Package org.biojava.nbio.structure

Interface Structure

All Superinterfaces:
Cloneable, Serializable
All Known Implementing Classes:
StructureImpl
public interface Structure extends Cloneable, Serializable
Interface for a structure object. Provides access to the data of a PDB file.

A structure object allows to access the PDB header information as well as to the data from the ATOM records. The header information is currently available through the following objects:

The structure object provides access to the data from the ATOM records through a hierarchy of sub-object: 
 Structure
         |
         Chain
             |
             Group
                 |
                 Atom
For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure

The tutorial for the BioJava structure modules can be found at github.

Q: How can I get a Structure object from a PDB file?

A: 

  Structure loadStructure(String pathToPDBFile) {
                PDBFileReader pdbreader = new PDBFileReader();
                Structure structure = pdbreader.getStructure(pathToPDBFile);
                System.out.println(structure);
                return structure;
        }

Q: How can I calculate Phi and Psi angles of AminoAcids?

A: 


  void calcPhiPsi(Structure structure) {

 		// get the first chain from the structure
 		Chain chain  = structure.getChain(0);

 		// A protein chain consists of a number of groups. These can be either
 		// AminoAcid, HetatomImpl or NucleotideImpl groups.
 		//
 		// Note: BioJava provides access to both the ATOM and SEQRES data in a PDB file.
 		// since we are interested in doing calculations here, we only request the groups
 		// from the ATOM records

 		//  get the Groups of the chain that are AminoAcids.
 		List<Group> groups = chain.getAtomGroups(GroupType.AMINOACID);

 		AminoAcid a;
 		AminoAcid b;
 		AminoAcid c;
 		for (int i=0; i < groups.size(); i++) {
 			// since we requested only groups of type AMINOACID they will always be amino acids
 			// Nucleotide and Hetatom groups will not be present in the groups list.
 			b = (AminoAcid)groups.get(i);
 			double phi = 360.0;
 			double psi = 360.0;

 			if (i > 0) {
 				a = (AminoAcid)groups.get(i-1) ;
 				// the Calc class provides utility methods for various calculations on
 				// structures, groups and atoms
 				phi = Calc.getPhi(a,b);
 			}
 			if (i < groups.size()-1) {
 				c = (AminoAcid)groups.get(i+1) ;
 				psi = Calc.getPsi(b, c);
 			}
 			System.out.print(b.getPDBCode() + " " + b.getPDBName() + ":"  );
 			System.out.println(String.format("\tphi: %+7.2f psi: %+7.2f", phi, psi));
 		}
 	}
Since:
1.4
Author:
Andreas Prlic

  • Method Details

    • clone

      Structure clone()
      Return an identical copy of this Structure object
      Returns:
      identical copy of this Structure object

    • toString

      String toString()
      String representation of object.
      Overrides:
      toString in class Object

    • setName

      void setName(String name)
      Set biological name of Structure .
      Parameters:
      name - a String specifying the biological name of the Structure
      See Also:

    • getName

      String getName()
      Get biological name of Structure.
      Returns:
      a String representing the biological name of the Structure
      See Also:

    • getStructureIdentifier

      StructureIdentifier getStructureIdentifier()
      Get an identifier corresponding to this structure
      Returns:
      The StructureIdentifier used to create this structure

    • setStructureIdentifier

      void setStructureIdentifier(StructureIdentifier structureIdentifier)
      Set the identifier corresponding to this structure
      Parameters:
      structureIdentifier - the structureIdentifier corresponding to this structure

    • size

      int size()
      Return number of polymer Chains in this Structure for first model.
      Returns:
      the number of polymer Chains in this Structure

    • size

      int size(int modelnr)
      Return number of chains of model.
      Parameters:
      modelnr - an int specifying the number of the Model that should be used
      Returns:
      an int representing the number of Chains in this Model

    • nrModels

      int nrModels()
      Return the number of models . In this implementation also XRAY structures have "1 model", since model is the container for the chains. to test if a Structure is an NMR structure use isNmr().
      Returns:
      an int representing the number of models in this Structure
      See Also:

    • isNmr

      boolean isNmr()
      Test if this structure is an NMR structure.
      Returns:
      true if this Structure has been solved by NMR
      See Also:

    • isCrystallographic

      boolean isCrystallographic()
      Test if this structure is a crystallographic structure, i.e. it is an asymmetric unit from which it is possible to reconstruct the crystal lattice given cell parameters and space group.
      Returns:
      true if crystallographic, false otherwise

    • addModel

      void addModel(List<Chain> model)
      Add a new model.
      Parameters:
      model - a List object containing the Chains of the new Model

    • setModel

      void setModel(int position, List<Chain> model)
      A convenience function if one wants to edit and replace the models in a structure. Allows to set (replace) the model at position with the new List of Chains.
      Parameters:
      position - starting at 0
      model - list of chains representing a model

    • getModel

      List<Chain> getModel(int modelnr)
      Retrieve all Chains belonging to a model .
      Parameters:
      modelnr - an int
      Returns:
      a List object containing the Chains of Model nr. modelnr
      See Also:

    • getChains

      List<Chain> getChains()
      Retrieve all chains for the first model. This is the same as getChains(0);
      Returns:
      a List object containing the Chains of Model nr. modelnr
      See Also:

    • setChains

      void setChains(List<Chain> chains)
      Set the chains of a structure, if this is a NMR structure, this will only set model 0.
      Parameters:
      chains - the list of chains for this structure.
      See Also:

    • getChains

      List<Chain> getChains(int modelnr)
      Retrieve all chains of a model.
      Parameters:
      modelnr - an int
      Returns:
      a List object containing the Chains of Model nr. modelnr
      See Also:

    • setChains

      void setChains(int modelnr, List<Chain> chains)
      Set the chains for a model
      Parameters:
      modelnr - the number of the model
      chains - the chains for a model

    • getPolyChains

      List<Chain> getPolyChains()
      Return all polymeric chains for the first model
      Returns:
      all polymeric chains.
      Since:
      5.0

    • getPolyChains

      List<Chain> getPolyChains(int modelIdx)
      Return all polymeric chains for the given model index.
      Parameters:
      modelIdx - the model index
      Returns:
      all polymeric chains.
      Since:
      5.0

    • getNonPolyChains

      List<Chain> getNonPolyChains()
      Return all non-polymeric chains for the first model
      Returns:
      all non-polymeric chains.
      Since:
      5.0

    • getNonPolyChains

      List<Chain> getNonPolyChains(int modelIdx)
      Return all non-polymeric chains for the given model index.
      Parameters:
      modelIdx - the model index
      Returns:
      all non-polymeric chains.
      Since:
      5.0

    • getWaterChains

      List<Chain> getWaterChains()
      Return all water chains for the first model
      Returns:
      Since:
      5.0

    • getWaterChains

      List<Chain> getWaterChains(int modelIdx)
      Return all water chains for the given model index
      Parameters:
      modelIdx -
      Returns:
      Since:
      5.0

    • addChain

      void addChain(Chain chain)
      Add a new chain to the first model
      Parameters:
      chain - a Chain object

    • addChain

      void addChain(Chain chain, int modelnr)
      Add a new chain to the model specified by the given index
      Parameters:
      chain - a Chain object
      modelnr - an int specifying to which model the Chain should be added

    • getChainByIndex

      Chain getChainByIndex(int chainIndex)
      Retrieve a chain by its index within the Structure .
      Parameters:
      chainIndex - the index of the desired chain in the structure
      Returns:
      a Chain object

    • getChainByIndex

      Chain getChainByIndex(int modelnr, int chainIndex)
      Retrieve a chain by its indices within the Structure and model.
      Parameters:
      modelnr - the model the desired chain is in
      chainIndex - the index of the desired chain in the structure
      Returns:
      a Chain object

    • hasChain

      boolean hasChain(String asymId)
      Check if a chain with the chainId aymId is contained in this structure.
      Parameters:
      asymId - the Id of the chain
      Returns:
      true if a chain with the id asymId is found

    • hasNonPolyChain

      boolean hasNonPolyChain(String asymId)
      Check if a non polymeric chain with chainId asymId is contained in the structure.
      Parameters:
      asymId - the id of the chain
      Returns:
      true if a nonpolymeric chain with the asymId is found
      Since:
      5.0

    • hasPdbChain

      boolean hasPdbChain(String authId)
      Check if a chain with chain name authId is contained in the structure
      Parameters:
      authId - the chain name
      Returns:
      true if a chain with the name authId is found

    • findGroup

      Group findGroup(String authId, String pdbResnum) throws StructureException
      Request a particular group from a structure. by default considers only the first model in the structure.
      Parameters:
      authId - the name of the chain to use
      pdbResnum - the PDB residue number of the requested group
      Returns:
      Group the requested Group
      Throws:
      StructureException

    • findGroup

      Group findGroup(String authId, String pdbResnum, int modelnr) throws StructureException
      Request a particular group from a structure. considers only model nr X. count starts with 0.
      Parameters:
      authId - the chain name of the chain to use
      pdbResnum - the PDB residue number of the requested group
      modelnr - the number of the model to use
      Returns:
      Group the requested Group
      Throws:
      StructureException

    • getChain

      Chain getChain(String asymId)
      Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model
      Parameters:
      asymId - the asymId (chainId)
      Returns:
      See Also:

    • getChain

      Chain getChain(String asymId, int modelIdx)
      Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index
      Parameters:
      asymId - the asymId (chainId)
      modelIdx - the index of the required model (0-based)
      Returns:
      See Also:

    • getPolyChain

      Chain getPolyChain(String asymId)
      Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first model

      See getPolyChainByPDB(String) for a similar method using the chain name (authId).

      Parameters:
      asymId - the asymId (chainId)
      Returns:
      a polymeric Chain or null if it can't be found
      Since:
      5.0

    • getPolyChain

      Chain getPolyChain(String asymId, int modelIdx)
      Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model index

      See getPolyChainByPDB(String, int) for a similar method using the chain name (authId).

      Parameters:
      asymId - the asymId (chainId)
      modelIdx - the index of the required model (0-based)
      Returns:
      a polymeric Chain or null if it can't be found
      Since:
      5.0

    • getPolyChainByPDB

      Chain getPolyChainByPDB(String authId)
      Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first model

      See getPolyChain(String) for a similar method using the chain id (asymId).

      Parameters:
      authId - the author id (chainName, public chain id)
      Returns:
      a polymeric Chain or null if it can't be found
      Since:
      5.0

    • getPolyChainByPDB

      Chain getPolyChainByPDB(String authId, int modelIdx)
      Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.

      See getPolyChain(String, int) for a similar method using the chain id (asymId).

      Parameters:
      authId - the author id (chainName, public chain id)
      modelIdx - the index of the required model (0-based)
      Returns:
      a polymeric Chain or null if it can't be found
      Since:
      5.0

    • getNonPolyChain

      Chain getNonPolyChain(String asymId)
      Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first model
      Parameters:
      asymId - the asymId (chainId)
      Returns:
      a non-polymeric chain or null if it can't be found
      Since:
      5.0

    • getNonPolyChain

      Chain getNonPolyChain(String asymId, int modelIdx)
      Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model index
      Parameters:
      asymId - the asymId (chainId)
      modelIdx - the index of the required model (0-based)
      Returns:
      a non-polymeric Chain or null if it can't be found
      Since:
      5.0

    • getNonPolyChainsByPDB

      List<Chain> getNonPolyChainsByPDB(String authId)
      Retrieve all non-polymeric Chains corresponding to the given 'public' chain name (authId) for the first model.
      Parameters:
      authId - the author id (chainName, public chain id)
      Returns:
      a list of non-polymeric Chains, if none found the list will be empty
      Since:
      5.0

    • getNonPolyChainsByPDB

      List<Chain> getNonPolyChainsByPDB(String authId, int modelIdx)
      Retrieve all non-polymeric Chains corresponding to the 'public' chain name (authId) and the given model index.
      Parameters:
      authId - the author id (chainName, public chain id)
      modelIdx - the index of the required model (0-based)
      Returns:
      a list of non-polymeric Chains, if none found the list will be empty
      Since:
      5.0

    • getWaterChain

      Chain getWaterChain(String asymId)
      Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model
      Parameters:
      asymId - the asymId (chainId)
      Returns:
      a water Chain or null if it can't be found
      Since:
      5.0

    • getWaterChain

      Chain getWaterChain(String asymId, int modelIdx)
      Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index
      Parameters:
      asymId - the asymId (chainId)
      modelIdx - the index of the required model (0-based)
      Returns:
      Since:
      5.0

    • getWaterChainByPDB

      Chain getWaterChainByPDB(String authId)
      Retrieve a water Chain based on the 'public' chain name (authId) for the first model
      Parameters:
      authId - the author id (chainName, public chain id)
      Returns:
      Since:
      5.0

    • getWaterChainByPDB

      Chain getWaterChainByPDB(String authId, int modelIdx)
      Retrieve a water Chain based on the 'public' chain name (authId) for the given model index
      Parameters:
      authId - the author id (chainName, public chain id)
      modelIdx - the index of the required model (0-based)
      Returns:
      Since:
      5.0

    • toPDB

      String toPDB()
      Create a String that contains this Structure's contents in PDB file format.
      Returns:
      a String that looks like a PDB file
      See Also:

    • toMMCIF

      String toMMCIF()
      Create a String that contains this Structure's contents in MMCIF file format.
      Returns:
      a String representation of the Structure object in mmCIF.

    • setEntityInfos

      void setEntityInfos(List<EntityInfo> molList)
      Set the EntityInfo
      Parameters:
      molList - list of entityinfo objects

    • getEntityInfos

      List<EntityInfo> getEntityInfos()
      Get all the EntityInfo for this Structure.
      Returns:
      a list of EntityInfos

    • addEntityInfo

      void addEntityInfo(EntityInfo entityInfo)
      Add an EntityInfo to this Structure

    • setDBRefs

      void setDBRefs(List<DBRef> dbrefs)
      Set the list of database references for this structure
      Parameters:
      dbrefs - list of DBRef objects

    • getDBRefs

      List<DBRef> getDBRefs()
      Get the list of database references
      Returns:
      list of DBRef objects

    • getEntityById

      EntityInfo getEntityById(int entityId)
      Request a particular entity by its entity id (mol id in legacy PDB format)
      Parameters:
      entityId - the number of the entity
      Returns:
      an entity, or null if the molId was not found

    • getPDBHeader

      PDBHeader getPDBHeader()
      Return the header information for this PDB file. N.B. Take care when you blindly use the returned object from this method, because it might be null in some cases.
      Returns:
      the PDBHeader object

    • hasJournalArticle

      boolean hasJournalArticle()
      Return whether or not the entry has an associated journal article or ation. The JRNL section is not mandatory and thus may not be present.
      Returns:
      flag if a JournalArticle has been found.

    • getJournalArticle

      JournalArticle getJournalArticle()
      Get the associated publication as defined by the JRNL records in a PDB file.
      Returns:
      a JournalArticle

    • setJournalArticle

      void setJournalArticle(JournalArticle journalArticle)
      Set the associated publication as defined by the JRNL records in a PDB file.
      Parameters:
      journalArticle - a JournalArticle object

    • getSSBonds

      List<Bond> getSSBonds()
      Get the list of disulfide Bonds as they have been defined in the PDB files
      Returns:
      a list of Bonds

    • setSSBonds

      void setSSBonds(List<Bond> ssbonds)
      Set the list of SSBonds for this structure
      Parameters:
      ssbonds -

    • addSSBond

      void addSSBond(Bond ssbond)
      Add a single disulfide Bond to this structure
      Parameters:
      ssbond - a disulfide bond

    • setPDBHeader

      void setPDBHeader(PDBHeader header)
      Set the the header information for this PDB file
      Parameters:
      header - the PDBHeader object

    • setSites

      void setSites(List<Site> sites)
      Parameters:
      sites - the sites to set in the structure

    • getSites

      List<Site> getSites()
      Returns:
      the sites contained in this structure

    • setBiologicalAssembly

      void setBiologicalAssembly(boolean biologicalAssembly)
      Set a flag to indicate if this structure is a biological assembly
      Parameters:
      biologicalAssembly - true if biological assembly, otherwise false
      Since:
      3.2

    • isBiologicalAssembly

      boolean isBiologicalAssembly()
      Get flag that indicates if this structure is a biological assembly
      Returns:
      true if biological assembly, otherwise false
      Since:
      3.2

    • setCrystallographicInfo

      void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)
      Set crystallographic information for this structure
      Parameters:
      crystallographicInfo - crystallographic information
      Since:
      3.2

    • getCrystallographicInfo

      PDBCrystallographicInfo getCrystallographicInfo()
      Get crystallographic information for this structure
      Returns:
      PDBCrystallographicInfo crystallographic information
      Since:
      3.2

    • resetModels

      void resetModels()
      Resets all models of this Structure
      Since:
      4.0.1

    • getIdentifier

      String getIdentifier()
      Get a string representing this structure's contents. The following places are searched for a non-null value, with the first being returned:
      1. getStructureIdentifier().getIdentifier(), which should give the string originally used to create the structure
      2. getName()
      3. A combination of getPDBCode() with a heuristic description of the residue ranges, in SubstructureIdentifier format.
      Returns:
      A SubstructureIdentifier-format string describing the residue ranges in this structure
      Since:
      The behavior of this method changed in BioJava 4.2. Previously it returned the same value as getPDBCode()

    • getPDBCode

      @Deprecated String getPDBCode()
      Deprecated.
      use getPdbId() to get a PdbId object or getPdbId().getId() to get a String
      Get PDB code of structure.
      Returns:
      a String representing the PDBCode value
      See Also:

    • setPDBCode

      @Deprecated void setPDBCode(String pdb_id)
      Deprecated.
      use setPdbId(PdbId)
      Set PDB code of structure .
      Parameters:
      pdb_id - a String specifying the PDBCode
      See Also:

    • getPdbId

      PdbId getPdbId()
      Returns the PDB identifier associated with this StructureIdentifier.
      Returns:
      the PdbId object
      Since:
      6.0.0

    • setPdbId

      void setPdbId(PdbId pdbId)
      Sets the PdbId identifier associated with this structure.
      Parameters:
      pdbId - the PdbId identifier object to set
      Since:
      6.0.0