public class DebugPDBAtom extends PDBAtom implements IPDBAtom
IAtomType.Hybridization
exactMass, naturalAbundance
Constructor and Description |
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DebugPDBAtom(IElement element) |
DebugPDBAtom(String symbol) |
DebugPDBAtom(String symbol,
javax.vecmath.Point3d point3d) |
Modifier and Type | Method and Description |
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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() |
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) |
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.
|
clone, compare, getCharge, getFractionalPoint3d, getImplicitHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setPoint2d, setPoint3d, setStereoParity
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
addListener, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
getCharge, getFractionalPoint3d, getImplicitHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setPoint2d, setPoint3d, setStereoParity
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
addListener, clone, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
getBuilder
public DebugPDBAtom(IElement element)
public DebugPDBAtom(String symbol)
public DebugPDBAtom(String symbol, javax.vecmath.Point3d point3d)
public String getRecord()
PDBAtom
public void setRecord(String newRecord)
PDBAtom
public Double getTempFactor()
PDBAtom
getTempFactor
in interface IPDBAtom
getTempFactor
in class PDBAtom
public void setTempFactor(Double newTempFactor)
PDBAtom
setTempFactor
in interface IPDBAtom
setTempFactor
in class PDBAtom
newTempFactor
- the Temperature factor of this atompublic void setResName(String newResName)
PDBAtom
setResName
in interface IPDBAtom
setResName
in class PDBAtom
newResName
- the Residue name of this atompublic String getResName()
PDBAtom
getResName
in interface IPDBAtom
getResName
in class PDBAtom
public void setICode(String newICode)
PDBAtom
public String getICode()
PDBAtom
public void setName(String newName)
PDBAtom
public String getName()
PDBAtom
public void setChainID(String newChainID)
PDBAtom
setChainID
in interface IPDBAtom
setChainID
in class PDBAtom
newChainID
- the Chain identifier of this atompublic String getChainID()
PDBAtom
getChainID
in interface IPDBAtom
getChainID
in class PDBAtom
public void setAltLoc(String newAltLoc)
PDBAtom
public String getAltLoc()
PDBAtom
public void setSegID(String newSegID)
PDBAtom
public String getSegID()
PDBAtom
public void setSerial(Integer newSerial)
PDBAtom
public Integer getSerial()
PDBAtom
public void setResSeq(String newResSeq)
PDBAtom
public String getResSeq()
PDBAtom
public void setOxt(Boolean newOxt)
public Boolean getOxt()
public void setHetAtom(Boolean newHetAtom)
IPDBAtom
setHetAtom
in interface IPDBAtom
setHetAtom
in class PDBAtom
newHetAtom
- if true, the atom will be marked as a heteroatompublic Boolean getHetAtom()
IPDBAtom
getHetAtom
in interface IPDBAtom
getHetAtom
in class PDBAtom
public void setOccupancy(Double newOccupancy)
PDBAtom
setOccupancy
in interface IPDBAtom
setOccupancy
in class PDBAtom
newOccupancy
- the Occupancy of this atompublic Double getOccupancy()
PDBAtom
getOccupancy
in interface IPDBAtom
getOccupancy
in class PDBAtom