Class PDBCrystallographicInfo

Method Details

• getA

  public float getA()

  Returns:

  the unit cell parameter a

• getB

  public float getB()

  Returns:

  the unit cell parameter b

• getC

  public float getC()

  Returns:

  the unit cell parameter c

• getAlpha

  public float getAlpha()

  Returns:

  the unit cell parameter alpha (degrees)

• getBeta

  public float getBeta()

  Returns:

  the unit cell parameter beta (degrees)

• getGamma

  public float getGamma()

  Returns:

  the unit cell parameter gamma (degrees)

• getCrystalCell

  public CrystalCell getCrystalCell()

  Return the crystal cell

  Returns:

• setCrystalCell

  public void setCrystalCell(CrystalCell cell)

  Set the crystal cell

  Parameters:

  cell -

• getSpaceGroup

  public SpaceGroup getSpaceGroup()

  Get the SpaceGroup

  Returns:

  the spaceGroup

• setSpaceGroup

  public void setSpaceGroup(SpaceGroup spaceGroup)

  Set the SpaceGroup

  Parameters:

  spaceGroup -

• getZ

  @Deprecated public int getZ()

  Deprecated.

  As of 4.0, use SpaceGroup.getMultiplicity() and Structure.size()

  Return the z, i.e. the multiplicity of the space group times the number of chains in asymmetric unit

  Returns:

  0

• getTransformationsOrthonormal

  public javax.vecmath.Matrix4d[] getTransformationsOrthonormal()

  Gets all symmetry transformation operators corresponding to this structure's space group (including the identity, at index 0) expressed in the orthonormal basis. Using PDB axes convention (NCODE=1).

  Returns:

  an array of size SpaceGroup.getNumOperators()

• getNcsOperators

  public javax.vecmath.Matrix4d[] getNcsOperators()

  Get the NCS operators. Some PDB files contain NCS operators necessary to create the full AU. Usually this happens for viral proteins. See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn . Note that the "given" operators (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format) are not stored.

  Returns:

  the operators or null if no operators present

• setNcsOperators

  public void setNcsOperators(javax.vecmath.Matrix4d[] ncsOperators)

  Set the NCS operators. Some PDB files contain NCS operators necessary to create the full AU. Usually this happens for viral proteins. See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn . Note that the "given" operators (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format) are not stored.

  Parameters:

  ncsOperators -

• isNonStandardSg

  public boolean isNonStandardSg()

  Whether this structure has a non-standard space group not supported by Biojava. If this is true getSpaceGroup() will be null.

  Since:

  4.2.5

• setNonStandardSg

  public void setNonStandardSg(boolean nonStandardSg)

  Set the non-standard space group field

  Parameters:

  nonStandardSg -

  Since:

  4.2.5

• isNonStandardCoordFrameConvention

  public boolean isNonStandardCoordFrameConvention()

  Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect. There's ~ 200 old structures in the PDB affected by the non-standard frame problem, hopefully they will be remediated in the future. For more info see: https://github.com/eppic-team/owl/issues/4

  Since:

  4.2.5

• setNonStandardCoordFrameConvention

  public void setNonStandardCoordFrameConvention(boolean nonStandardCoordFrameConvention)

  Set the non-standard coordinate frame convention field

  Parameters:

  nonStandardCoordFrameConvention -

  Since:

  4.2.5

• toString

  public String toString()

  Overrides:

  toString in class Object