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889 lines (795 loc) · 24.1 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on 26.04.2004
* @author Andreas Prlic
*
*/
package org.biojava.nbio.structure;
import org.biojava.nbio.structure.io.FileConvert;
import org.biojava.nbio.structure.io.PDBFileReader;
import java.io.Serializable;
import java.util.List;
/**
*
* 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:
* <ul>
* <li>{@link PDBHeader}</li>
* <li>{@link DBRef}</li>
* <li>{@link EntityInfo}</li>
* </ul>
*
* The structure object provides access to the data from the ATOM records through
* a hierarchy of sub-object:
* <pre>
* Structure
* |
* {@link Chain}
* |
* {@link Group}
* |
* {@link Atom}
* </pre>
*
* For more documentation on how to work with the Structure API please
* see <a href="http://biojava.org/wiki/BioJava:CookBook#Protein_Structure">
* http://biojava.org/wiki/BioJava:CookBook#Protein_Structure</a>
*
* <p>
* The tutorial for the BioJava structure modules can be found at <a href="https://github.com/biojava/biojava3-tutorial/tree/master/structure">github</a>.
* </p>
*
*
* <hr/>
* </hr>
* <p>
* Q: How can I get a Structure object from a PDB file?
* </p>
* <p>
* A:
* </p>
* <pre>
* {@link Structure} loadStructure(String pathToPDBFile){
* {@link PDBFileReader} pdbreader = new {@link PDBFileReader}();
*
* {@link Structure} structure = null;
* try{
* structure = pdbreader.getStructure(pathToPDBFile);
* System.out.println(structure);
* } catch (IOException e) {
* e.printStackTrace();
* }
* return structure;
* }
* </pre>
*
* <hr>
* </hr>
* <p>
* Q: How can I calculate Phi and Psi angles of AminoAcids?
* </p>
* <p>
* A:
* </p>
* <pre>
* void calcPhiPsi({@link Structure} structure){
*
*
* // get the first chain from the structure
*
* {@link Chain} chain = structure.getChain(0);
*
* // A protein chain consists of a number of groups. These can be either
* // {@link AminoAcid}, {@link HetatomImpl Hetatom} or {@link NucleotideImpl 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<Group> groups = chain.getAtomGroups(GroupType.AMINOACID);
*
* {@link AminoAcid} a;
* {@link AminoAcid} b;
* {@link 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 = ({@link AminoAcid})groups.get(i);
*
* double phi =360.0;
* double psi =360.0;
*
* if ( i > 0) {
* a = ({@link AminoAcid})groups.get(i-1) ;
* try {
*
* // the Calc class provides utility methods for various calculations on
* // structures, groups and atoms
*
* phi = {@link Calc}.getPhi(a,b);
* } catch ({@link StructureException} e){
* e.printStackTrace();
* phi = 360.0 ;
* }
* }
* if ( i < groups.size()-1) {
* c = ({@link AminoAcid})groups.get(i+1) ;
* try {
* psi = {@link Calc}.getPsi(b,c);
* }catch ({@link 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));
*
* }
* </pre>
* <hr>
* </hr>
*
*
*
*
* @author Andreas Prlic
* @since 1.4
* @version %I% %G%
*/
public interface Structure extends Cloneable, Serializable {
/**
* Return an identical copy of this Structure object
*
* @return identical copy of this Structure object
*/
Structure clone();
/**
* String representation of object.
*/
@Override
String toString();
/**
* Set PDB code of structure .
*
* @param pdb_id a String specifying the PDBCode
* @see #getPDBCode
*/
void setPDBCode (String pdb_id) ;
/**
* Get PDB code of structure.
*
* @return a String representing the PDBCode value
* @see #setPDBCode
*/
String getPDBCode () ;
/**
* Set biological name of Structure .
*
* @param name a String specifying the biological name of the Structure
* @see #getName
*/
void setName(String name);
/**
* Get biological name of Structure.
*
* @return a String representing the biological name of the Structure
* @see #setName
*/
String getName();
/**
* Get an identifier corresponding to this structure
* @return The StructureIdentifier used to create this structure
*/
StructureIdentifier getStructureIdentifier();
/**
* Set the identifier corresponding to this structure
* @param structureIdentifier the structureIdentifier corresponding to this structure
*/
void setStructureIdentifier(StructureIdentifier structureIdentifier);
/**
* Return number of polymer Chains in this Structure for first model.
* @return the number of polymer Chains in this Structure
*/
int size() ;
/**
* Return number of chains of model.
*
* @param modelnr an int specifying the number of the Model that should be used
* @return an int representing the number of Chains in this Model
*/
int size(int modelnr);
/**
* 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 {@link #isNmr()}.
*
* @return an int representing the number of models in this Structure
* @see #isNmr()
*/
int nrModels() ;
/**
* Test if this structure is an NMR structure.
*
* @return true if this Structure has been solved by NMR
* @see #nrModels()
*/
boolean isNmr() ;
/**
* 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.
*
* @return true if crystallographic, false otherwise
*/
boolean isCrystallographic();
/**
* Add a new model.
*
* @param model a List object containing the Chains of the new Model
*/
void addModel(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.
* @param position starting at 0
* @param model list of chains representing a model
*/
void setModel(int position, List<Chain> model);
/**
* Retrieve all Chains belonging to a model .
* @see #getChains(int modelnr)
*
* @param modelnr an int
* @return a List object containing the Chains of Model nr. modelnr
*/
List<Chain> getModel(int modelnr);
/**
* Retrieve all chains for the first model.
* This is the same as getChains(0);
* @see #getModel(int modelnr)
* @see #getChains(int modelnr)
*
* @return a List object containing the Chains of Model nr. modelnr
*/
List<Chain> getChains();
/**
* Set the chains of a structure, if this is a NMR structure,
* this will only set model 0.
*
* @see #setChains(int, List)
*
* @param chains the list of chains for this structure.
*/
void setChains(List<Chain> chains);
/**
* Retrieve all chains of a model.
* @see #getModel
*
* @param modelnr an int
* @return a List object containing the Chains of Model nr. modelnr
*/
List<Chain> getChains(int modelnr);
/**
* Set the chains for a model
* @param chains the chains for a model
* @param modelnr the number of the model
*/
void setChains( int modelnr, List<Chain> chains);
/**
* Return all polymeric chains for the first model
*
* @return all polymeric chains.
* @since 5.0
*/
List<Chain> getPolyChains();
/**
* Return all polymeric chains for the given model index.
* @param modelIdx the model index
* @return all polymeric chains.
* @since 5.0
*/
List<Chain> getPolyChains(int modelIdx);
/**
* Return all non-polymeric chains for the first model
*
* @return all non-polymeric chains.
* @since 5.0
*/
List<Chain> getNonPolyChains();
/**
* Return all non-polymeric chains for the given model index.
*
* @param modelIdx the model index
* @return all non-polymeric chains.
* @since 5.0
*/
List<Chain> getNonPolyChains(int modelIdx);
/**
* Return all water chains for the first model
* @return
* @since 5.0
*/
List<Chain> getWaterChains();
/**
* Return all water chains for the given model index
* @param modelIdx
* @return
* @since 5.0
*/
List<Chain> getWaterChains(int modelIdx);
/**
* Add a new chain to the first model
*
* @param chain a Chain object
*/
void addChain(Chain chain);
/**
* Add a new chain to the model specified by the given index
*
* @param chain a Chain object
* @param modelnr an int specifying to which model the Chain should be added
*/
void addChain(Chain chain, int modelnr);
/**
* Retrieve a chain by its index within the Structure .
*
* @param chainIndex the index of the desired chain in the structure
* @return a Chain object
*/
Chain getChainByIndex(int chainIndex);
/**
* Retrieve a chain by its indices within the Structure and model.
*
* @param chainIndex the index of the desired chain in the structure
* @param modelnr the model the desired chain is in
* @return a Chain object
*/
Chain getChainByIndex(int modelnr, int chainIndex);
/**
* Request a particular chain from a structure.
* by default considers only the first model.
* @param authId name of a chain that should be returned
* @return Chain the requested chain
* @throws StructureException
* @Deprecated use {@link #getPolyChainByPDB(String)} or {@link #getNonPolyChainsByPDB(String)} instead
*/
@Deprecated
Chain findChain(String authId) throws StructureException;
/**
* Request a particular chain from a particular model
* @param authId the name of a chain that should be returned
* @param modelnr the number of the model to use
* @return Chain the requested chain
* @throws StructureException
* @Deprecated use {@link #getPolyChainByPDB(String, int)} or {@link #getNonPolyChainsByPDB(String, int)} instead
*/
@Deprecated
Chain findChain(String authId, int modelnr) throws StructureException;
/**
* Check if a chain with the chainId aymId is contained in this structure.
*
* @param asymId the Id of the chain
* @return true if a chain with the id asymId is found
*/
boolean hasChain(String asymId);
/**
* Check if a non polymeric chain with chainId asymId is contained in the structure.
*
* @param asymId the id of the chain
* @return true if a nonpolymeric chain with the asymId is found
* @since 5.0
*/
boolean hasNonPolyChain(String asymId);
/**
* Check if a chain with chain name authId is contained in the structure
*
* @param authId the chain name
* @return true if a chain with the name authId is found
*/
boolean hasPdbChain(String authId) ;
/**
* Request a particular group from a structure.
* by default considers only the first model in the structure.
* @param authId the name of the chain to use
* @param pdbResnum the PDB residue number of the requested group
* @return Group the requested Group
* @throws StructureException
*/
Group findGroup(String authId, String pdbResnum) throws StructureException;
/**
* Request a particular group from a structure.
* considers only model nr X. count starts with 0.
* @param authId the chain name of the chain to use
* @param pdbResnum the PDB residue number of the requested group
* @param modelnr the number of the model to use
* @return Group the requested Group
* @throws StructureException
*/
Group findGroup(String authId, String pdbResnum, int modelnr) throws StructureException;
/**
* 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.
*
* @param authId the author id (chainName, public chain id)
* @return the Chain that matches the authId
* @throws StructureException if chain can't be found
* @deprecated use {@link #getPolyChainByPDB(String)} instead
*/
@Deprecated
Chain getChainByPDB(String authId) throws StructureException;
/**
* 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.
*
* @param authId the author id (chainName, public chain id)
* @param modelIdx the index of the required model (0-based)
* @return the Chain that matches the authId in the model
* @throws StructureException if chain can't be found
* @deprecated use {@link #getPolyChainByPDB(String,int)} instead
*/
@Deprecated
Chain getChainByPDB(String authId, int modelIdx) throws StructureException;
/**
* Retrieve a Chain (polymeric, non-polymeric or water) based on
* the 'internal' chain id (asymId) for the first model
* @param asymId the asymId (chainId)
* @return
* @see #getPolyChain(String)
* @see #getNonPolyChain(String)
* @see #getWaterChain(String)
*/
Chain getChain(String asymId);
/**
* Retrieve a Chain (polymeric, non-polymeric or water) based on
* the 'internal' chain id (asymId) for the given model index
* @param asymId the asymId (chainId)
* @param modelIdx the index of the required model (0-based)
* @return
* @see #getPolyChain(String, int)
* @see #getNonPolyChain(String, int)
* @see #getWaterChain(String, int)
*/
Chain getChain(String asymId, int modelIdx);
/**
* Retrieve a polymeric Chain based on the 'internal' chain
* id (asymId) for the first model
*
* <p>See {@link #getPolyChainByPDB(String)} for a similar
* method using the chain name (authId).
* @param asymId the asymId (chainId)
* @return a polymeric Chain or null if it can't be found
* @since 5.0
*/
Chain getPolyChain(String asymId);
/**
* Retrieve a polymeric Chain based on the 'internal' chain
* id (asymId) for the given model index
*
* <p>See {@link #getPolyChainByPDB(String, int)} for a similar
* method using the chain name (authId).
* @param asymId the asymId (chainId)
* @param modelIdx the index of the required model (0-based)
* @return a polymeric Chain or null if it can't be found
* @since 5.0
*/
Chain getPolyChain(String asymId, int modelIdx);
/**
* Retrieve a polymeric Chain based on the 'public' chain
* name (authId) for the first model
*
* <p>See {@link #getPolyChain(String)} for a similar
* method using the chain id (asymId).
* @param authId the author id (chainName, public chain id)
* @return a polymeric Chain or null if it can't be found
* @since 5.0
*/
Chain getPolyChainByPDB(String authId);
/**
* Retrieve a polymeric Chain based on the 'public' chain
* name (authId) for the given model index.
*
* <p>See {@link #getPolyChain(String, int)} for a similar
* method using the chain id (asymId).
* @param authId the author id (chainName, public chain id)
* @param modelIdx the index of the required model (0-based)
* @return a polymeric Chain or null if it can't be found
* @since 5.0
*
*/
Chain getPolyChainByPDB(String authId, int modelIdx);
/**
* Retrieve a non-polymeric Chain based on the 'internal' chain
* id (asymId) for the first model
* @param asymId the asymId (chainId)
* @return a non-polymeric chain or null if it can't be found
* @since 5.0
*/
Chain getNonPolyChain(String asymId);
/**
* Retrieve a non-polymeric Chain based on the 'internal' chain
* id (asymId) for the given model index
* @param asymId the asymId (chainId)
* @param modelIdx the index of the required model (0-based)
* @return a non-polymeric Chain or null if it can't be found
* @since 5.0
*/
Chain getNonPolyChain(String asymId, int modelIdx);
/**
* Retrieve all non-polymeric Chains corresponding to the given 'public' chain
* name (authId) for the first model.
* @param authId the author id (chainName, public chain id)
* @return a list of non-polymeric Chains, if none found the list will be empty
* @since 5.0
*/
List<Chain> getNonPolyChainsByPDB(String authId);
/**
* Retrieve all non-polymeric Chains corresponding to the 'public' chain
* name (authId) and the given model index.
* @param authId the author id (chainName, public chain id)
* @param modelIdx the index of the required model (0-based)
* @return a list of non-polymeric Chains, if none found the list will be empty
* @since 5.0
*/
List<Chain> getNonPolyChainsByPDB(String authId, int modelIdx);
/**
* Retrieve a water Chain based on the 'internal' chain id (asymId)
* for the first model
* @param asymId the asymId (chainId)
* @return a water Chain or null if it can't be found
* @since 5.0
*/
Chain getWaterChain(String asymId);
/**
* Retrieve a water chain based on the 'internal' chain id (asymId)
* for the given model index
* @param asymId the asymId (chainId)
* @param modelIdx the index of the required model (0-based)
* @return
* @since 5.0
*/
Chain getWaterChain(String asymId, int modelIdx);
/**
* Retrieve a water Chain based on the 'public' chain name (authId)
* for the first model
* @param authId the author id (chainName, public chain id)
* @return
* @since 5.0
*/
Chain getWaterChainByPDB(String authId);
/**
* Retrieve a water Chain based on the 'public' chain name (authId)
* for the given model index
* @param authId the author id (chainName, public chain id)
* @param modelIdx the index of the required model (0-based)
* @return
* @since 5.0
*/
Chain getWaterChainByPDB(String authId, int modelIdx);
/**
* Create a String that contains this Structure's contents in PDB file format.
*
* @return a String that looks like a PDB file
* @see FileConvert
*/
String toPDB();
/**
* Create a String that contains this Structure's contents in MMCIF file format.
* @return a String representation of the Structure object in mmCIF.
*/
String toMMCIF();
/**
* Set the EntityInfo
*
* @param molList list of entityinfo objects
*/
void setEntityInfos(List<EntityInfo> molList);
/**
* Get all the EntityInfo for this Structure.
*
* @return a list of EntityInfos
*/
List<EntityInfo> getEntityInfos();
/**
* Add an EntityInfo to this Structure
*/
void addEntityInfo(EntityInfo entityInfo);
/**
* Set the list of database references for this structure
* @param dbrefs list of DBRef objects
*
*/
void setDBRefs(List<DBRef> dbrefs);
/**
* Get the list of database references
*
* @return list of DBRef objects
*/
List<DBRef> getDBRefs();
/**
* Request a particular entity by its entity id (mol id in legacy PDB format)
*
* @param entityId the number of the entity
* @return a entityInfo
* @deprecated use {@link #getEntityById(int)} instead
*/
@Deprecated
EntityInfo getCompoundById(int entityId);
/**
* Request a particular entity by its entity id (mol id in legacy PDB format)
*
* @param entityId the number of the entity
* @return an entity, or null if the molId was not found
*/
EntityInfo getEntityById(int entityId);
/**
* Return the header information for this PDB file
*
* @return the PDBHeader object
*/
PDBHeader getPDBHeader();
/**
* 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.
* @return flag if a JournalArticle has been found.
*/
boolean hasJournalArticle();
/**
* Get the associated publication as defined by the JRNL records in a PDB
* file.
* @return a JournalArticle
*/
JournalArticle getJournalArticle();
/**
* Set the associated publication as defined by the JRNL records in a PDB
* file.
* @param journalArticle a JournalArticle object
*/
void setJournalArticle(JournalArticle journalArticle);
/**
* Get the list of disulfide Bonds as they have been defined in the PDB files
*
* @return a list of Bonds
*/
List<Bond> getSSBonds();
/**
* Set the list of SSBonds for this structure
*
* @param ssbonds
*/
void setSSBonds(List<Bond> ssbonds);
/**
* Add a single disulfide Bond to this structure
*
* @param ssbond a disulfide bond
*/
void addSSBond(Bond ssbond);
/**
* Set the the header information for this PDB file
*
* @param header the PDBHeader object
*/
void setPDBHeader(PDBHeader header);
/**
* Get the ID used by Hibernate
*
* @return the ID used by Hibernate
*/
Long getId() ;
/** set the ID used by Hibernate
*
* @param id the id
*/
void setId(Long id) ;
/**
* @param sites the sites to set in the structure
*/
void setSites(List<Site> sites);
/**
* @return the sites contained in this structure
*/
List<Site> getSites();
/**
* Set a flag to indicate if this structure is a biological assembly
* @param biologicalAssembly true if biological assembly, otherwise false
* @since 3.2
*/
void setBiologicalAssembly(boolean biologicalAssembly);
/**
* Get flag that indicates if this structure is a biological assembly
* @return true if biological assembly, otherwise false
* @since 3.2
*/
boolean isBiologicalAssembly();
/**
* Set crystallographic information for this structure
* @param crystallographicInfo crystallographic information
* @since 3.2
*/
void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo);
/**
* Get crystallographic information for this structure
* @return PDBCrystallographicInfo crystallographic information
* @since 3.2
*/
PDBCrystallographicInfo getCrystallographicInfo();
/**
* Resets all models of this Structure
* @since 4.0.1
*/
void resetModels();
/**
* Returns the PDB identifier associated with this StructureIdentifier.
* @deprecated From BioJava 4.2, use {@link #getPDBCode()} or
* <code>getStructureIdentifier().toCanonical().getPdbId()</code>
*/
@Deprecated
String getPdbId();
/**
* Returns the list of {@link ResidueRange ResidueRanges} that this StructureIdentifier defines.
* This is a unique representation.
* @deprecated From BioJava 4.2, use
* <code>getStructureIdentifier().toCanonical().getResidueRanges()</code>
*/
@Deprecated
List<? extends ResidueRange> getResidueRanges();
/**
* Returns a list of residue ranges. For example:
* <pre>
* getRanges().get(0): 'A'
* getRanges().get(1): 'B_5-100'
* </pre>
* This is a unique representation.
* @deprecated From BioJava 4.2, use
* <code>getStructureIdentifier().toCanonical().getRanges()</code>
*/
@Deprecated
List<String> getRanges();
/**
* Get a string representing this structure's contents. The following places
* are searched for a non-null value, with the first being returned:
* <ol>
* <li>{@link #getStructureIdentifier()}.getIdentifier(), which should give
* the string originally used to create the structure
* <li>{@link #getName()}
* <li>A combination of {@link #getPDBCode()} with a heuristic description
* of the residue ranges, in {@link SubstructureIdentifier} format.
* </ol>
* @return A {@link 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 {@link #getPDBCode()}
*/
String getIdentifier();
}