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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/
*
*/
package org.biojava.nbio.structure;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.text.DateFormat;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.EnumSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Set;
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* A class that contains PDB Header information.
* In contrast to what the name suggests, this class does not represent a
* direct mapping of the Header section of the PDB legacy file format.
* Instead, it holds the information that is not directly related to the
* structure data. Such information may exist in some cases and may not exist in
* other cases.
*
* @author Andreas Prlic
* @since 1.6
*
*/
public class PDBHeader implements PDBRecord {
private static final long serialVersionUID = -5834326174085429508L;
private static final Logger logger = LoggerFactory.getLogger(PDBHeader.class);
private String title;
/**@deprecated This field should not be used. It will be removed later.
* Use {@link #getKeywords()} instead. */
private String description;
private List keywords;
private PdbId pdbId;
private String classification;
private Date depDate;
private Date relDate;
private Date modDate;
private Set techniques;
private PDBCrystallographicInfo crystallographicInfo;
private float resolution;
private float rFree;
private float rWork;
private JournalArticle journalArticle;
private String authors;
public static final float DEFAULT_RESOLUTION = 99;
public static final float DEFAULT_RFREE = 1; // worst possible rfree is the default
private Long id;
public static final String newline = System.getProperty("line.separator");
private DateFormat dateFormat;
private Map bioAssemblies ;
List revisionRecords;
public PDBHeader(){
depDate = new Date(0);
modDate = new Date(0);
relDate = new Date(0);
dateFormat = new SimpleDateFormat("dd-MMM-yy",Locale.US);
resolution = DEFAULT_RESOLUTION;
rFree = DEFAULT_RFREE;
rWork = DEFAULT_RFREE;
bioAssemblies = new LinkedHashMap<>();
crystallographicInfo = new PDBCrystallographicInfo();
keywords = new ArrayList<>();
}
/** String representation
*
*/
@Override
public String toString(){
StringBuilder buf = new StringBuilder();
try {
Class c = Class.forName(PDBHeader.class.getName());
Method[] methods = c.getMethods();
for (Method m : methods) {
String name = m.getName();
if ("get".equals(name.substring(0, 3))) {
if ("getClass".equals(name)) {
continue;
}
Object o = m.invoke(this);
if (o != null) {
buf.append(name.substring(3, name.length()));
buf.append(": ").append(o).append(" ");
}
}
}
} catch (ClassNotFoundException e) {
logger.error("Exception caught while creating toString ",e);
} catch (InvocationTargetException e) {
logger.error("Exception caught while creating toString ",e);
} catch (IllegalAccessException e) {
logger.error("Exception caught while creating toString ",e);
}
return buf.toString();
}
/** Return a PDB representation of the PDB Header
*
* @return a PDB file style display
*/
@Override
public String toPDB(){
StringBuffer buf = new StringBuffer();
toPDB(buf);
return buf.toString();
}
/** Appends a PDB representation of the PDB header to the provided StringBuffer
*
* @param buf
*/
@Override
public void toPDB(StringBuffer buf){
// 1 2 3 4 5 6 7
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//HEADER COMPLEX (SERINE PROTEASE/INHIBITORS) 06-FEB-98 1A4W
//TITLE CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING
//TITLE 2 INHIBITORS: PROBES OF THE S1' BINDING SITE
printHeader(buf);
printTitle(buf);
printExpdata(buf);
printAuthors(buf);
printResolution(buf);
}
private void printResolution(StringBuffer buf){
if (getResolution() == DEFAULT_RESOLUTION){
return;
}
DecimalFormat d2 = (DecimalFormat)NumberFormat.getInstance(java.util.Locale.UK);
d2.setMaximumIntegerDigits(2);
d2.setMinimumFractionDigits(2);
d2.setMaximumFractionDigits(2);
buf.append("REMARK 2 RESOLUTION. ");
String x = d2.format(resolution);
buf.append(x);
buf.append(" ANGSTROMS.");
fillLine(buf,34+x.length());
buf.append(newline);
}
private void printExpdata(StringBuffer buf){
Set exp = getExperimentalTechniques();
if ( exp == null )
return;
buf.append("EXPDTA ");
int length = 0;
int i = 0;
for (ExperimentalTechnique et:exp) {
if (i>0) {
buf.append("; ");
length+=2;
}
buf.append(et.getName());
length+=et.getName().length();
i++;
}
// fill up the white space to the right column
int l = length + 10;
fillLine(buf,l);
buf.append(newline);
}
private void printAuthors(StringBuffer buf){
String authors = getAuthors();
if ( authors == null)
return;
if ( "".equals(authors)){
return;
}
printMultiLine(buf, "AUTHOR ", authors,',');
}
private void printMultiLine(StringBuffer buf, String lineStart, String data, char breakChar){
if ( lineStart.length() != 9)
logger.info("lineStart != 9, there will be problems :" + lineStart);
if ( data.length() < 58) {
buf.append(lineStart);
buf.append(" ");
buf.append(data);
buf.append(newline);
return;
}
String thisLine = "";
int count = 1;
while (data.length() > 57) {
// find first whitespace from left
// there are 10 chars to the left, so the cutoff position is 56
boolean charFound = false;
for ( int i =57;i>-1;i--){
char c = data.charAt(i);
if (c == breakChar){
// found the whitespace
thisLine = data.substring(0,i+1);
// prevent endless loop
if (i == 0 )
i++;
data = data.substring(i);
charFound = true;
break;
}
}
// for emergencies... prevents an endless loop
if ( ! charFound){
thisLine = data.substring(0,58);
data = data.substring(57);
}
if ( ( breakChar == ',' ) && ( data.charAt(0)== ',')) {
data = data.substring(1);
}
//TODO: check structures that have more than 10 lines...
// start printing..
buf.append(lineStart);
if ( count > 1) {
buf.append(count);
if ( breakChar != ' ' )
buf.append(" ");
}
else
buf.append(" ");
buf.append(thisLine);
// fill up the white space to the right column
int l = thisLine.length()+ 10;
while (l < 67){
l++;
buf.append(" ");
}
buf.append(newline);
count++;
}
// last line...
if (!data.trim().isEmpty()){
buf.append(lineStart);
buf.append(count);
int filledLeft = 10;
if ( breakChar != ' ' ) {
buf.append(" ");
filledLeft++;
}
buf.append(data);
// fill up the white space to the right column
int l = data.length()+ filledLeft;
fillLine(buf,l);
buf.append(newline);
}
}
private void fillLine(StringBuffer buf, int currentPos){
int l = currentPos;
while (l < 67){
l++;
buf.append(" ");
}
}
private void printHeader(StringBuffer buf){
String classification = getClassification();
if (classification == null || classification.isEmpty()) return;
// we can;t display this line since the classification is not there...
buf.append("HEADER ");
buf.append(classification);
buf.append(" ");
// fill up the white space to the right column
int l = classification.length() + 10 ;
while (l < 49){
l++;
buf.append(" ");
}
Date d = getDepDate();
if ( d != null){
// provide correct display of Dep date...
buf.append(dateFormat.format(d));
} else {
buf.append(" ");
}
buf.append(" ");
String id = getIdCode();
if ( id != null){
buf.append(getIdCode());
buf.append(" ");
}
else
buf.append(" ");
buf.append(newline);
}
private void printTitle(StringBuffer buf) {
// 1 2 3 4 5 6 7
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//HEADER COMPLEX (SERINE PROTEASE/INHIBITORS) 06-FEB-98 1A4W
//TITLE CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING
//TITLE 2 INHIBITORS: PROBES OF THE S1' BINDING SITE
String title = getTitle();
if ( (title == null) || (title.trim().isEmpty()) )
return;
printMultiLine(buf, "TITLE ", title,' ');
}
/** Get the ID used by Hibernate.
*
* @return the ID used by Hibernate
* @see #setId(Long)
*/
public Long getId() {
return id;
}
/** Set the ID used by Hibernate.
*
* @param id the id assigned by Hibernate
* @see #getId()
*
*/
@SuppressWarnings("unused")
private void setId(Long id) {
this.id = id;
}
/** Compare two PDBHeader objects
*
* @param other a PDBHeader object to compare this one to.
* @return true if they are equal or false if they are not.
*/
public boolean equals(PDBHeader other){
try {
Class c = Class.forName(PDBHeader.class.getName());
Method[] methods = c.getMethods();
for (Method m : methods) {
String name = m.getName();
if ("get".equals(name.substring(0, 3))) {
if ("getClass".equals(name)) {
continue;
}
Object a = m.invoke(this);
Object b = m.invoke(other);
if (a == null) {
if (b == null) {
continue;
} else {
logger.warn(name + " a is null, where other is " + b);
return false;
}
}
if (b == null) {
logger.warn(name + " other is null, where a is " + a);
return false;
}
if (!(a.equals(b))) {
logger.warn("mismatch with " + name + " >" + a + "< >" + b + "<");
return false;
}
}
}
} catch (ClassNotFoundException e) {
logger.error("Exception caught while comparing PDBHeader objects ",e);
return false;
} catch (InvocationTargetException e) {
logger.error("Exception caught while comparing PDBHeader objects ",e);
return false;
} catch (IllegalAccessException e) {
logger.error("Exception caught while comparing PDBHeader objects ",e);
return false;
}
return true;
}
/**
* The PDB code for this protein structure.
*
* @return the PDB identifier
* @see #setIdCode(String)
* @deprecated use {@link #getPdbId()}
*/
@Deprecated
public String getIdCode() {
if(this.pdbId == null)
return null;
return this.pdbId.getId();
}
/**
* The PDB code for this protein structure.
*
* @param idCode the PDB identifier
* @see #getIdCode()
* @deprecated use {@link #setPdbId(PdbId)}
*/
@Deprecated
public void setIdCode(String idCode) {
if(idCode == null) {
this.pdbId = null;
}else {
this.pdbId = new PdbId(idCode);
}
}
/**
* Gets the PDB identifier for this protein structure.
*
* @return the {@link PdbId} PDB identifier
* @see #setPdbId(PdbId)
* @since 6.0.0
*/
public PdbId getPdbId() {
return pdbId;
}
/**
* Sets the PDB identifier code for this protein structure.
*
* @param pdbId the PDB identifier
* @see #getPdbId()
* @since 6.0.0
*/
public void setPdbId(PdbId pdbId) {
this.pdbId = pdbId;
}
public String getClassification() {
return classification;
}
public void setClassification(String classification) {
this.classification = classification;
}
/**
* Return the deposition date of the structure in the PDB.
*
* @return the deposition date
*/
public Date getDepDate() {
return depDate;
}
/**
* The deposition date of the structure in the PDB
*
* @param depDate the deposition date
*/
public void setDepDate(Date depDate) {
this.depDate = depDate;
}
/**
* Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid
* experimental techniques when the Set will contain 2 or more values
* @return the Set of ExperimentalTechniques or null if not set
*/
public Set getExperimentalTechniques() {
return techniques;
}
/**
* Adds the experimental technique to the set of experimental techniques of this header.
* Note that if input is not a recognised technique string then no errors will be produced but
* false will be returned
* @param techniqueStr
* @return true if the input corresponds to a recognised technique string (see {@link ExperimentalTechnique})
* and it was not already present in the current set of ExperimentalTechniques
*/
public boolean setExperimentalTechnique(String techniqueStr) {
ExperimentalTechnique et = ExperimentalTechnique.getByName(techniqueStr);
if (et==null) return false;
if (techniques==null) {
techniques = EnumSet.of(et);
return true;
} else {
return techniques.add(et);
}
}
public PDBCrystallographicInfo getCrystallographicInfo() {
return crystallographicInfo;
}
public void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo) {
this.crystallographicInfo = crystallographicInfo;
}
/**
* Returns the resolution (or effective resolution) of the experiment. This is
* related to _refine.ls_d_res_high (DIFFRACTION) or
* _em_3d_reconstruction.resolution (ELECTRON MICROSCOPY) for mmCif
* format, or to REMARK 2 or REMARK 3 for PDB legacy
* format. If more than one value is available (in rare cases), the last one is
* reported. If no value is available, it defaults to
* {@link #DEFAULT_RESOLUTION} ({@value #DEFAULT_RESOLUTION}).
*
* @return The reported experiment resolution, {@link #DEFAULT_RESOLUTION}
* ({@value #DEFAULT_RESOLUTION}) if no value is available.
*/
public float getResolution() {
return resolution;
}
public void setResolution(float resolution) {
this.resolution = resolution;
}
public float getRfree() {
return rFree;
}
public void setRfree(float rFree) {
this.rFree = rFree;
}
/**
* Return the latest modification date of the structure.
*
* @return the latest modification date
*/
public Date getModDate() {
return modDate;
}
/**
* The latest modification date of the structure.
*
* @param modDate the latest modification date
*/
public void setModDate(Date modDate) {
this.modDate = modDate;
}
/**
* Return the release date of the structure in the PDB.
*
* @return the release date
*/
public Date getRelDate() {
return relDate;
}
/**
*
* The release date of the structure in the PDB.
*
* @param relDate the release date
*/
public void setRelDate(Date relDate) {
this.relDate = relDate;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
/**@deprecated will be removed later. Use {@link #getKeywords()} if you use
* description to keep the keywords.
* @return
*/
@Deprecated
public String getDescription() {
return description;
}
/**@deprecated will be removed later. Use {@link #getKeywords()} if you use
* description to keep the keywords.
* @param description
*/
@Deprecated
public void setDescription(String description) {
this.description = description;
}
/**
* Return the names of the authors as listed in the AUTHORS section of a PDB file.
* Not necessarily the same authors as listed in the AUTH section of the primary citation!
*
* @return Authors as a string
*/
public String getAuthors()
{
return authors;
}
public void setAuthors(String authors)
{
this.authors = authors;
}
/**
* 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 could be found.
*/
public boolean hasJournalArticle() {
return this.journalArticle != null;
}
/**
* Get the associated publication as defined by the JRNL records in a PDB
* file.
* @return a JournalArticle
*/
public JournalArticle getJournalArticle() {
return this.journalArticle;
}
/**
* Set the associated publication as defined by the JRNL records in a PDB
* file.
* @param journalArticle the article
*/
public void setJournalArticle(JournalArticle journalArticle) {
this.journalArticle = journalArticle;
}
/**
* Return the map of biological assemblies. The keys are the
* biological assembly identifiers (starting at 1). Non-numerical identifiers
* such as PAU or XAU are not supported.
* @return
*/
public Map getBioAssemblies() {
return bioAssemblies ;
}
public void setBioAssemblies(Map bioAssemblies) {
this.bioAssemblies = bioAssemblies;
}
/**
* Get the number of biological assemblies available in the PDB header
* @return
*/
public int getNrBioAssemblies() {
return this.bioAssemblies.size();
}
public List getRevisionRecords() {
return revisionRecords;
}
public void setRevisionRecords(List revisionRecords) {
this.revisionRecords = revisionRecords;
}
/**
* @return the R-work for this structure.
*/
public float getRwork() {
return rWork;
}
/**
* @param rWork the R-work for this structure.
*/
public void setRwork(float rWork) {
this.rWork = rWork;
}
/**
* Gets the keywords (KEYWODS) record of the structure
* @return The keywords in a List<String>
* @since 6.0.0
*/
public List getKeywords() {
return keywords;
}
/**
* Sets the KEYWODS record of the structure.
* @param keywords The keywords in a List<String> to set.
* @since 6.0.0
*/
public void setKeywords(List keywords) {
this.keywords = keywords;
}
}