Package org.openscience.cdk.silent
Class PDBAtom
- All Implemented Interfaces:
Serializable
,Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IIsotope
,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:
- Source code:
- main
- Belongs to CDK module:
- silent
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Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
IAtomType.Hybridization
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Field Summary
Fields inherited from class org.openscience.cdk.silent.Atom
charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity
Fields inherited from class org.openscience.cdk.silent.AtomType
electronValency, formalCharge, formalNeighbourCount, hybridization
Fields inherited from class org.openscience.cdk.silent.Isotope
exactMass, naturalAbundance
Fields inherited from class org.openscience.cdk.silent.Element
atomicNumber
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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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionget the Alternate location indicator of this atom.get the Chain identifier of this atom.Determine whether this is a heteroatom or not.getICode()
get Code for insertion of residues of this atom.getName()
get the Atom name of this atom.get the Occupancy of this atom.getOxt()
Returns true of this atom is a PDB OXT atom.get one entire line from the PDB entry file which describe the IPDBAtom.get the Residue name of this atom.get the Residue sequence number of this atom.getSegID()
get the Segment identifier, left-justified of this atom.get the Atom serial number of this atom.get the Temperature factor of this atom.void
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
set the Code for insertion of residues of this atom.void
set the Atom name of this atom.void
setOccupancy
(Double newOccupancy) set the Occupancy of this atom.void
Change the state of this atom in being the PDB OXT atom.void
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
set the Residue sequence number of this atom.void
set the Segment identifier, left-justified of this atom.void
set the Atom serial number of this atom.void
setTempFactor
(Double newTempFactor) set the Temperature factor of this atom.toString()
Returns a one line string representation of this Atom.Methods inherited from class org.openscience.cdk.silent.Atom
bonds, clone, compare, equals, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, hashCode, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d, setStereoParity
Methods inherited from class org.openscience.cdk.silent.AtomType
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
Methods inherited from class org.openscience.cdk.silent.Isotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
Methods inherited from class org.openscience.cdk.silent.Element
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
Methods inherited from class org.openscience.cdk.silent.ChemObject
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, 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, 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
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
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Constructor Details
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PDBAtom
Constructs an IPDBAtom from a Element.- Parameters:
element
- IElement to copy information from
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PDBAtom
Constructs anIPDBAtom
from a String containing an element symbol.- Parameters:
symbol
- The String describing the element for the PDBAtom
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PDBAtom
Constructs anIPDBAtom
from an Element and a Point3d.- Parameters:
symbol
- The symbol of the atomcoordinate
- The 3D coordinates of the atom
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Method Details
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getRecord
get one entire line from the PDB entry file which describe the IPDBAtom. It consists of 80 columns. -
setRecord
set one entire line from the PDB entry file which describe the IPDBAtom. It consists of 80 columns. -
getTempFactor
get the Temperature factor of this atom.- Specified by:
getTempFactor
in interfaceIPDBAtom
- Returns:
- the Temperature factor of this atom
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setTempFactor
set the Temperature factor of this atom.- Specified by:
setTempFactor
in interfaceIPDBAtom
- Parameters:
newTempFactor
- the Temperature factor of this atom
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setResName
set the Residue name of this atom.- Specified by:
setResName
in interfaceIPDBAtom
- Parameters:
newResName
- the Residue name of this atom
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getResName
get the Residue name of this atom.- Specified by:
getResName
in interfaceIPDBAtom
- Returns:
- the Residue name of this atom
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setICode
set the Code for insertion of residues of this atom. -
getICode
get Code for insertion of residues of this atom. -
setName
set the Atom name of this atom. -
getName
get the Atom name of this atom. -
setChainID
set the Chain identifier of this atom.- Specified by:
setChainID
in interfaceIPDBAtom
- Parameters:
newChainID
- the Chain identifier of this atom
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getChainID
get the Chain identifier of this atom.- Specified by:
getChainID
in interfaceIPDBAtom
- Returns:
- the Chain identifier of this atom
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setAltLoc
set the Alternate location indicator of this atom. -
getAltLoc
get the Alternate location indicator of this atom. -
setSegID
set the Segment identifier, left-justified of this atom. -
getSegID
get the Segment identifier, left-justified of this atom. -
setSerial
set the Atom serial number of this atom. -
getSerial
get the Atom serial number of this atom. -
setResSeq
set the Residue sequence number of this atom. -
getResSeq
get the Residue sequence number of this atom. -
setOxt
Description copied from interface:IPDBAtom
Change the state of this atom in being the PDB OXT atom. -
getOxt
Description copied from interface:IPDBAtom
Returns true of this atom is a PDB OXT atom. -
setHetAtom
Description copied from interface:IPDBAtom
Mark the atom as a heteroatom.- Specified by:
setHetAtom
in interfaceIPDBAtom
- Parameters:
newHetAtom
- if true, the atom will be marked as a heteroatom
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getHetAtom
Description copied from interface:IPDBAtom
Determine whether this is a heteroatom or not.- Specified by:
getHetAtom
in interfaceIPDBAtom
- Returns:
- true if the atom is a heteroatom, otherwise false
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setOccupancy
set the Occupancy of this atom.- Specified by:
setOccupancy
in interfaceIPDBAtom
- Parameters:
newOccupancy
- the Occupancy of this atom
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getOccupancy
get the Occupancy of this atom.- Specified by:
getOccupancy
in interfaceIPDBAtom
- Returns:
- the Occupancy of this atom
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toString
Returns a one line string representation of this Atom. Methods is conform RFC #9.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classAtom
- Returns:
- The string representation of this Atom
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