/** {@inheritDoc} */ @Override public String toPDB() { FileConvert f = new FileConvert(this) ; return f.toPDB(); }
/** {@inheritDoc} */ @Override public String toMMCIF() { FileConvert f = new FileConvert(this); return f.toMMCIF(); }
toPDB(g,str); toPDB(g,str); toPDB(g,str); if ( doPrintConnections() ) str.append(printPDBConnections());
@Override public String toPDB() { return FileConvert.toPDB(this); }
String fullName = formatAtomName(a); if ( hasInsertionCode(pdbcode) ) resseq = String.format("%5s",pdbcode); else
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())); if ( doPrintConnections() ) {
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(); }
@Override public String toMMCIF() { return FileConvert.toMMCIF(this, true); }
@Override public String toPDB() { return FileConvert.toPDB(this); }
sb.append(FileConvert.getAtomSiteHeader());
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(); }
@Override public void toPDB(StringBuffer buf) { FileConvert.toPDB(this,buf); }
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(); }
/** 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 Group object to PDB representation * * @param g * @return */ public static String toPDB(Group g){ StringBuffer w = new StringBuffer(); toPDB(g,w); 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(); }
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); } } }
public static void toPDB(Atom a, StringBuffer str) { toPDB(a,str,a.getGroup().getChain().getName()); }