Package org.openscience.cdk.interfaces
Interface IPDBAtom
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
IAtomType.Hybridization
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Field Summary
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Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
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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
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Method Summary
All Methods Instance Methods Abstract Methods 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, getTotalHydrogenCount, isAromatic, isInRing, neighbors, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d, setStereoParity
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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
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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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, toString
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Methods inherited from interface org.openscience.cdk.interfaces.IElement
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
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Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
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Method Detail
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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
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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
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getTempFactor
Double getTempFactor()
get the Temperature factor of this atom.- Returns:
- the Temperature factor of this atom
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setTempFactor
void setTempFactor(Double newTempFactor)
set the Temperature factor of this atom.- Parameters:
newTempFactor
- the Temperature factor of this atom
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getResName
String getResName()
get the Residue name of this atom.- Returns:
- the Residue name of this atom
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setResName
void setResName(String newResName)
set the Residue name of this atom.- Parameters:
newResName
- the Residue name of this atom
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getICode
String getICode()
get Code for insertion of residues of this atom.- Returns:
- the Code for insertion of residues of this atom
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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
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getName
String getName()
get the Atom name of this atom.- Returns:
- the Atom name of this atom
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setName
void setName(String newName)
set the Atom name of this atom.- Parameters:
newName
- the Atom name of this atom
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getChainID
String getChainID()
get the Chain identifier of this atom.- Returns:
- the Chain identifier of this atom
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setChainID
void setChainID(String newChainID)
set the Chain identifier of this atom.- Parameters:
newChainID
- the Chain identifier of this atom
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getAltLoc
String getAltLoc()
get the Alternate location indicator of this atom.- Returns:
- the Alternate location indicator of this atom
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setAltLoc
void setAltLoc(String newAltLoc)
set the Alternate location indicator of this atom.- Parameters:
newAltLoc
- the Alternate location indicator of this atom
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getSegID
String getSegID()
get the Segment identifier, left-justified of this atom.- Returns:
- the Segment identifier, left-justified of this atom
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setSegID
void setSegID(String newSegID)
set the Segment identifier, left-justified of this atom.- Parameters:
newSegID
- the Segment identifier, left-justified of this atom
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getSerial
Integer getSerial()
get the Atom serial number of this atom.- Returns:
- the Atom serial number of this atom
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setSerial
void setSerial(Integer newSerial)
set the Atom serial number of this atom.- Parameters:
newSerial
- the Atom serial number of this atom
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getResSeq
String getResSeq()
get the Residue sequence number of this atom.- Returns:
- the Residue sequence number of this atom
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setResSeq
void setResSeq(String newResSeq)
set the Residue sequence number of this atom.- Parameters:
newResSeq
- the Residue sequence number of this atom
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getOxt
Boolean getOxt()
Returns true of this atom is a PDB OXT atom.- Returns:
- true if this atom is a PDB OXT atom.
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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.
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getHetAtom
Boolean getHetAtom()
Determine whether this is a heteroatom or not.- Returns:
- true if the atom is a heteroatom, otherwise false
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setHetAtom
void setHetAtom(Boolean newHetAtom)
Mark the atom as a heteroatom.- Parameters:
newHetAtom
- if true, the atom will be marked as a heteroatom
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getOccupancy
Double getOccupancy()
get the Occupancy of this atom.- Returns:
- the Occupancy of this atom
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setOccupancy
void setOccupancy(Double newOccupancy)
set the Occupancy of this atom.- Parameters:
newOccupancy
- the Occupancy of this atom
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