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The protein structure modules of BioJava.
/*
* 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.util.List;
import java.util.Map;
/**
*
* 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:
*
* - {@link PDBHeader}
* - {@link DBRef}
* - {@link EntityInfo}
*
*
* The structure object provides access to the data from the ATOM records through
* a hierarchy of sub-object:
*
* Structure
* |
* {@link Chain}
* |
* {@link Group}
* |
* {@link 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:
*
*
* public {@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;
* }
*
*
*
*
*
* Q: How can I calculate Phi and Psi angles of AminoAcids?
*
*
* A:
*
*
* public 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 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));
*
* }
*
*
*
*
*
*
*
* @author Andreas Prlic
* @since 1.4
* @version %I% %G%
*/
public interface Structure extends Cloneable {
/**
* Return an identical copy of this Structure object
*
* @return identical copy of this Structure object
*/
public Structure clone();
/**
* String representation of object.
*/
@Override
public String toString();
/**
* Set PDB code of structure .
*
* @param pdb_id a String specifying the PDBCode
* @see #getPDBCode
*/
public void setPDBCode (String pdb_id) ;
/**
* Get PDB code of structure.
*
* @return a String representing the PDBCode value
* @see #setPDBCode
*/
public String getPDBCode () ;
/**
* Set biological name of Structure .
*
* @param name a String specifying the biological name of the Structure
* @see #getName
*/
public void setName(String name);
/**
* Get biological name of Structure.
*
* @return a String representing the biological name of the Structure
* @see #setName
*/
public String getName();
/**
* Get an identifier corresponding to this structure
* @return The StructureIdentifier used to create this structure
*/
public StructureIdentifier getStructureIdentifier();
/**
* Set the identifier corresponding to this structure
* @param structureIdentifier the structureIdentifier corresponding to this structure
*/
public void setStructureIdentifier(StructureIdentifier structureIdentifier);
/**
sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
COLUMNS DATA TYPE FIELD DEFINITION
---------------------------------------------------------------------------------
1 - 6 Record name "CONECT"
7 - 11 Integer serial Atom serial number
12 - 16 Integer serial Serial number of bonded atom
17 - 21 Integer serial Serial number of bonded atom
22 - 26 Integer serial Serial number of bonded atom
27 - 31 Integer serial Serial number of bonded atom
32 - 36 Integer serial Serial number of hydrogen bonded
atom
37 - 41 Integer serial Serial number of hydrogen bonded
atom
42 - 46 Integer serial Serial number of salt bridged
atom
47 - 51 Integer serial Serial number of hydrogen bonded
atom
52 - 56 Integer serial Serial number of hydrogen bonded
atom
57 - 61 Integer serial Serial number of salt bridged
atom
the HashMap for a single CONECT line contains the following fields:
atomserial (mandatory) : Atom serial number
bond1 .. bond4 (optional): Serial number of bonded atom
hydrogen1 .. hydrogen4 (optional):Serial number of hydrogen bonded atom
salt1 .. salt2 (optional): Serial number of salt bridged atom
*
* @param connections a List object specifying the connections
* @see #getConnections
* @deprecated use {@link Atom#addBond(Bond)} instead
*/
@Deprecated
public void setConnections(List> connections);
/**
* Return the connections value.
* @return a List object representing the connections value
* @see #setConnections
* @deprecated use {@link Atom#getBonds()} instead
*/
@Deprecated
public List> getConnections();
/**
* Return number of Chains in this Structure.
* @return an int representing the number of Chains in this Structure
*/
public 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
*/
public 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()
*/
public int nrModels() ;
/**
* Test if this structure is an NMR structure.
*
* @return true if this Structure has been solved by NMR
* @see #nrModels()
*/
public 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
*/
public boolean isCrystallographic();
/** set NMR flag.
*
* @param nmr true to declare that this Structure has been solved by NMR.
*/
@Deprecated
public void setNmr(boolean nmr);
/**
* Add a new model.
*
* @param model a List object containing the Chains of the new Model
*/
public void addModel(List 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
*/
public void setModel(int position, List 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
*/
public List getModel(int modelnr);
/**
* Retrieve all chains - if it is a NMR structure will return the chains of 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
*/
public List 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.
*/
public void setChains(List chains);
/**
* Retrieve all chains of a model.
* @see #getModel
*
* @param modelnr an int
* @return a List object containing the Chains of Model nr. modelnr
*/
public List getChains(int modelnr);
/**
* Set the chains for a model
* @param chains
* @param modelnr
*/
public void setChains( int modelnr, List chains);
/**
* Add a new chain.
*
* @param chain a Chain object
*/
public void addChain(Chain chain);
/**
* Add a new chain, if several models are available.
*
* @param chain a Chain object
* @param modelnr an int specifying to which model the Chain should be added
*/
public void addChain(Chain chain, int modelnr);
/**
* Retrieve a chain by its position within the Structure .
*
* @param pos an int for the position in the List of Chains.
* @return a Chain object
*/
public Chain getChain(int pos);
/**
* Retrieve a chain by its position within the Structure and model number.
*
* @param pos an int
* @param modelnr an int
* @return a Chain object
*/
public Chain getChain( int modelnr, int pos);
/**
* Request a particular chain from a structure.
* by default considers only the first model.
* @param chainId the ID of a chain that should be returned
* @return Chain the requested chain
* @throws StructureException
*/
public Chain findChain(String chainId)
throws StructureException;
/**
* Check if a chain with the id chainId is contained in this structure.
*
* @param chainId the name of the chain
* @return true if a chain with the id (name) chainId is found
*/
public boolean hasChain(String chainId);
/**
* Request a particular chain from a particular model
* @param modelnr the number of the model to use
* @param chainId the ID of a chain that should be returned
* @return Chain the requested chain
* @throws StructureException
*/
public Chain findChain(String chainId, int modelnr)
throws StructureException;
/**
* Request a particular group from a structure.
* by default considers only the first model in the structure.
* @param chainId the ID of the chain to use
* @param pdbResnum the PDB residue number of the requested group
* @return Group the requested Group
* @throws StructureException
*/
public Group findGroup(String chainId, String pdbResnum)
throws StructureException;
/**
* Request a particular group from a structure.
* considers only model nr X. count starts with 0.
* @param chainId the ID 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
*/
public Group findGroup(String chainId, String pdbResnum, int modelnr)
throws StructureException;
/**
* Request a chain by its PDB code
* by default takes only the first model
*
* @param chainId the chain identifier
* @return the Chain that matches the chainID
* @throws StructureException
*/
public Chain getChainByPDB(String chainId)
throws StructureException;
/**
* Request a chain by its PDB code
* by default takes only the first model
*
* @param chainId the chain identifier
* @param modelnr request a particular model;
* @return the Chain that matches the chainID in the model
* @throws StructureException
*/
public Chain getChainByPDB(String chainId, int modelnr)
throws StructureException;
/**
* Create a String that contains this Structure's contents in PDB file format.
*
* @return a String that looks like a PDB file
* @see FileConvert
*/
public String toPDB();
/**
* Create a String that contains this Structure's contents in MMCIF file format.
* @return
*/
public String toMMCIF();
/**
* Set the EntityInfo
*
* @param molList
*/
public void setEntityInfos(List molList);
/**
* Get all the EntityInfo for this Structure.
*
* @return a list of EntityInfos
*/
public List getEntityInfos();
/**
* Add an EntityInfo to this Structure
*/
public void addEntityInfo(EntityInfo entityInfo);
/**
* Set the list of database references for this structure
* @param dbrefs list of DBRef objects
*
*/
public void setDBRefs(List dbrefs);
/**
* Get the list of database references
*
* @return list of DBRef objects
*/
public List getDBRefs();
/**
* Request a particular entity by its entity id (mol id in legacy PDB format)
*
* @param entityId
* @return a entityInfo
* @deprecated use {@link #getEntityById(int)} instead
*/
public EntityInfo getCompoundById(int entityId);
/**
* Request a particular entity by its entity id (mol id in legacy PDB format)
*
* @param entityId
* @return an entity
*/
public EntityInfo getEntityById(int entityId);
/**
* Return the header information for this PDB file
*
* @return the PDBHeader object
*/
public PDBHeader getPDBHeader();
/**
* Return whether or not the entry has an associated journal article
* or publication. The JRNL section is not mandatory and thus may not be
* present.
* @return flag if a JournalArticle has been found.
*/
public boolean hasJournalArticle();
/**
* Get the associated publication as defined by the JRNL records in a PDB
* file.
* @return a JournalArticle
*/
public JournalArticle getJournalArticle();
/**
* Set the associated publication as defined by the JRNL records in a PDB
* file.
* @param journalArticle
*/
public void setJournalArticle(JournalArticle journalArticle);
/**
* Get the list of disulfide Bonds as they have been defined in the PDB files
*
* @return a list of Bonds
*/
public List getSSBonds();
/**
* Set the list of SSBonds for this structure
*
* @param ssbonds
*/
public void setSSBonds(List ssbonds);
/**
* Add a single disulfide Bond to this structure
*
* @param ssbond
*/
public void addSSBond(Bond ssbond);
/**
* Set the the header information for this PDB file
*
* @param header the PDBHeader object
*/
public void setPDBHeader(PDBHeader header);
/**
* Get the ID used by Hibernate
*
* @return the ID used by Hibernate
*/
public Long getId() ;
/** set the ID used by Hibernate
*
* @param id
*/
public void setId(Long id) ;
/**
* @param sites the sites to set in the structure
*/
public void setSites(List sites);
/**
* @return the sites contained in this structure
*/
public List getSites();
public List getHetGroups();
/**
* Set a flag to indicate if this structure is a biological assembly
* @param biologicalAssembly true if biological assembly, otherwise false
* @since 3.2
*/
public 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
*/
public boolean isBiologicalAssembly();
/**
* Set crystallographic information for this structure
* @param PDBCrystallographicInfo crystallographic information
* @since 3.2
*/
public void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo);
/**
* Get crystallographic information for this structure
* @return PDBCrystallographicInfo crystallographic information
* @since 3.2
*/
public PDBCrystallographicInfo getCrystallographicInfo();
/**
* Resets all models of this Structure
* @since 4.0.1
*/
public void resetModels();
/**
* Returns the PDB identifier associated with this StructureIdentifier.
* @deprecated From BioJava 4.2, use {@link #getPDBCode()} or
* getStructureIdentifier().toCanonical().getPdbId()
*/
@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
* getStructureIdentifier().toCanonical().getResidueRanges()
*/
@Deprecated
List getResidueRanges();
/**
* Returns a list of residue ranges. For example:
*
* getRanges().get(0): 'A'
* getRanges().get(1): 'B_5-100'
*
* This is a unique representation.
* @deprecated From BioJava 4.2, use
* getStructureIdentifier().toCanonical().getRanges()
*/
@Deprecated
List getRanges();
/**
* Get a string representing this structure's contents. The following places
* are searched for a non-null value, with the first being returned:
*
* - {@link #getStructureIdentifier()}.getIdentifier(), which should give
* the string originally used to create the structure
*
- {@link #getName()}
*
- A combination of {@link #getPDBCode()} with a heuristic description
* of the residue ranges, in {@link SubstructureIdentifier} format.
*
* @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();
}
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