Class 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:
Source code:
main
Belongs to CDK module:
data
  • 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