Class DebugPDBAtom

All Implemented Interfaces:
Serializable, Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IIsotope, IPDBAtom

public class DebugPDBAtom extends PDBAtom implements IPDBAtom
Debugging data class.
Author:
Miguel Rojas
See Also:
Source code:
main
Belongs to CDK module:
datadebug
  • Constructor Details

    • DebugPDBAtom

      public DebugPDBAtom(IElement element)
    • DebugPDBAtom

      public DebugPDBAtom(String symbol)
    • DebugPDBAtom

      public DebugPDBAtom(String symbol, javax.vecmath.Point3d point3d)
  • 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
      Overrides:
      getRecord in class PDBAtom
      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
      Overrides:
      setRecord in class PDBAtom
      Parameters:
      newRecord - A String with all information
    • getTempFactor

      public Double getTempFactor()
      get the Temperature factor of this atom.
      Specified by:
      getTempFactor in interface IPDBAtom
      Overrides:
      getTempFactor in class PDBAtom
      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
      Overrides:
      setTempFactor in class PDBAtom
      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
      Overrides:
      setResName in class PDBAtom
      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
      Overrides:
      getResName in class PDBAtom
      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
      Overrides:
      setICode in class PDBAtom
      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
      Overrides:
      getICode in class PDBAtom
      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
      Overrides:
      setName in class PDBAtom
      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
      Overrides:
      getName in class PDBAtom
      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
      Overrides:
      setChainID in class PDBAtom
      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
      Overrides:
      getChainID in class PDBAtom
      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
      Overrides:
      setAltLoc in class PDBAtom
      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
      Overrides:
      getAltLoc in class PDBAtom
      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
      Overrides:
      setSegID in class PDBAtom
      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
      Overrides:
      getSegID in class PDBAtom
      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
      Overrides:
      setSerial in class PDBAtom
      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
      Overrides:
      getSerial in class PDBAtom
      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
      Overrides:
      setResSeq in class PDBAtom
      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
      Overrides:
      getResSeq in class PDBAtom
      Returns:
      the Residue sequence number of this atom
    • setOxt

      public void setOxt(Boolean newOxt)
      Change the state of this atom in being the PDB OXT atom.
      Specified by:
      setOxt in interface IPDBAtom
      Overrides:
      setOxt in class PDBAtom
      Parameters:
      newOxt - new boolean indicating whether this atom is a PDB OXT atom.
    • getOxt

      public Boolean getOxt()
      Returns true of this atom is a PDB OXT atom.
      Specified by:
      getOxt in interface IPDBAtom
      Overrides:
      getOxt in class PDBAtom
      Returns:
      true if this atom is a PDB OXT atom.
    • setHetAtom

      public void setHetAtom(Boolean newHetAtom)
      Mark the atom as a heteroatom.
      Specified by:
      setHetAtom in interface IPDBAtom
      Overrides:
      setHetAtom in class PDBAtom
      Parameters:
      newHetAtom - if true, the atom will be marked as a heteroatom
    • getHetAtom

      public Boolean getHetAtom()
      Determine whether this is a heteroatom or not.
      Specified by:
      getHetAtom in interface IPDBAtom
      Overrides:
      getHetAtom in class PDBAtom
      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
      Overrides:
      setOccupancy in class PDBAtom
      Parameters:
      newOccupancy - the Occupancy of this atom
    • getOccupancy

      public Double getOccupancy()
      get the Occupancy of this atom.
      Specified by:
      getOccupancy in interface IPDBAtom
      Overrides:
      getOccupancy in class PDBAtom
      Returns:
      the Occupancy of this atom