempFactor

public Double getTempFactor()

get the Temperature factor of this atom.

Specified by:

getTempFactor in interface IPDBAtom

Returns:

the Temperature factor of this atom

setTempFactor

public void setTempFactor(Double newTempFactor)

set the Temperature factor of this atom.

Specified by:

setTempFactor in interface IPDBAtom

Parameters:

newTempFactor - the Temperature factor of this atom

setResName

public void setResName(String newResName)

set the Residue name of this atom.

Specified by:

setResName in interface IPDBAtom

Parameters:

newResName - the Residue name of this atom

getResName

public String getResName()

get the Residue name of this atom.

Specified by:

getResName in interface IPDBAtom

Returns:

the Residue name of this atom

setICode

public void setICode(String newICode)

set the Code for insertion of residues of this atom.

Specified by:

setICode in interface IPDBAtom

Parameters:

newICode - the Code for insertion of residues of this atom

getICode

public String getICode()

get Code for insertion of residues of this atom.

Specified by:

getICode in interface IPDBAtom

Returns:

the Code for insertion of residues of this atom

setName

public void setName(String newName)

set the Atom name of this atom.

Specified by:

setName in interface IPDBAtom

Parameters:

newName - the Atom name of this atom

getName

public String getName()

get the Atom name of this atom.

Specified by:

getName in interface IPDBAtom

Returns:

the Atom name of this atom

setChainID

public void setChainID(String newChainID)

set the Chain identifier of this atom.

Specified by:

setChainID in interface IPDBAtom

Parameters:

newChainID - the Chain identifier of this atom

getChainID

public String getChainID()

get the Chain identifier of this atom.

Specified by:

getChainID in interface IPDBAtom

Returns:

the Chain identifier of this atom

setAltLoc

public void setAltLoc(String newAltLoc)

set the Alternate location indicator of this atom.

Specified by:

setAltLoc in interface IPDBAtom

Parameters:

newAltLoc - the Alternate location indicator of this atom

getAltLoc

public String getAltLoc()

get the Alternate location indicator of this atom.

Specified by:

getAltLoc in interface IPDBAtom

Returns:

the Alternate location indicator of this atom

setSegID

public void setSegID(String newSegID)

set the Segment identifier, left-justified of this atom.

Specified by:

setSegID in interface IPDBAtom

Parameters:

newSegID - the Segment identifier, left-justified of this atom

getSegID

public String getSegID()

get the Segment identifier, left-justified of this atom.

Specified by:

getSegID in interface IPDBAtom

Returns:

the Segment identifier, left-justified of this atom

setSerial

public void setSerial(Integer newSerial)

set the Atom serial number of this atom.

Specified by:

setSerial in interface IPDBAtom

Parameters:

newSerial - the Atom serial number of this atom

getSerial

public Integer getSerial()

get the Atom serial number of this atom.

Specified by:

getSerial in interface IPDBAtom

Returns:

the Atom serial number of this atom

setResSeq

public void setResSeq(String newResSeq)

set the Residue sequence number of this atom.

Specified by:

setResSeq in interface IPDBAtom

Parameters:

newResSeq - the Residue sequence number of this atom

getResSeq

public String getResSeq()

get the Residue sequence number of this atom.

Specified by:

getResSeq in interface IPDBAtom

Returns:

the Residue sequence number of this atom

setOxt

public void setOxt(Boolean newOxt)

Description copied from interface: IPDBAtom

Change the state of this atom in being the PDB OXT atom.

Specified by:

setOxt in interface IPDBAtom

Parameters:

newOxt - new boolean indicating whether this atom is a PDB OXT atom.

getOxt

public Boolean getOxt()

Description copied from interface: IPDBAtom

Returns true of this atom is a PDB OXT atom.

Specified by:

getOxt in interface IPDBAtom

Returns:

true if this atom is a PDB OXT atom.

setHetAtom

public void setHetAtom(Boolean newHetAtom)

Description copied from interface: IPDBAtom

Mark the atom as a heteroatom.

Specified by:

setHetAtom in interface IPDBAtom

Parameters:

newHetAtom - if true, the atom will be marked as a heteroatom

getHetAtom

public Boolean getHetAtom()

Description copied from interface: IPDBAtom

Determine whether this is a heteroatom or not.

Specified by:

getHetAtom in interface IPDBAtom

Returns:

true if the atom is a heteroatom, otherwise false

setOccupancy

public void setOccupancy(Double newOccupancy)

set the Occupancy of this atom.

Specified by:

setOccupancy in interface IPDBAtom

Parameters:

newOccupancy - the Occupancy of this atom

getOccupancy

public Double getOccupancy()

get the Occupancy of this atom.

Specified by:

getOccupancy in interface IPDBAtom

Returns:

the Occupancy of this atom

toString

public String toString()

Returns a one line string representation of this Atom. Methods is conform RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Atom

Returns:

The string representation of this Atom