Constructor Detail

• StructureIO

  public StructureIO()

Method Detail

• getStructure

  public static Structure getStructure​(java.lang.String name)
                                throws java.io.IOException,
                                       StructureException

  Loads a structure based on a name. Supported naming conventions are: *

                  Formal specification for how to specify the name:
  
                  name     := pdbID
                                 | pdbID '.' chainID
                                 | pdbID '.' range
                                 | scopID
                                 | biol
                                 | pdp
                  range         := '('? range (',' range)? ')'?
                                 | chainID
                                 | chainID '_' resNum '-' resNum
                  pdbID         := [0-9][a-zA-Z0-9]{3}
                  chainID       := [a-zA-Z0-9]
                  scopID        := 'd' pdbID [a-z_][0-9_]
                  biol              := 'BIOL:' pdbID [:]? [0-9]+
                  pdp                       := 'PDP:' pdbID[A-Za-z0-9_]+
                  resNum        := [-+]?[0-9]+[A-Za-z]?
  
  
                  Example structures:
                  1TIM            #whole structure - asym unit
                  4HHB.C          #single chain
                  4GCR.A_1-83 #one domain, by residue number
                  3AA0.A,B    #two chains treated as one structure
                  d2bq6a1     #scop domain
                  BIOL:1fah   #biological assembly nr 1 for 1fah
                  BIOL:1fah:0 #asym unit for 1fah
                  BIOL:1fah:1 #biological assembly nr 1 for 1fah
                  BIOL:1fah:2 #biological assembly nr 2 for 1fah
  
                  

  With the additional set of rules:

  • If only a PDB code is provided, the whole structure will be return including ligands, but the first model only (for NMR).
  • Chain IDs are case sensitive, PDB ids are not. To specify a particular chain write as: 4hhb.A or 4HHB.A
  • To specify a SCOP domain write a scopId e.g. d2bq6a1. Some flexibility can be allowed in SCOP domain names, see #setStrictSCOP(boolean)
  • URLs are accepted as well

  Parameters:

  name -

  Returns:

  a Structure object, or null if name appears improperly formated (eg too short, etc)

  Throws:

  java.io.IOException - The PDB file cannot be cached due to IO errors

  StructureException - The name appeared valid but did not correspond to a structure. Also thrown by some submethods upon errors, eg for poorly formatted subranges.

• setAtomCache

  public static void setAtomCache​(AtomCache c)

• getAtomCache

  public static AtomCache getAtomCache()

• getBiologicalAssembly

  public static Structure getBiologicalAssembly​(java.lang.String pdbId)
                                         throws java.io.IOException,
                                                StructureException

  Returns the first biologicalAssembly that is available for a protein structure. For more documentation on quaternary structures see: {@link http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html}

  Parameters:

  pdbId -

  Returns:

  a Structure object or null if that assembly is not available

  Throws:

  StructureException

  java.io.IOException

• getBiologicalAssembly

  public static Structure getBiologicalAssembly​(java.lang.String pdbId,
                                                int biolAssemblyNr)
                                         throws java.io.IOException,
                                                StructureException

  By default the getStructure method loads asym units. This access method allows to recreate the quaternary structure for a protein if it is available.

  Parameters:

  pdbId -

  biolAssemblyNr - - the ith biological assembly that is available for a PDB ID (we start counting at 1, 0 represents the asym unit).

  Returns:

  a Structure object or null if that assembly is not available

  Throws:

  StructureException - if there is no bioassembly available for given biolAssemblyNr or some other problems encountered while loading it

  java.io.IOException

• getBiologicalAssembly

  public static Structure getBiologicalAssembly​(java.lang.String pdbId,
                                                int biolAssemblyNr,
                                                AtomCache cache)
                                         throws java.io.IOException,
                                                StructureException

  Throws:

  java.io.IOException

  StructureException

• getBiologicalAssembly

  public static Structure getBiologicalAssembly​(java.lang.String pdbId,
                                                int biolAssemblyNr,
                                                AtomCache cache,
                                                BioUnitDataProvider provider)
                                         throws java.io.IOException,
                                                StructureException

  Throws:

  java.io.IOException

  StructureException

• hasBiologicalAssembly

  public static boolean hasBiologicalAssembly​(java.lang.String pdbId)

  Does the provider PDB ID have a biological assembly?

  Parameters:

  pdbId -

  Returns:

  flag if one or more biological assemblies are available

• getNrBiologicalAssemblies

  public static int getNrBiologicalAssemblies​(java.lang.String pdbId)

• setPdbPath

  public static void setPdbPath​(java.lang.String pathToPDBFiles)

  Utility method to set the location where PDB files can be found

  Parameters:

  pathToPDBFiles -

• guessFiletype

  public static StructureIO.StructureFiletype guessFiletype​(java.lang.String filename)

  Attempts to guess the type of a structure file based on the extension

  Parameters:

  filename -

  Returns: