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

private List<Group> getGroupList(int size, String type, Chain chain, Point3d center) {
    List<Group> list = new ArrayList<>();
    double offsetx = 0;
    double offsety = 0;
    double offsetz = 0;
    for (int i=0;i<size;i++) {
        Group g = new AminoAcidImpl();
        g.setPDBName(type);
        g.setResidueNumber(new ResidueNumber(chain.getId(), i+1, null));
        chain.addGroup(g);
        Atom a = new AtomImpl();
        a.setName(StructureTools.CA_ATOM_NAME);
        a.setX(center.x + offsetx);
        a.setY(center.y + offsety);
        a.setZ(center.z + offsetz);
        g.addAtom(a);
        list.add(g);

        if (i%3 == 0) offsetx += 1;
        if (i%3 == 1) offsety += 1;
        if (i%3 == 2) offsetz += 1;
    }

    return list;
}
 

/**
 * Convert a mmCIF AtomSite object to a BioJava Atom object
 *
 * @param atom the mmmcif AtomSite record
 * @return an Atom
 */
private Atom convertAtom(AtomSite atom){


	Atom a = new AtomImpl();

	a.setPDBserial(Integer.parseInt(atom.getId()));
	a.setName(atom.getLabel_atom_id());

	double x = Double.parseDouble (atom.getCartn_x());
	double y = Double.parseDouble (atom.getCartn_y());
	double z = Double.parseDouble (atom.getCartn_z());
	a.setX(x);
	a.setY(y);
	a.setZ(z);

	float occupancy = Float.parseFloat (atom.getOccupancy());
	a.setOccupancy(occupancy);

	float temp = Float.parseFloat (atom.getB_iso_or_equiv());
	a.setTempFactor(temp);

	String alt = atom.getLabel_alt_id();
	if (( alt != null ) && ( alt.length() > 0) && (! alt.equals("."))){
		a.setAltLoc(new Character(alt.charAt(0)));
	} else {
		a.setAltLoc(new Character(' '));
	}

	Element element = Element.R;
	try {
		element = Element.valueOfIgnoreCase(atom.getType_symbol());
	}  catch (IllegalArgumentException e) {
		logger.info("Element {} was not recognised as a BioJava-known element, the element will be represented as the generic element {}", atom.getType_symbol(), Element.R.name());
	}
	a.setElement(element);

	return a;

}
 

private Atom getAtom(double x, double y, double z) {
	Atom atom = new AtomImpl();
	AminoAcidImpl g = new AminoAcidImpl();
	g.setAminoType('A');
	atom.setGroup(g);
	atom.setName("CA");
	atom.setElement(Element.C);
	atom.setX(x);
	atom.setY(y);
	atom.setZ(z);
	return atom;
}
 

private List<Group> getGroupList(int size, String type, Chain chain) {
	List<Group> list = new ArrayList<>();
	for (int i=0;i<size;i++) {
		Group g = new AminoAcidImpl();
		g.setPDBName(type);
		g.setResidueNumber(new ResidueNumber(chain.getId(), i+1, null));
		chain.addGroup(g);
		Atom a = new AtomImpl();
		a.setName(StructureTools.CA_ATOM_NAME);
		g.addAtom(a);
		list.add(g);
	}
	return list;
}
 

private static Atom getAtom(String name, Element e, int id, double x, double y, double z) {
	Atom a = new AtomImpl();
	a.setX(x);
	a.setY(y);
	a.setZ(z);
	a.setPDBserial(id);
	a.setName(name);
	a.setElement(e);
	return a;
}
 

private static Atom getAtom(String name, Element e, int id, double x, double y, double z) {
    Atom a = new AtomImpl();
    a.setX(x);
    a.setY(y);
    a.setZ(z);
    a.setPDBserial(id);
    a.setName(name);
    a.setElement(e);
    return a;
}
 

@Override
public void setAtomInfo(String atomName,
		int serialNumber, char alternativeLocationId, float x,
		float y, float z, float occupancy,
		float temperatureFactor,
		String element, int charge) {
	Atom atom = new AtomImpl();
	Group altGroup = null;
	atom.setPDBserial(serialNumber);
	atom.setName(atomName.trim());
	atom.setElement(Element.valueOfIgnoreCase(element));
	if(alternativeLocationId==MmtfStructure.UNAVAILABLE_CHAR_VALUE){
		alternativeLocationId = ' ';
	}
	if (alternativeLocationId != ' ') {
		// Get the altGroup
		altGroup = getCorrectAltLocGroup(alternativeLocationId);
		atom.setAltLoc(alternativeLocationId);
	} else {
		atom.setAltLoc(Character.valueOf(' '));
	}
	atom.setX(x);
	atom.setY(y);
	atom.setZ(z);
	atom.setOccupancy(occupancy);
	atom.setTempFactor(temperatureFactor);
	atom.setCharge((short) charge);
	if (altGroup == null) {
		group.addAtom(atom);
	} else {
		altGroup.setChain(chain);
		altGroup.addAtom(atom);
	}

	// IF the main group doesn't have this atom
	if (!group.hasAtom(atom.getName())) {

		// If it's not a microheterogenity case
		if (group.getPDBName().equals(atom.getGroup().getPDBName())) {
			// And it's not a deuterated case.  'nanoheterogenity'
			if(!StructureTools.hasNonDeuteratedEquiv(atom,group)){
				group.addAtom(atom);
			}
		}
	}
	atomsInGroup.add(atom);
	allAtoms[atomCounter] = atom;
	atomCounter++;
}
 

/**
 * Test the writing of Structure objects to a file.
 * @throws IOException
 */
@Test
public void testWrite() throws IOException {

	// Create a structure
	Structure structure = new StructureImpl();

	// Add some header information
	PDBHeader pdbHeader = new PDBHeader();
	pdbHeader.setExperimentalTechnique("X-RAY DIFFRACTION");
	structure.setPDBHeader(pdbHeader);

	// Create one chain
	structure.setEntityInfos(new ArrayList<EntityInfo>());
	Chain chain = new ChainImpl();
	chain.setId("A");
	chain.setName("A");
	Group group = new AminoAcidImpl();
	group.setPDBName("FKF");
	ChemComp chemComp = new ChemComp();
	chemComp.setType("TYPfdl");
	chemComp.setOne_letter_code("A");
	group.setChemComp(chemComp);

	// Create one Atom
	Atom atom = new AtomImpl();
	atom.setName("A");
	atom.setElement(Element.Ag);
	atom.setCoords(new double[] { 1.0, 2.0, 3.0 });

	// Link together the objects
	chain.addGroup(group);
	group.addAtom(atom);

	ResidueNumber residueNumber = new ResidueNumber();
	residueNumber.setInsCode('A');
	residueNumber.setSeqNum(100);
	group.setResidueNumber(residueNumber);

	structure.addChain(chain);

	File tempFile = testFolder.newFile("tmpfile");
	MmtfActions.writeToFile(structure, tempFile.toPath());
}