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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 22.01.2007
*
*/
package org.biojava.nbio.structure;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
/**
* An object to contain the info from the PDB header for a Molecule.
* In mmCIF dictionary, it is called an Entity. In the case of polymers it
* is defined as each group of sequence identical NCS-related chains
*
* Now PDB file format 3.2 aware - contains the new TAX_ID fields for the
* organism studied and the expression system.
*
* @author Jules Jacobsen
* @author Jose Duarte
* @author Anthony Bradley
* @since 1.5
*/
public class EntityInfo implements Serializable {
private final static Logger logger = LoggerFactory.getLogger(EntityInfo.class);
// TODO We could drop a lot of the stuff here that is PDB-file related (actually many PDB files don't contain many of these fields) - JD 2016-03-25
// The only really essential part of a EntityInfo is the member chains and the entity_id/mol_id
// See also issue https://github.com/biojava/biojava/issues/219
private static final long serialVersionUID = 2991897825657586356L;
/**
* The list of chains that are described by this EntityInfo
*/
private List chains;
/**
* The Molecule identifier, called entity_id in mmCIF dictionary
*/
private int molId;
/**
* A map to cache residue number mapping, between ResidueNumbers and index (1-based) in aligned sequences (SEQRES).
* Initialised lazily upon call to {@link #getAlignedResIndex(Group, Chain)}
*/
private Map> chains2pdbResNums2ResSerials;
private String refChainId;
private String description = null;
private String title = null;
/**
* The type of entity (polymer, non-polymer, water)
*/
private EntityType type = null;
private List synonyms = null;
private List ecNums = null;
private String engineered = null;
private String mutation = null;
private String biologicalUnit = null;
private String details = null;
private String numRes = null;
private String resNames = null;
private String headerVars = null;
private String synthetic = null;
private String fragment = null;
private String organismScientific = null;
private String organismTaxId = null;
private String organismCommon = null;
private String strain = null;
private String variant = null;
private String cellLine = null;
private String atcc = null;
private String organ = null;
private String tissue = null;
private String cell = null;
private String organelle = null;
private String secretion = null;
private String gene = null;
private String cellularLocation = null;
private String expressionSystem = null;
private String expressionSystemTaxId = null;
private String expressionSystemStrain = null;
private String expressionSystemVariant = null;
private String expressionSystemCellLine = null;
private String expressionSystemAtccNumber = null;
private String expressionSystemOrgan = null;
private String expressionSystemTissue = null;
private String expressionSystemCell = null;
private String expressionSystemOrganelle = null;
private String expressionSystemCellularLocation = null;
private String expressionSystemVectorType = null;
private String expressionSystemVector = null;
private String expressionSystemPlasmid = null;
private String expressionSystemGene = null;
private String expressionSystemOtherDetails = null;
private Long id;
public EntityInfo () {
chains = new ArrayList();
chains2pdbResNums2ResSerials = new HashMap>();
molId = -1;
}
/**
* Constructs a new EntityInfo copying all data from the given one
* but not setting the Chains
* @param c
*/
public EntityInfo (EntityInfo c) {
this.chains = new ArrayList();
this.chains2pdbResNums2ResSerials = new HashMap>();
this.molId = c.molId;
this.type = c.type;
this.refChainId = c.refChainId;
this.description = c.description;
this.title = c.title;
if (c.synonyms!=null) {
this.synonyms = new ArrayList();
synonyms.addAll(c.synonyms);
}
if (c.ecNums!=null) {
this.ecNums = new ArrayList();
ecNums.addAll(c.ecNums);
}
this.engineered = c.engineered;
this.mutation = c.mutation;
this.biologicalUnit = c.biologicalUnit;
this.details = c.details;
this.numRes = c.numRes;
this.resNames = c.resNames;
this.headerVars = c.headerVars;
this.synthetic = c.synthetic;
this.fragment = c.fragment;
this.organismScientific = c.organismScientific;
this.organismTaxId = c.organismTaxId;
this.organismCommon = c.organismCommon;
this.strain = c.strain;
this.variant = c.variant;
this.cellLine = c.cellLine;
this.atcc = c.atcc;
this.organ = c.organ;
this.tissue = c.tissue;
this.cell = c.cell;
this.organelle = c.organelle;
this.secretion = c.secretion;
this.gene = c.gene;
this.cellularLocation = c.cellularLocation;
this.expressionSystem = c.expressionSystem;
this.expressionSystemTaxId = c.expressionSystemTaxId;
this.expressionSystemStrain = c.expressionSystemStrain;
this.expressionSystemVariant = c.expressionSystemVariant;
this.expressionSystemCellLine = c.expressionSystemCellLine;
this.expressionSystemAtccNumber = c.expressionSystemAtccNumber;
this.expressionSystemOrgan = c.expressionSystemOrgan;
this.expressionSystemTissue = c.expressionSystemTissue;
this.expressionSystemCell = c.expressionSystemCell;
this.expressionSystemOrganelle = c.expressionSystemOrganelle;
this.expressionSystemCellularLocation = c.expressionSystemCellularLocation;
this.expressionSystemVectorType = c.expressionSystemVectorType;
this.expressionSystemVector = c.expressionSystemVector;
this.expressionSystemPlasmid = c.expressionSystemPlasmid;
this.expressionSystemGene = c.expressionSystemGene;
this.expressionSystemOtherDetails = c.expressionSystemOtherDetails;
}
@Override
public String toString(){
StringBuilder buf = new StringBuilder();
buf.append("EntityInfo: ").append(molId).append(" ");
buf.append(description==null?"(no name)":"("+description+")");
buf.append(" chains: ");
if (chains!=null) {
for (int i=0;i chainIds = new ArrayList();
for (Chain chain:chains) {
chainIds.add(chain.getChainID());
}
Collections.sort(chainIds, String.CASE_INSENSITIVE_ORDER);
for (Chain chain:chains) {
if (chain.getChainID().equals(chainIds.get(0))) {
return chain;
}
}
logger.error("Could not find a representative chain for EntityInfo '{}'", this.toString());
return null;
}
/** get the ID used by Hibernate
*
* @return the ID used by Hibernate
*/
public Long getId() {
return id;
}
/** set the ID used by Hibernate
*
* @param id
*/
public void setId(Long id) {
this.id = id;
}
/**
* Print some debug statements to System.out
*
*
*/
public void showHeader(){
this.showEntityInfo();
this.showSource();
}
public void showEntityInfo() {
System.out.println("ENTITY INFO:");
if (this.molId != -1) {
System.out.println("Mol ID: " + this.molId);
}
if (this.chains != null) {
StringBuilder buf = new StringBuilder();
for (int i=0;i getChainIds() {
Set uniqChainIds = new TreeSet();
for (int i=0;i(uniqChainIds);
}
/**
* Given a Group g of Chain c (member of this EnityInfo) return the corresponding position in the
* alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence.
* This allows for comparisons of residues belonging to different chains of the same EnityInfo (entity).
*
* If {@link FileParsingParameters#setAlignSeqRes(boolean)} is not used or SEQRES not present, a mapping
* will not be available and this method will return {@link ResidueNumber#getSeqNum()} for all residues, which
* in some cases will be correctly aligned indices (when no insertion codes are
* used and when all chains within the entity are numbered in the same way), but
* in general they will be neither unique (because of insertion codes) nor aligned.
*
* @param g
* @param c
* @return the aligned residue index (1 to n), if no SEQRES groups are available at all then {@link ResidueNumber#getSeqNum()}
* is returned as a fall-back, if the group is not found in the SEQRES groups then -1 is returned
* for the given group and chain
* @throws IllegalArgumentException if the given Chain is not a member of this EnityInfo
* @see {@link Chain#getSeqResGroup(int)}
*/
public int getAlignedResIndex(Group g, Chain c) {
boolean contained = false;
for (Chain member:getChains()) {
if (c.getChainID().equals(member.getChainID())) {
contained = true;
break;
}
}
if (!contained)
throw new IllegalArgumentException("Given chain "+c.getChainID()+" is not a member of this entity: "+getChainIds().toString());
if (!chains2pdbResNums2ResSerials.containsKey(c.getChainID())) {
// we do lazy initialisation of the map
initResSerialsMap(c);
}
// if no seqres groups are available at all the map will be null
Map map = chains2pdbResNums2ResSerials.get(c.getChainID());
int serial;
if (map!=null) {
ResidueNumber resNum = g.getResidueNumber();
// the resNum will be null for groups that are SEQRES only and not in ATOM,
// still it can happen that a group is in ATOM in one chain but not in other of the same entity.
// This is what we try to find out here (analogously to what we do in initResSerialsMap() ):
if (resNum==null && c.getSeqResGroups()!=null && !c.getSeqResGroups().isEmpty()) {
int index = -1;
for (int i=0;i resNums2ResSerials = new HashMap();
chains2pdbResNums2ResSerials.put(c.getChainID(), resNums2ResSerials);
for (int i=0;i getSynonyms() {
return synonyms;
}
public void setSynonyms(List synonyms) {
this.synonyms = synonyms;
}
public List getEcNums() {
return ecNums;
}
public void setEcNums(List ecNums) {
this.ecNums = ecNums;
}
public String getEngineered() {
return engineered;
}
public void setEngineered(String engineered) {
this.engineered = engineered;
}
public String getMutation() {
return mutation;
}
public void setMutation(String mutation) {
this.mutation = mutation;
}
public String getBiologicalUnit() {
return biologicalUnit;
}
public void setBiologicalUnit(String biologicalUnit) {
this.biologicalUnit = biologicalUnit;
}
public String getDetails() {
return details;
}
public void setDetails(String details) {
this.details = details;
}
public String getNumRes() {
return numRes;
}
public void setNumRes(String numRes) {
this.numRes = numRes;
}
public String getResNames() {
return resNames;
}
public void setResNames(String resNames) {
this.resNames = resNames;
}
public String getHeaderVars() {
return headerVars;
}
public void setHeaderVars(String headerVars) {
this.headerVars = headerVars;
}
public String getSynthetic() {
return synthetic;
}
public void setSynthetic(String synthetic) {
this.synthetic = synthetic;
}
public String getFragment() {
return fragment;
}
public void setFragment(String fragment) {
this.fragment = fragment;
}
public String getOrganismScientific() {
return organismScientific;
}
public void setOrganismScientific(String organismScientific) {
this.organismScientific = organismScientific;
}
public String getOrganismTaxId() {
return organismTaxId;
}
public void setOrganismTaxId(String organismTaxId) {
this.organismTaxId = organismTaxId;
}
public String getOrganismCommon() {
return organismCommon;
}
public void setOrganismCommon(String organismCommon) {
this.organismCommon = organismCommon;
}
public String getStrain() {
return strain;
}
public void setStrain(String strain) {
this.strain = strain;
}
public String getVariant() {
return variant;
}
public void setVariant(String variant) {
this.variant = variant;
}
public String getCellLine() {
return cellLine;
}
public void setCellLine(String cellLine) {
this.cellLine = cellLine;
}
public String getAtcc() {
return atcc;
}
public void setAtcc(String atcc) {
this.atcc = atcc;
}
public String getOrgan() {
return organ;
}
public void setOrgan(String organ) {
this.organ = organ;
}
public String getTissue() {
return tissue;
}
public void setTissue(String tissue) {
this.tissue = tissue;
}
public String getCell() {
return cell;
}
public void setCell(String cell) {
this.cell = cell;
}
public String getOrganelle() {
return organelle;
}
public void setOrganelle(String organelle) {
this.organelle = organelle;
}
public String getSecretion() {
return secretion;
}
public void setSecretion(String secretion) {
this.secretion = secretion;
}
public String getGene() {
return gene;
}
public void setGene(String gene) {
this.gene = gene;
}
public String getCellularLocation() {
return cellularLocation;
}
public void setCellularLocation(String cellularLocation) {
this.cellularLocation = cellularLocation;
}
public String getExpressionSystem() {
return expressionSystem;
}
public String getExpressionSystemTaxId() {
return expressionSystemTaxId;
}
public void setExpressionSystemTaxId(String expressionSystemTaxId) {
this.expressionSystemTaxId = expressionSystemTaxId;
}
public void setExpressionSystem(String expressionSystem) {
this.expressionSystem = expressionSystem;
}
public String getExpressionSystemStrain() {
return expressionSystemStrain;
}
public void setExpressionSystemStrain(String expressionSystemStrain) {
this.expressionSystemStrain = expressionSystemStrain;
}
public String getExpressionSystemVariant() {
return expressionSystemVariant;
}
public void setExpressionSystemVariant(String expressionSystemVariant) {
this.expressionSystemVariant = expressionSystemVariant;
}
public String getExpressionSystemCellLine() {
return expressionSystemCellLine;
}
public void setExpressionSystemCellLine(String expressionSystemCellLine) {
this.expressionSystemCellLine = expressionSystemCellLine;
}
public String getExpressionSystemAtccNumber() {
return expressionSystemAtccNumber;
}
public void setExpressionSystemAtccNumber(String expressionSystemAtccNumber) {
this.expressionSystemAtccNumber = expressionSystemAtccNumber;
}
public String getExpressionSystemOrgan() {
return expressionSystemOrgan;
}
public void setExpressionSystemOrgan(String expressionSystemOrgan) {
this.expressionSystemOrgan = expressionSystemOrgan;
}
public String getExpressionSystemTissue() {
return expressionSystemTissue;
}
public void setExpressionSystemTissue(String expressionSystemTissue) {
this.expressionSystemTissue = expressionSystemTissue;
}
public String getExpressionSystemCell() {
return expressionSystemCell;
}
public void setExpressionSystemCell(String expressionSystemCell) {
this.expressionSystemCell = expressionSystemCell;
}
public String getExpressionSystemOrganelle() {
return expressionSystemOrganelle;
}
public void setExpressionSystemOrganelle(String expressionSystemOrganelle) {
this.expressionSystemOrganelle = expressionSystemOrganelle;
}
public String getExpressionSystemCellularLocation() {
return expressionSystemCellularLocation;
}
public void setExpressionSystemCellularLocation(String expressionSystemCellularLocation) {
this.expressionSystemCellularLocation = expressionSystemCellularLocation;
}
public String getExpressionSystemVectorType() {
return expressionSystemVectorType;
}
public void setExpressionSystemVectorType(String expressionSystemVectorType) {
this.expressionSystemVectorType = expressionSystemVectorType;
}
public String getExpressionSystemVector() {
return expressionSystemVector;
}
public void setExpressionSystemVector(String expressionSystemVector) {
this.expressionSystemVector = expressionSystemVector;
}
public String getExpressionSystemPlasmid() {
return expressionSystemPlasmid;
}
public void setExpressionSystemPlasmid(String expressionSystemPlasmid) {
this.expressionSystemPlasmid = expressionSystemPlasmid;
}
public String getExpressionSystemGene() {
return expressionSystemGene;
}
public void setExpressionSystemGene(String expressionSystemGene) {
this.expressionSystemGene = expressionSystemGene;
}
public String getExpressionSystemOtherDetails() {
return expressionSystemOtherDetails;
}
public void setExpressionSystemOtherDetails(String expressionSystemOtherDetails) {
this.expressionSystemOtherDetails = expressionSystemOtherDetails;
}
/**
* Get the list of chains that are part of this EntityInfo. Note that for multi-model
* structures chains from all models are returned.
*
* @return a List of Chain objects
*/
public List getChains(){
return this.chains;
}
/**
* Add new Chain to this EntityInfo
* @param chain
*/
public void addChain(Chain chain){
this.chains.add(chain);
}
/**
* Set the chains for this EntityInfo
* @param chains
*/
public void setChains(List chains){
this.chains = chains;
}
/**
* Get the type of entity this EntityInfo describes.
* Options are polymer, non-polymer or water.
* @return a string describing the type of entity. (polymer, non-polymer or water).
*/
public EntityType getType() {
return this.type;
}
/**
* Set the type of entity this EntityInfo describes.
* Options are polymer, non-polymer or water.
* @param type a string describing the type of entity. (polymer, non-polymer or water).
*/
public void setType(EntityType type) {
this.type = type;
}
}
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