/*
* 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.bio.structure;
import java.util.List;
import java.util.Map;
import org.biojava.bio.structure.io.FileConvert;
import org.biojava.bio.structure.io.PDBFileReader;
import org.biojava.bio.structure.HetatomImpl;
import org.biojava.bio.structure.NucleotideImpl;
/**
*
* 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 Compound}
*
*
* 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
*
*
*
*
*
* 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("amino");
{@link AminoAcid} a;
{@link AminoAcid} b;
{@link AminoAcid} c ;
for ( int i=0; i < groups.size(); i++){
// since we requested only groups of type "amino" 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{
/** returns an identical copy of this Structure object
*
* @return identical copy of this Structure object
*/
public Structure clone();
/**
* String representation of object.
*/
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();
/** set the Header data .
*
* @param h a Map object specifying the header
* @see #getHeader
*/
public void setHeader(Map h) ;
/** get Header data .
*
* @return a Map object representing the header value
* @see #setHeader
* @deprecated use getPDBHeader instead
* @see #getPDBHeader
*/
public Map getHeader() ;
/**
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
*/
public void setConnections(List> connections);
/**
* Returns the connections value.
* @return a List object representing the connections value
* @see #setConnections
*/
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 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 @see isNMR ,
* since this is based on the info in the PDB file header.
*
* @return an int representing the number of models in this Structure
*/
public int nrModels() ;
/** test if this structure is an nmr structure.
*
* @return true if this Structure has been resolved by NMR
*/
public boolean isNmr() ;
/** set NMR flag.
*
* @param nmr true to declare that this Structure has been solved by NMR.
*/
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 it's 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 it's position within the Structure and model number.
*
* @param pos an int
* @param modelnr an int
* @return a Chain object
*/
public Chain getChain(int pos, int modelnr);
/** 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 it's 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 it's 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 the contents of a PDB file .
*
* @return a String that looks like a PDB file
* @see FileConvert
*/
public String toPDB();
/** set the compounts
*
* @param molList
*/
public void setCompounds(ListmolList);
/** get all the Compounds that are defined in the PDB Header
*
* @return a list of compound
*/
public List getCompounds();
/** 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 compound by its id
*
* @param molId
* @return a compound
*/
public Compound getCompoundById(String molId);
/** 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 SSBonds as they have been defined in the PDB files
*
* @return a list of SSBonds
*/
public List getSSBonds();
/** set the list of SSBonds for this structure
*
* @param ssbonds
*/
public void setSSBonds(List ssbonds);
/** add a single SSBond to this structure
*
* @param ssbond
*/
public void addSSBond(SSBond ssbond);
/** 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) ;
}