Structure (biojava 5.3.0 API)

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?

  Structure loadStructure(String pathToPDBFile){
                PDBFileReader pdbreader = new PDBFileReader();

                Structure structure = null;
                try{
                        structure = pdbreader.getStructure(pathToPDBFile);
                        System.out.println(structure);
                } catch (IOException e) {
                        e.printStackTrace();
                }
                return structure;
        }

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

  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, Hetatom or Nucleotide 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 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) ;
                                try {

                                        // the Calc class provides utility methods for various calculations on
                                        // structures, groups and atoms

                                        phi = Calc.getPhi(a,b);
                                } catch (StructureException e){
                                        e.printStackTrace();
                                        phi = 360.0 ;
                                }
                        }
                        if ( i < groups.size()-1) {
                                c = (AminoAcid)groups.get(i+1) ;
                                try {
                                        psi = Calc.getPsi(b,c);
                                }catch (StructureException e){
                                        e.printStackTrace();
                                        psi = 360.0 ;
                                }
                        }

                        System.out.print(b.getPDBCode() + " " + b.getPDBName() + ":"  );

                        System.out.println(String.format("\tphi: %+7.2f psi: %+7.2f", phi, psi));

                }

Since:: 1.4
Version:: %I% %G%
Author:: Andreas Prlic

Method Summary

All Methods Instance Methods Abstract Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`addChain(Chain chain)` Add a new chain to the first model
`void`	`addChain(Chain chain, int modelnr)` Add a new chain to the model specified by the given index
`void`	`addEntityInfo(EntityInfo entityInfo)` Add an EntityInfo to this Structure
`void`	`addModel(List<Chain> model)` Add a new model.
`void`	`addSSBond(Bond ssbond)` Add a single disulfide Bond to this structure
`Structure`	`clone()` Return an identical copy of this Structure object
`Chain`	`findChain(String authId)` Deprecated.
`Chain`	`findChain(String authId, int modelnr)` Deprecated.
`Group`	`findGroup(String authId, String pdbResnum)` Request a particular group from a structure.
`Group`	`findGroup(String authId, String pdbResnum, int modelnr)` Request a particular group from a structure.
`Chain`	`getChain(String asymId)` Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model
`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
`Chain`	`getChainByIndex(int chainIndex)` Retrieve a chain by its index within the Structure .
`Chain`	`getChainByIndex(int modelnr, int chainIndex)` Retrieve a chain by its indices within the Structure and model.
`Chain`	`getChainByPDB(String authId)` Deprecated. use `getPolyChainByPDB(String)` instead
`Chain`	`getChainByPDB(String authId, int modelIdx)` Deprecated. use `getPolyChainByPDB(String,int)` instead
`List<Chain>`	`getChains()` Retrieve all chains for the first model.
`List<Chain>`	`getChains(int modelnr)` Retrieve all chains of a model.
`EntityInfo`	`getCompoundById(int entityId)` Deprecated. use `getEntityById(int)` instead
`PDBCrystallographicInfo`	`getCrystallographicInfo()` Get crystallographic information for this structure
`List<DBRef>`	`getDBRefs()` Get the list of database references
`EntityInfo`	`getEntityById(int entityId)` Request a particular entity by its entity id (mol id in legacy PDB format)
`List<EntityInfo>`	`getEntityInfos()` Get all the EntityInfo for this Structure.
`Long`	`getId()` Get the ID used by Hibernate
`String`	`getIdentifier()` Get a string representing this structure's contents.
`JournalArticle`	`getJournalArticle()` Get the associated publication as defined by the JRNL records in a PDB file.
`List<Chain>`	`getModel(int modelnr)` Retrieve all Chains belonging to a model .
`String`	`getName()` Get biological name of Structure.
`Chain`	`getNonPolyChain(String asymId)` Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first model
`Chain`	`getNonPolyChain(String asymId, int modelIdx)` Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model index
`List<Chain>`	`getNonPolyChains()` Return all non-polymeric chains for the first model
`List<Chain>`	`getNonPolyChains(int modelIdx)` Return all non-polymeric chains for the given model index.
`List<Chain>`	`getNonPolyChainsByPDB(String authId)` Retrieve all non-polymeric Chains corresponding to the given 'public' chain name (authId) for the first model.
`List<Chain>`	`getNonPolyChainsByPDB(String authId, int modelIdx)` Retrieve all non-polymeric Chains corresponding to the 'public' chain name (authId) and the given model index.
`String`	`getPDBCode()` Get PDB code of structure.
`PDBHeader`	`getPDBHeader()` Return the header information for this PDB file
`String`	`getPdbId()` Deprecated. From BioJava 4.2, use `getPDBCode()` or `getStructureIdentifier().toCanonical().getPdbId()`
`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).
`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).
`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).
`Chain`	`getPolyChainByPDB(String authId, int modelIdx)` Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.
`List<Chain>`	`getPolyChains()` Return all polymeric chains for the first model
`List<Chain>`	`getPolyChains(int modelIdx)` Return all polymeric chains for the given model index.
`List<String>`	`getRanges()` Deprecated. From BioJava 4.2, use `getStructureIdentifier().toCanonical().getRanges()`
`List<? extends ResidueRange>`	`getResidueRanges()` Deprecated. From BioJava 4.2, use `getStructureIdentifier().toCanonical().getResidueRanges()`
`List<Site>`	`getSites()`
`List<Bond>`	`getSSBonds()` Get the list of disulfide Bonds as they have been defined in the PDB files
`StructureIdentifier`	`getStructureIdentifier()` Get an identifier corresponding to this structure
`Chain`	`getWaterChain(String asymId)` Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model
`Chain`	`getWaterChain(String asymId, int modelIdx)` Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index
`Chain`	`getWaterChainByPDB(String authId)` Retrieve a water Chain based on the 'public' chain name (authId) for the first model
`Chain`	`getWaterChainByPDB(String authId, int modelIdx)` Retrieve a water Chain based on the 'public' chain name (authId) for the given model index
`List<Chain>`	`getWaterChains()` Return all water chains for the first model
`List<Chain>`	`getWaterChains(int modelIdx)` Return all water chains for the given model index
`boolean`	`hasChain(String asymId)` Check if a chain with the chainId aymId is contained in this structure.
`boolean`	`hasJournalArticle()` Return whether or not the entry has an associated journal article or ation.
`boolean`	`hasNonPolyChain(String asymId)` Check if a non polymeric chain with chainId asymId is contained in the structure.
`boolean`	`hasPdbChain(String authId)` Check if a chain with chain name authId is contained in the structure
`boolean`	`isBiologicalAssembly()` Get flag that indicates if this structure is a biological assembly
`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.
`boolean`	`isNmr()` Test if this structure is an NMR structure.
`int`	`nrModels()` Return the number of models .
`void`	`resetModels()` Resets all models of this Structure
`void`	`setBiologicalAssembly(boolean biologicalAssembly)` Set a flag to indicate if this structure is a biological assembly
`void`	`setChains(int modelnr, List<Chain> chains)` Set the chains for a model
`void`	`setChains(List<Chain> chains)` Set the chains of a structure, if this is a NMR structure, this will only set model 0.
`void`	`setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)` Set crystallographic information for this structure
`void`	`setDBRefs(List<DBRef> dbrefs)` Set the list of database references for this structure
`void`	`setEntityInfos(List<EntityInfo> molList)` Set the EntityInfo
`void`	`setId(Long id)` set the ID used by Hibernate
`void`	`setJournalArticle(JournalArticle journalArticle)` Set the associated publication as defined by the JRNL records in a PDB file.
`void`	`setModel(int position, List<Chain> model)` A convenience function if one wants to edit and replace the models in a structure.
`void`	`setName(String name)` Set biological name of Structure .
`void`	`setPDBCode(String pdb_id)` Set PDB code of structure .
`void`	`setPDBHeader(PDBHeader header)` Set the the header information for this PDB file
`void`	`setSites(List<Site> sites)`
`void`	`setSSBonds(List<Bond> ssbonds)` Set the list of SSBonds for this structure
`void`	`setStructureIdentifier(StructureIdentifier structureIdentifier)` Set the identifier corresponding to this structure
`int`	`size()` Return number of polymer Chains in this Structure for first model.
`int`	`size(int modelnr)` Return number of chains of model.
`String`	`toMMCIF()` Create a String that contains this Structure's contents in MMCIF file format.
`String`	`toPDB()` Create a String that contains this Structure's contents in PDB file format.
`String`	`toString()` String representation of object.

- Method Detail
  - 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
  - setPDBCode
```
void setPDBCode(String pdb_id)
```
    Set PDB code of structure .
    
    Parameters:
    
    pdb_id - a String specifying the PDBCode
    
    See Also:
    
    getPDBCode()
  - getPDBCode
```
String getPDBCode()
```
    Get PDB code of structure.
    
    Returns:
    
    a String representing the PDBCode value
    
    See Also:
    
    setPDBCode(java.lang.String)
  - setName
```
void setName(String name)
```
    Set biological name of Structure .
    
    Parameters:
    
    name - a String specifying the biological name of the Structure
    
    See Also:
    
    getName()
  - getName
```
String getName()
```
    Get biological name of Structure.
    
    Returns:
    
    a String representing the biological name of the Structure
    
    See Also:
    
    setName(java.lang.String)
  - 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()
  - isNmr
```
boolean isNmr()
```
    Test if this structure is an NMR structure.
    
    Returns:
    
    true if this Structure has been solved by NMR
    
    See Also:
    
    nrModels()
  - 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(int modelnr)
  - 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:
    
    getModel(int modelnr), getChains(int modelnr)
  - 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:
    
    setChains(int, List)
  - 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:
    
    getModel(int)
  - setChains
```
void setChains(int modelnr,
               List<Chain> chains)
```
    Set the chains for a model
    
    Parameters:
    
    chains - the chains for a model
    
    modelnr - the number of the 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:
    
    chainIndex - the index of the desired chain in the structure
    
    modelnr - the model the desired chain is in
    
    Returns:
    
    a Chain object
  - findChain
```
@Deprecated
Chain findChain(String authId)
                     throws StructureException
```
    Deprecated.
    
    Request a particular chain from a structure. by default considers only the first model.
    
    Parameters:
    
    authId - name of a chain that should be returned
    
    Returns:
    
    Chain the requested chain
    
    Throws:
    
    StructureException
  - findChain
```
@Deprecated
Chain findChain(String authId,
                            int modelnr)
                     throws StructureException
```
    Deprecated.
    
    Request a particular chain from a particular model
    
    Parameters:
    
    authId - the name of a chain that should be returned
    
    modelnr - the number of the model to use
    
    Returns:
    
    Chain the requested chain
    
    Throws:
    
    StructureException
  - 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
  - getChainByPDB
```
@Deprecated
Chain getChainByPDB(String authId)
                         throws StructureException
```
    Deprecated. use getPolyChainByPDB(String) instead
    
    Request a chain by its public id (author id) for the first model. Before 5.0 it returned a Chain that had both polymeric and non-polymeric groups following the PDB-file data model. Since 5.0 it only returns the polymeric part of the chain.
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    Returns:
    
    the Chain that matches the authId
    
    Throws:
    
    StructureException - if chain can't be found
  - getChainByPDB
```
@Deprecated
Chain getChainByPDB(String authId,
                                int modelIdx)
                         throws StructureException
```
    Deprecated. use getPolyChainByPDB(String,int) instead
    
    Request a chain by its public id (author id) for the given model index. Before 5.0 it returned a Chain that had both polymeric and non-polymeric groups following the PDB-file data model. Since 5.0 it only returns the polymeric part of the chain.
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    modelIdx - the index of the required model (0-based)
    
    Returns:
    
    the Chain that matches the authId in the model
    
    Throws:
    
    StructureException - if chain can't be found
  - 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:
    
    getPolyChain(String), getNonPolyChain(String), getWaterChain(String)
  - 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(String, int), getNonPolyChain(String, int), getWaterChain(String, int)
  - 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:
    
    FileConvert
  - 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
  - getCompoundById
```
@Deprecated
EntityInfo getCompoundById(int entityId)
```
    Deprecated. use getEntityById(int) instead
    
    Request a particular entity by its entity id (mol id in legacy PDB format)
    
    Parameters:
    
    entityId - the number of the entity
    
    Returns:
    
    a entityInfo
  - 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
    
    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
  - getId
```
Long getId()
```
    Get the ID used by Hibernate
    
    Returns:
    
    the ID used by Hibernate
  - setId
```
void setId(Long id)
```
    set the ID used by Hibernate
    
    Parameters:
    
    id - the id
  - 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
  - getPdbId
```
@Deprecated
String getPdbId()
```
    Deprecated. From BioJava 4.2, use getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()
    
    Returns the PDB identifier associated with this StructureIdentifier.
  - getResidueRanges
```
@Deprecated
List<? extends ResidueRange> getResidueRanges()
```
    Deprecated. From BioJava 4.2, use getStructureIdentifier().toCanonical().getResidueRanges()
    
    Returns the list of ResidueRanges that this StructureIdentifier defines. This is a unique representation.
  - getRanges
```
@Deprecated
List<String> getRanges()
```
    Deprecated. From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()
    Returns a list of residue ranges. For example:
```
 getRanges().get(0): 'A'
 getRanges().get(1): 'B_5-100'
 
```
    This is a unique representation.
  - 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()

Interface Structure

Method Summary

Method Detail

clone

toString

setPDBCode

getPDBCode

setName

getName

getStructureIdentifier

setStructureIdentifier

size

size

nrModels

isNmr

isCrystallographic

addModel

setModel

getModel

getChains

setChains

getChains

setChains

getPolyChains

getPolyChains

getNonPolyChains

getNonPolyChains

getWaterChains

getWaterChains

addChain

addChain

getChainByIndex

getChainByIndex

findChain

findChain

hasChain

hasNonPolyChain

hasPdbChain

findGroup

findGroup

getChainByPDB

getChainByPDB

getChain

getChain

getPolyChain

getPolyChain

getPolyChainByPDB

getPolyChainByPDB

getNonPolyChain

getNonPolyChain

getNonPolyChainsByPDB

getNonPolyChainsByPDB

getWaterChain

getWaterChain

getWaterChainByPDB

getWaterChainByPDB

toPDB

toMMCIF

setEntityInfos

getEntityInfos

addEntityInfo

setDBRefs

getDBRefs

getCompoundById

getEntityById

getPDBHeader

hasJournalArticle

getJournalArticle

setJournalArticle

getSSBonds

setSSBonds

addSSBond

setPDBHeader

getId

setId

setSites

getSites

setBiologicalAssembly

isBiologicalAssembly

setCrystallographicInfo