Java Code Examples for org.biojava.nbio.structure.Atom#getGroup()

/**
 * Returns and array of all non-Hydrogen atoms in the given molecule, including all
 * main chain HETATOM groups. Non main-chain HETATOM groups with fewer than minSizeHetAtomToInclude
 * non-Hydrogen atoms are not included.
 * @param m
 * @param minSizeHetAtomToInclude HETATOM groups (non main-chain) with fewer number of
 * non-Hydrogen atoms are not included
 * @return
 */
private static Atom[] getAllNonHAtomArray(Atom[] m, int minSizeHetAtomToInclude) {
	List<Atom> atoms = new ArrayList<>();

	for (Atom a:m){

		if (a.getElement()==Element.H) continue;

		Group g = a.getGroup();
		if (g.getType().equals(GroupType.HETATM) &&
			!isInChain(g) &&
			getSizeNoH(g)<minSizeHetAtomToInclude) {
			continue;
		}

		atoms.add(a);

	}
	return atoms.toArray(new Atom[atoms.size()]);
}
 

/**
 * Returns the List of Groups of the corresponding representative Atom
 * array. The representative Atom array needs to fulfill: no two Atoms are
 * from the same Group and Groups are sequential (connected in the original
 * Structure), except if they are from different Chains.
 *
 * @param rAtoms
 *            array of representative Atoms (CA, P, etc).
 * @return List of Groups
 */
public static List<Group> getGroups(Atom[] rAtoms) {

	List<Group> groups = new ArrayList<Group>(rAtoms.length);

	for (Atom a : rAtoms) {
		Group g = a.getGroup();
		if (g != null)
			groups.add(g);
		else
			logger.info("Group not found for representative Atom {}", a);
	}
	return groups;
}
 

/**
 * Converts an Atom object to an {@link AtomSite} object.
 * @param a the atom
 * @param model the model number for the output AtomSites
 * @param chainName the chain identifier (author id) for the output AtomSites
 * @param chainId the internal chain identifier (asym id) for the output AtomSites
 * @param atomId the atom id to be written to AtomSite
 * @return
 */
public static AtomSite convertAtomToAtomSite(Atom a, int model, String chainName, String chainId, int atomId) {

	/*
	ATOM 7    C CD  . GLU A 1 24  ? -10.109 15.374 38.853 1.00 50.05 ? ? ? ? ? ? 24  GLU A CD  1
	ATOM 8    O OE1 . GLU A 1 24  ? -9.659  14.764 37.849 1.00 49.80 ? ? ? ? ? ? 24  GLU A OE1 1
	ATOM 9    O OE2 . GLU A 1 24  ? -11.259 15.171 39.310 1.00 50.51 ? ? ? ? ? ? 24  GLU A OE2 1
	ATOM 10   N N   . LEU A 1 25  ? -5.907  18.743 37.412 1.00 41.55 ? ? ? ? ? ? 25  LEU A N   1
	ATOM 11   C CA  . LEU A 1 25  ? -5.168  19.939 37.026 1.00 37.55 ? ? ? ? ? ? 25  LEU A CA  1
	*/

	Group g = a.getGroup();

	String record ;
	if ( g.getType().equals(GroupType.HETATM) ) {
		record = "HETATM";
	} else {
		record = "ATOM";
	}

	String entityId = "0";
	String labelSeqId = Integer.toString(g.getResidueNumber().getSeqNum());
	if (g.getChain()!=null && g.getChain().getEntityInfo()!=null) {
		entityId = Integer.toString(g.getChain().getEntityInfo().getMolId());
		if (g.getChain().getEntityInfo().getType() == EntityType.POLYMER) {
			// this only makes sense for polymeric chains, non-polymer chains will never have seqres groups and there's no point in calling getAlignedResIndex
			labelSeqId = Integer.toString(g.getChain().getEntityInfo().getAlignedResIndex(g, g.getChain()));
		}
	}

	Character  altLoc = a.getAltLoc();
	String altLocStr;
	if (altLoc==null || altLoc == ' ') {
		altLocStr = MMCIF_DEFAULT_VALUE;
	} else {
		altLocStr = altLoc.toString();
	}

	Element e = a.getElement();
	String eString = e.toString().toUpperCase();
	if ( e.equals(Element.R)) {
		eString = "X";
	}

	String insCode = MMCIF_MISSING_VALUE;
	if (g.getResidueNumber().getInsCode()!=null ) {
		insCode = Character.toString(g.getResidueNumber().getInsCode());
	}

	AtomSite atomSite = new AtomSite();
	atomSite.setGroup_PDB(record);
	atomSite.setId(Integer.toString(atomId));
	atomSite.setType_symbol(eString);
	atomSite.setLabel_atom_id(a.getName());
	atomSite.setLabel_alt_id(altLocStr);
	atomSite.setLabel_comp_id(g.getPDBName());
	atomSite.setLabel_asym_id(chainId);
	atomSite.setLabel_entity_id(entityId);
	atomSite.setLabel_seq_id(labelSeqId);
	atomSite.setPdbx_PDB_ins_code(insCode);
	atomSite.setCartn_x(FileConvert.d3.format(a.getX()));
	atomSite.setCartn_y(FileConvert.d3.format(a.getY()));
	atomSite.setCartn_z(FileConvert.d3.format(a.getZ()));
	atomSite.setOccupancy(FileConvert.d2.format(a.getOccupancy()));
	atomSite.setB_iso_or_equiv(FileConvert.d2.format(a.getTempFactor()));
	atomSite.setAuth_seq_id(Integer.toString(g.getResidueNumber().getSeqNum()));
	atomSite.setAuth_comp_id(g.getPDBName());
	atomSite.setAuth_asym_id(chainName);
	atomSite.setAuth_atom_id(a.getName());
	atomSite.setPdbx_PDB_model_num(Integer.toString(model));

	return atomSite;
}
 

@Override
public void accept(WrappedAtom wrappedAtom) {
    Atom atom = wrappedAtom.getAtom();
    Group group = atom.getGroup();
    Chain chain = group.getChain();

    groupPDB.add(group.getType().equals(GroupType.HETATM) ? "HETATM" : "ATOM");
    id.add(wrappedAtom.getAtomId());
    Element element = atom.getElement();
    typeSymbol.add(element.equals(Element.R) ? "X" : element.toString().toUpperCase());
    labelAtomId.add(atom.getName());
    Character altLoc = atom.getAltLoc();
    if (altLoc == null || altLoc == ' ') {
        labelAltId.markNextNotPresent();
    } else {
        labelAltId.add(String.valueOf(altLoc));
    }
    labelCompId.add(group.getPDBName());
    labelAsymId.add(wrappedAtom.getChainId());
    String entityId = "0";
    int seqId = group.getResidueNumber().getSeqNum();
    if (chain.getEntityInfo() != null) {
        entityId = Integer.toString(chain.getEntityInfo().getMolId());
        if (chain.getEntityInfo().getType() == EntityType.POLYMER) {
            // this only makes sense for polymeric chains, non-polymer chains will never have seqres groups and
            // there's no point in calling getAlignedResIndex
            seqId = chain.getEntityInfo().getAlignedResIndex(group, chain);
        }
    }
    labelEntityId.add(entityId);
    labelSeqId.add(seqId);
    String insCode = "";
    if (group.getResidueNumber().getInsCode() != null ) {
        insCode = Character.toString(group.getResidueNumber().getInsCode());
    }
    if (insCode.isEmpty()) {
        pdbxPDBInsCode.markNextUnknown();
    } else {
        pdbxPDBInsCode.add(insCode);
    }
    cartnX.add(atom.getX());
    cartnY.add(atom.getY());
    cartnZ.add(atom.getZ());
    occupancy.add(atom.getOccupancy());
    bIsoOrEquiv.add(atom.getTempFactor());
    authSeqId.add(group.getResidueNumber().getSeqNum());
    authCompId.add(group.getPDBName());
    authAsymId.add(wrappedAtom.getChainName());
    authAtomId.add(atom.getName());
    pdbxPDBModelNum.add(wrappedAtom.getModel());
}
 

/**
 * 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);

}