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
  • Method Details

    • 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