Interface Group

Method Details

• size

  int size()

  Get number of atoms.

  Returns:

  number of atoms of this Group

• has3D

  boolean has3D()

  Return true or false, depending if this group has 3D coordinates or not.

  Returns:

  true if Group has 3D coordinates

• setPDBFlag

  void setPDBFlag(boolean flag)

  Flag if group has 3D data .

  Parameters:

  flag - true to set flag that this Group has 3D coordinates

• getType

  GroupType getType()

  Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE

  Returns:

  a String representing the type value

• addAtom

  void addAtom(Atom atom)

  Add an atom to this group.

  Parameters:

  atom - an Atom object

• getAtoms

  List<Atom> getAtoms()

  Get list of atoms.

  Returns:

  a List object representing the atoms

  See Also:

  • setAtoms(List)

• setAtoms

  void setAtoms(List<Atom> atoms)

  Set the atoms of this group.

  Parameters:

  atoms - a list of atoms

• clearAtoms

  void clearAtoms()

  Remove all atoms from this group.

• getAtom

  Atom getAtom(String name)

  Get an atom given its PDB name. Beware that some PDB atom names are ambiguous (e.g. CA, which means C-alpha or Calcium), ambiguities should not occur within the same group though. To solve these ambiguities one would need to check the atom returned for the required element with Atom.getElement()

  Parameters:

  name - a trimmed String representing the atom's PDB name, e.g. "CA"

  Returns:

  an Atom object or null if no such atom exists within this group

• getAtom

  Atom getAtom(int position)

  Get at atom by position.

  Parameters:

  position - an int

  Returns:

  an Atom object or null if no Atom exists for given position

• hasAtom

  boolean hasAtom(String name)

  Tell whether a particular atom exists within this group. Beware that some PDB atom names are ambiguous (e.g. CA, which means C-alpha or Calcium), ambiguities should not occur within the same group though.

  Parameters:

  name - a trimmed String representing the atom's PDB name, e.g. "CA"

  Returns:

  true if Atom with name exists within this group

• getPDBName

  String getPDBName()

  Get the PDB 3-letter name for this group. (e.g. ALA)

  Returns:

  a String representing the PDBName value

  See Also:

  • setPDBName(java.lang.String)

• setPDBName

  void setPDBName(String s)

  Set the PDB 3-letter name for this group. (e.g. ALA)

  Parameters:

  s - a String specifying the PDBName value

  See Also:

  • getPDBName()

• hasAminoAtoms

  boolean hasAminoAtoms()

  Calculate if this group has all atoms required for an amino acid backbone. This allows to include chemically modified amino acids that are labeled hetatoms into some computations, the usual way to identify if a group is an amino acid is getType()

  amino atoms are : N, CA, C, O

  Example: 1DW9 chain A first group is a Selenomethionine, provided as HETATM, but here returns true.

   HETATM    1  N   MSE A   1      11.720  20.973   1.584  0.00  0.00           N
   HETATM    2  CA  MSE A   1      10.381  20.548   1.139  0.00  0.00           C
   HETATM    3  C   MSE A   1       9.637  20.037   2.398  0.00  0.00           C
   HETATM    4  O   MSE A   1      10.198  19.156   2.985  0.00  0.00           O
   HETATM    5  CB  MSE A   1      10.407  19.441   0.088  0.00  0.00           C
   

  Returns:

  true if all Atoms required for an AminoAcid are available (N, CA, C, O)

  See Also:

  • getType()

• setProperties

  void setProperties(Map<String,Object> properties)

  Properties of this amino acid. Currently available properties are: phi psi secstruc

  Parameters:

  properties - a Map object specifying the properties value

  See Also:

  • getProperties()

• getProperties

  Map<String,Object> getProperties()

  return properties.

  Returns:

  a HashMap object representing the properties value

  See Also:

  • setProperties(java.util.Map<java.lang.String, java.lang.Object>)

• setProperty

  void setProperty(String key, Object value)

  set a single property .

  Parameters:

  key - a String

  value - an Object

  See Also:

  • getProperty(java.lang.String)

• getProperty

  Object getProperty(String key)

  get a single property .

  Parameters:

  key - a String

  Returns:

  an Object

  See Also:

  • setProperty(java.lang.String, java.lang.Object)

• iterator

  Iterator<Atom> iterator()

  get an Atom Iterator.

  Returns:

  an Iterator object

• clone

  Object clone()

  returns and identical copy of this Group object .

  Returns:

  and identical copy of this Group object

• setChain

  void setChain(Chain chain)

  Sets the back-reference to its parent Chain.

  Parameters:

  chain - the parent Chain

  Since:

  3.0

  See Also:

  • getChain()

• getChain

  Chain getChain()

  Returns the parent Chain of the Group.

  Returns:

  Chain the Chain object that contains the Group

  Since:

  3.0

  See Also:

  • setChain(Chain)

• getResidueNumber

  ResidueNumber getResidueNumber()

  returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.

  Returns:

  ResidueNumber for the group.

  Since:

  3.0

  See Also:

  • ResidueNumber

• setResidueNumber

  void setResidueNumber(ResidueNumber residueNumber)

  sets the ResidueNumber for this Group

  Parameters:

  residueNumber - the PDB residueNumber

• setResidueNumber

  void setResidueNumber(String chainId, Integer residueNumber, Character iCode)

  Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet. Not recommended for general use other than parsing.

  Parameters:

  chainId -

  residueNumber -

  iCode -

• getChainId

  String getChainId()

  Utility method for returning the chainId of the Group or null if no Chain has been set. This replaces the need to use the expression group.getChain().getId()

  Returns:

  the ID of the chain

  Since:

  3.0

• setChemComp

  void setChemComp(ChemComp cc)

  Set the Chemical Component that closer describes this group.

  Parameters:

  cc - the chemical component

• getChemComp

  ChemComp getChemComp()

  Get the chemical component that closer describes this group. If the information does not exist yet, fetches the information from PDB web site.

  Returns:

  the Chemical Component definition for this Group.

• hasAltLoc

  boolean hasAltLoc()

  Test if this group has alternate locations.

  Returns:

  boolean flag if there are alternate locations.

• getAltLocs

  List<Group> getAltLocs()

  Get the list of alternate locations.

  Returns:

  List of other groups that are on alternate locations

• addAltLoc

  void addAltLoc(Group g)

  Add a group that is an alternate location for this group.

• isWater

  boolean isWater()

  Determines if this group is water.

  Returns:

  true if it's water, false otherwise.

• getAltLocGroup

  Group getAltLocGroup(Character altLoc)

  Gets the alternate location group to this group that has the alt-loc character code passed.

  Parameters:

  altLoc - the alternate location code of the group desired

  Returns:

  the alternate location group if found, or null otherwise

• trimToSize

  void trimToSize()

  attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

• toSDF

  String toSDF()

  Function to get the Group as an MDL molblock

  Returns:

  the string of the MDL molblock