Package org.openscience.cdk.interfaces

Interface IPDBAtom

All Superinterfaces:

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

All Known Implementing Classes:

DebugPDBAtom, PDBAtom, PDBAtom

public interface IPDBAtom
extends IAtom

A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.

Author:

Miguel Rojas <miguel.rojas@uni-koeln.de>

Source code:

main

Belongs to CDK module:

interfaces

Keywords:

pdbpolymer

Created on:

2006-11-20

Nested Class Summary

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

IAtomType.Hybridization

Field Summary

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

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.

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

bonds, clone, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, 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, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

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

Method Detail

getRecord

String getRecord()

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

Returns:

a String with all information

setRecord

void setRecord(String newRecord)

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

Parameters:

newRecord - A String with all information

getTempFactor

Double getTempFactor()

get the Temperature factor of this atom.

Returns:

the Temperature factor of this atom

setTempFactor

void setTempFactor(Double newTempFactor)

set the Temperature factor of this atom.

Parameters:

newTempFactor - the Temperature factor of this atom

getResName

String getResName()

get the Residue name of this atom.

Returns:

the Residue name of this atom

setResName

void setResName(String newResName)

set the Residue name of this atom.

Parameters:

newResName - the Residue name of this atom

getICode

String getICode()

get Code for insertion of residues of this atom.

Returns:

the Code for insertion of residues of this atom

setICode

void setICode(String newICode)

set the Code for insertion of residues of this atom.

Parameters:

newICode - the Code for insertion of residues of this atom

getName

String getName()

get the Atom name of this atom.

Returns:

the Atom name of this atom

setName

void setName(String newName)

set the Atom name of this atom.

Parameters:

newName - the Atom name of this atom

getChainID

String getChainID()

get the Chain identifier of this atom.

Returns:

the Chain identifier of this atom

setChainID

void setChainID(String newChainID)

set the Chain identifier of this atom.

Parameters:

newChainID - the Chain identifier of this atom

getAltLoc

String getAltLoc()

get the Alternate location indicator of this atom.

Returns:

the Alternate location indicator of this atom

setAltLoc

void setAltLoc(String newAltLoc)

set the Alternate location indicator of this atom.

Parameters:

newAltLoc - the Alternate location indicator of this atom

getSegID

String getSegID()

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

Returns:

the Segment identifier, left-justified of this atom

setSegID

void setSegID(String newSegID)

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

Parameters:

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

getSerial

Integer getSerial()

get the Atom serial number of this atom.

Returns:

the Atom serial number of this atom

setSerial

void setSerial(Integer newSerial)

set the Atom serial number of this atom.

Parameters:

newSerial - the Atom serial number of this atom

getResSeq

String getResSeq()

get the Residue sequence number of this atom.

Returns:

the Residue sequence number of this atom

setResSeq

void setResSeq(String newResSeq)

set the Residue sequence number of this atom.

Parameters:

newResSeq - the Residue sequence number of this atom

getOxt

Boolean getOxt()

Returns true of this atom is a PDB OXT atom.

Returns:

true if this atom is a PDB OXT atom.

setOxt

void setOxt(Boolean newOxt)

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

Parameters:

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

getHetAtom

Boolean getHetAtom()

Determine whether this is a heteroatom or not.

Returns:

true if the atom is a heteroatom, otherwise false

setHetAtom

void setHetAtom(Boolean newHetAtom)

Mark the atom as a heteroatom.

Parameters:

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

getOccupancy

Double getOccupancy()

get the Occupancy of this atom.

Returns:

the Occupancy of this atom

setOccupancy

void setOccupancy(Double newOccupancy)

set the Occupancy of this atom.

Parameters:

newOccupancy - the Occupancy of this atom