/*
* 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.io;
import java.io.IOException;
import java.text.DateFormat;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.text.SimpleDateFormat;
import java.util.List;
import java.util.Locale;
import org.biojava.nbio.core.util.XMLWriter;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Bond;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.DBRef;
import org.biojava.nbio.structure.Element;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.GroupType;
import org.biojava.nbio.structure.PDBHeader;
import org.biojava.nbio.structure.Site;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Methods to convert a structure object into different file formats.
* @author Andreas Prlic
* @since 1.4
*/
public class FileConvert {
private static final Logger logger = LoggerFactory.getLogger(FileConvert.class);
private Structure structure ;
private boolean printConnections;
// Locale should be english, e.g. in DE separator is "," -> PDB files have "." !
public static DecimalFormat d3 = (DecimalFormat)NumberFormat.getInstance(Locale.US);
static {
d3.setMaximumIntegerDigits(4);
d3.setMinimumFractionDigits(3);
d3.setMaximumFractionDigits(3);
}
public static DecimalFormat d2 = (DecimalFormat)NumberFormat.getInstance(Locale.US);
static {
d2.setMaximumIntegerDigits(3);
d2.setMinimumFractionDigits(2);
d2.setMaximumFractionDigits(2);
}
private static final String newline = System.getProperty("line.separator");
/**
* Constructs a FileConvert object.
*
* @param struc a Structure object
*/
public FileConvert(Structure struc) {
structure = struc ;
printConnections = true;
}
/**
* Returns if the Connections should be added
* default is true;
* @return if the printConnections flag is set
*/
public boolean doPrintConnections() {
return printConnections;
}
/** enable/disable printing of connections
* connections are sometimes buggy in PDB files
* so there are some cases where one might turn this off.
* @param printConnections
*/
public void setPrintConnections(boolean printConnections) {
this.printConnections = printConnections;
}
/**
* Prints the connections in PDB style
*
* Rewritten since 5.0 to use {@link Bond}s
* Will produce strictly one CONECT record per bond (won't group several bonds in one line)
*/
private String printPDBConnections(){
StringBuilder str = new StringBuilder();
for (Chain c:structure.getChains()) {
for (Group g:c.getAtomGroups()) {
for (Atom a:g.getAtoms()) {
if (a.getBonds()!=null) {
for (Bond b:a.getBonds()) { //7890123456789012345678901234567890123456789012345678901234567890
str.append(String.format("CONECT%5d%5d "+newline, b.getAtomA().getPDBserial(), b.getAtomB().getPDBserial()));
}
}
}
}
}
return str.toString();
}
/** Convert a structure into a PDB file.
* @return a String representing a PDB file.
*/
public String toPDB() {
StringBuffer str = new StringBuffer();
//int i = 0 ;
// TODO: print all the PDB header informaton in PDB style
// some objects (PDBHeader, Compound) are still missing
//
PDBHeader header = structure.getPDBHeader();
header.toPDB(str);
//REMARK 800
if (!structure.getSites().isEmpty()) {
str.append("REMARK 800 ").append(newline);
str.append("REMARK 800 SITE ").append(newline);
for (Site site : structure.getSites()) {
site.remark800toPDB(str);
}
}
//DBREF
for (DBRef dbref : structure.getDBRefs()){
dbref.toPDB(str);
str.append(newline);
}
//SSBOND
List<SSBondImpl> ssbonds = SSBondImpl.getSsBondListFromBondList(structure.getSSBonds());
for (SSBondImpl ssbond : ssbonds){
ssbond.toPDB(str);
str.append(newline);
}
//SITE
for (Site site : structure.getSites()) {
try {
site.toPDB(str);
} catch (Exception e){
e.printStackTrace();
}
}
//
// print the atom records
//
// do for all models
int nrModels = structure.nrModels() ;
if ( structure.isNmr()) {
str.append("EXPDTA NMR, "+ nrModels+" STRUCTURES"+newline) ;
}
for (int m = 0 ; m < nrModels ; m++) {
if ( nrModels>1 ) {
str.append("MODEL " + (m+1)+ newline);
}
List<Chain> polyChains = structure.getPolyChains(m);
List<Chain> nonPolyChains = structure.getNonPolyChains(m);
List<Chain> waterChains = structure.getWaterChains(m);
for (Chain chain : polyChains) {
// do for all groups
int nrGroups = chain.getAtomLength();
for ( int h=0; h<nrGroups;h++){
Group g= chain.getAtomGroup(h);
toPDB(g,str);
}
// End any polymeric chain with a "TER" record
if (nrGroups > 0) str.append(String.format("%-80s","TER")).append(newline);
}
boolean nonPolyGroupsExist = false;
for (Chain chain : nonPolyChains) {
// do for all groups
int nrGroups = chain.getAtomLength();
for ( int h=0; h<nrGroups;h++){
Group g= chain.getAtomGroup(h);
toPDB(g,str);
nonPolyGroupsExist = true;
}
}
if (nonPolyGroupsExist) str.append(String.format("%-80s","TER")).append(newline);;
boolean waterGroupsExist = false;
for (Chain chain : waterChains) {
// do for all groups
int nrGroups = chain.getAtomLength();
for ( int h=0; h<nrGroups;h++){
Group g= chain.getAtomGroup(h);
toPDB(g,str);
waterGroupsExist = true;
}
}
if (waterGroupsExist) str.append(String.format("%-80s","TER")).append(newline);;
if ( nrModels>1) {
str.append(String.format("%-80s","ENDMDL")).append(newline);
}
}
if ( doPrintConnections() )
str.append(printPDBConnections());
return str.toString() ;
}
private static void toPDB(Group g, StringBuffer str) {
// iterate over all atoms ...
// format output ...
int groupsize = g.size();
for ( int atompos = 0 ; atompos < groupsize; atompos++) {
Atom a = null ;
a = g.getAtom(atompos);
if ( a == null)
continue ;
toPDB(a, str);
//line = record + serial + " " + fullname +altLoc
//+ leftResName + " " + chainID + resseq
//+ " " + x+y+z
//+ occupancy + tempfactor;
//str.append(line + newline);
//System.out.println(line);
}
if ( g.hasAltLoc()){
for (Group alt : g.getAltLocs() ) {
toPDB(alt,str);
}
}
}
/** Prints the content of an Atom object as a PDB formatted line.
*
* @param a
* @return
*/
public static String toPDB(Atom a){
StringBuffer w = new StringBuffer();
toPDB(a,w);
return w.toString();
}
public static String toPDB(Atom a, String chainId) {
StringBuffer w = new StringBuffer();
toPDB(a,w, chainId);
return w.toString();
}
/**
* Convert a Chain object to PDB representation
*
* @param chain
* @return
*/
public static String toPDB(Chain chain){
StringBuffer w = new StringBuffer();
int nrGroups = chain.getAtomLength();
for ( int h=0; h<nrGroups;h++){
Group g= chain.getAtomGroup(h);
toPDB(g,w);
}
return w.toString();
}
/**
* Convert a Group object to PDB representation
*
* @param g
* @return
*/
public static String toPDB(Group g){
StringBuffer w = new StringBuffer();
toPDB(g,w);
return w.toString();
}
/**
* Print ATOM record in the following syntax
* <pre>
* ATOM 1 N ASP A 15 110.964 24.941 59.191 1.00 83.44 N
*
* COLUMNS DATA TYPE FIELD DEFINITION
* ---------------------------------------------------------------------------------
* 1 - 6 Record name "ATOM "
* 7 - 11 Integer serial Atom serial number.
* 13 - 16 Atom name Atom name.
* 17 Character altLoc Alternate location indicator.
* 18 - 20 Residue name resName Residue name.
* 22 Character chainID Chain identifier.
* 23 - 26 Integer resSeq Residue sequence number.
* 27 AChar iCode Code for insertion of residues.
* 31 - 38 Real(8.3) x Orthogonal coordinates for X in
* Angstroms.
* 39 - 46 Real(8.3) y Orthogonal coordinates for Y in
* Angstroms.
* 47 - 54 Real(8.3) z Orthogonal coordinates for Z in
* Angstroms.
* 55 - 60 Real(6.2) occupancy Occupancy.
* 61 - 66 Real(6.2) tempFactor Temperature factor.
* 73 - 76 LString(4) segID Segment identifier, left-justified.
* 77 - 78 LString(2) element Element symbol, right-justified.
* 79 - 80 LString(2) charge Charge on the atom.
* </pre>
* @param a
* @param str
* @param chainID the chain ID that the Atom will have in the output string
*/
public static void toPDB(Atom a, StringBuffer str, String chainID) {
Group g = a.getGroup();
GroupType type = g.getType() ;
String record = "" ;
if ( type.equals(GroupType.HETATM) ) {
record = "HETATM";
} else {
record = "ATOM ";
}
// format output ...
String resName = g.getPDBName();
String pdbcode = g.getResidueNumber().toString();
int seri = a.getPDBserial() ;
String serial = String.format("%5d",seri);
String fullName = formatAtomName(a);
Character altLoc = a.getAltLoc();
if ( altLoc == null)
altLoc = ' ';
String resseq = "" ;
if ( hasInsertionCode(pdbcode) )
resseq = String.format("%5s",pdbcode);
else
resseq = String.format("%4s",pdbcode)+" ";
String x = String.format("%8s",d3.format(a.getX()));
String y = String.format("%8s",d3.format(a.getY()));
String z = String.format("%8s",d3.format(a.getZ()));
String occupancy = String.format("%6s",d2.format(a.getOccupancy())) ;
String tempfactor = String.format("%6s",d2.format(a.getTempFactor()));
String leftResName = String.format("%3s",resName);
StringBuffer s = new StringBuffer();
s.append(record);
s.append(serial);
s.append(" ");
s.append(fullName);
s.append(altLoc);
s.append(leftResName);
s.append(" ");
s.append(chainID);
s.append(resseq);
s.append(" ");
s.append(x);
s.append(y);
s.append(z);
s.append(occupancy);
s.append(tempfactor);
Element e = a.getElement();
String eString = e.toString().toUpperCase();
if ( e.equals(Element.R)) {
eString = "X";
}
str.append(String.format("%-76s%2s", s.toString(),eString));
str.append(newline);
}
public static void toPDB(Atom a, StringBuffer str) {
toPDB(a,str,a.getGroup().getChain().getName());
}
/** test if pdbserial has an insertion code */
private static boolean hasInsertionCode(String pdbserial) {
try {
Integer.parseInt(pdbserial) ;
} catch (NumberFormatException e) {
return true ;
}
return false ;
}
/**
* Convert a protein Structure to a DAS Structure XML response .
* Since 5.0, bond (CONECT records) information is not supported anymore.
* @param xw a XMLWriter object
* @throws IOException ...
*
*/
public void toDASStructure(XMLWriter xw)
throws IOException
{
/*xmlns="http://www.sanger.ac.uk/xml/das/2004/06/17/dasalignment.xsd" xmlns:align="http://www.sanger.ac.uk/xml/das/2004/06/17/alignment.xsd" xmlns:xsd="http://www.w3.org/2001/XMLSchema-instance" xsd:schemaLocation="http://www.sanger.ac.uk/xml/das/2004/06/17/dasalignment.xsd http://www.sanger.ac.uk/xml/das//2004/06/17/dasalignment.xsd"*/
if ( structure == null){
System.err.println("can not convert structure null");
return;
}
PDBHeader header = structure.getPDBHeader();
xw.openTag("object");
xw.attribute("dbAccessionId",structure.getPDBCode());
xw.attribute("intObjectId" ,structure.getPDBCode());
// missing modification date
DateFormat dateFormat = new SimpleDateFormat("dd-MMM-yy",Locale.US);
String modificationDate = dateFormat.format(header.getModDate());
xw.attribute("objectVersion",modificationDate);
xw.attribute("type","protein structure");
xw.attribute("dbSource","PDB");
xw.attribute("dbVersion","20070116");
xw.attribute("dbCoordSys","PDBresnum,Protein Structure");
// do we need object details ???
xw.closeTag("object");
// do for all models
for (int modelnr = 0;modelnr<structure.nrModels();modelnr++){
// do for all chains:
for (int chainnr = 0;chainnr<structure.size(modelnr);chainnr++){
Chain chain = structure.getChainByIndex(modelnr,chainnr);
xw.openTag("chain");
xw.attribute("id",chain.getId());
xw.attribute("SwissprotId",chain.getSwissprotId() );
if (structure.nrModels()>1){
xw.attribute("model",Integer.toString(modelnr+1));
}
//do for all groups:
for (int groupnr =0;
groupnr<chain.getAtomLength()
;groupnr++){
Group gr = chain.getAtomGroup(groupnr);
xw.openTag("group");
xw.attribute("name",gr.getPDBName());
xw.attribute("type",gr.getType().toString());
xw.attribute("groupID",gr.getResidueNumber().toString());
// do for all atoms:
//Atom[] atoms = gr.getAtoms();
List<Atom> atoms = gr.getAtoms();
for (int atomnr=0;atomnr<atoms.size();atomnr++){
Atom atom = atoms.get(atomnr);
xw.openTag("atom");
xw.attribute("atomID",Integer.toString(atom.getPDBserial()));
xw.attribute("atomName",formatAtomName(atom));
xw.attribute("x",Double.toString(atom.getX()));
xw.attribute("y",Double.toString(atom.getY()));
xw.attribute("z",Double.toString(atom.getZ()));
xw.closeTag("atom");
}
xw.closeTag("group") ;
}
xw.closeTag("chain");
}
}
if ( doPrintConnections() ) {
// not supported anymore since 5.0
}
}
private static String formatAtomName(Atom a) {
String fullName = null;
String name = a.getName();
Element element = a.getElement();
// RULES FOR ATOM NAME PADDING: 4 columns in total: 13, 14, 15, 16
// if length 4: nothing to do
if (name.length()==4)
fullName = name;
// if length 3: they stay at 14
else if (name.length()==3)
fullName = " "+name;
// for length 2 it depends:
// carbon, oxygens, nitrogens, phosphorous stay at column 14
// elements with 2 letters (e.g. NA, FE) will go to column 13
else if (name.length()==2) {
if (element == Element.C || element == Element.N || element == Element.O || element == Element.P || element == Element.S)
fullName = " "+name+" ";
else
fullName = name+" ";
}
// for length 1 (e.g. K but also C, O) they stay in column 14
else if (name.length()==1)
fullName = " "+name+" ";
//if (fullName.length()!=4)
// logger.warn("Atom name "+fullName+"to be written in PDB format does not have length 4. Formatting will be incorrect");
return fullName;
}
public String toMMCIF() {
StringBuilder str = new StringBuilder();
str.append(SimpleMMcifParser.MMCIF_TOP_HEADER+"BioJava_mmCIF_file"+newline);
if (structure.getPDBHeader()!=null && structure.getPDBHeader().getCrystallographicInfo()!=null &&
structure.getPDBHeader().getCrystallographicInfo().getSpaceGroup()!=null &&
structure.getPDBHeader().getCrystallographicInfo().getCrystalCell()!=null) {
str.append(MMCIFFileTools.toMMCIF("_cell",
MMCIFFileTools.convertCrystalCellToCell(structure.getPDBHeader().getCrystallographicInfo().getCrystalCell())));
str.append(MMCIFFileTools.toMMCIF("_symmetry",
MMCIFFileTools.convertSpaceGroupToSymmetry(structure.getPDBHeader().getCrystallographicInfo().getSpaceGroup())));
}
str.append(getAtomSiteHeader());
List<AtomSite> list = MMCIFFileTools.convertStructureToAtomSites(structure);
str.append(MMCIFFileTools.toMMCIF(list,AtomSite.class));
return str.toString();
}
public static String toMMCIF(Chain chain, String authId, String asymId, boolean writeHeader) {
StringBuilder str = new StringBuilder();
if (writeHeader)
str.append(getAtomSiteHeader());
List<AtomSite> list = MMCIFFileTools.convertChainToAtomSites(chain, 1, authId, asymId);
str.append(MMCIFFileTools.toMMCIF(list,AtomSite.class));
return str.toString();
}
public static String toMMCIF(Chain chain, boolean writeHeader) {
StringBuilder sb = new StringBuilder();
sb.append(SimpleMMcifParser.MMCIF_TOP_HEADER+"BioJava_mmCIF_file"+newline);
sb.append(toMMCIF(chain, chain.getName(), chain.getId(),writeHeader));
return sb.toString();
}
public static String getAtomSiteHeader() {
String header;
try {
header = MMCIFFileTools.toLoopMmCifHeaderString("_atom_site", AtomSite.class.getName());
} catch (ClassNotFoundException e) {
logger.error("Class not found, will not have a header for this MMCIF category: "+e.getMessage());
header = "";
}
return header;
}
}