/** * Adds the atom oAtom without specifying a {@link IMonomer} or a Strand. Therefore the * atom to this AtomContainer, but not to a certain Strand or {@link IMonomer} (intended * e.g. for HETATMs). * * @param oAtom The {@link IPDBAtom} to add */ @Override public void addAtom(IPDBAtom oAtom) { super.addAtom(oAtom); }
/** *{@inheritDoc} */ @Override public IPDBPolymer clone() throws CloneNotSupportedException { return (IPDBPolymer) super.clone(); }
/** * Removes a particular strand, specified by its name. * * @param name name of the strand to remove */ @Override public void removeStrand(String name) { if (strands.containsKey(name)) { Strand strand = (Strand) strands.get(name); this.remove(strand); strands.remove(name); } }
@Override public IBioPolymer clone() throws CloneNotSupportedException { BioPolymer clone = (BioPolymer) super.clone(); clone.strands.clear(); for (Iterator<String> strands = clone.getStrandNames().iterator(); strands.hasNext();) { Strand strand = (Strand) clone.getStrand(strands.next().toString()).clone(); for (Iterator<String> iter = strand.getMonomerNames().iterator(); iter.hasNext();) { IMonomer monomer = strand.getMonomer(iter.next().toString()); Iterator<IAtom> atoms = monomer.atoms().iterator(); while (atoms.hasNext()) { clone.addAtom((IAtom) atoms.next(), monomer, strand); } } } return clone; } }
@Override public IChemObject newTestObject() { return new BioPolymer(); } });
@Override public String toString() { StringBuilder stringContent = new StringBuilder(); stringContent.append("PDBPolymer("); stringContent.append(this.hashCode()).append(", "); stringContent.append(super.toString()); stringContent.append(')'); return stringContent.toString(); }
@Override public IBioPolymer clone() throws CloneNotSupportedException { BioPolymer clone = (BioPolymer) super.clone(); clone.strands.clear(); for (Iterator<String> strands = clone.getStrandNames().iterator(); strands.hasNext();) { Strand strand = (Strand) clone.getStrand(strands.next().toString()).clone(); for (Iterator<String> iter = strand.getMonomerNames().iterator(); iter.hasNext();) { IMonomer monomer = strand.getMonomer(iter.next().toString()); Iterator<IAtom> atoms = monomer.atoms().iterator(); while (atoms.hasNext()) { clone.addAtom((IAtom) atoms.next(), monomer, strand); } } } return clone; } }
@BeforeClass public static void setUp() { setTestObjectBuilder(new ITestObjectBuilder() { @Override public IChemObject newTestObject() { return new BioPolymer(); } }); }
@Override public String toString() { StringBuilder stringContent = new StringBuilder(); stringContent.append("PDBPolymer("); stringContent.append(this.hashCode()).append(", "); stringContent.append(super.toString()); stringContent.append(')'); return stringContent.toString(); }
/** * Adds the atom oAtom without specifying a {@link IMonomer} or a Strand. Therefore the * atom to this AtomContainer, but not to a certain Strand or {@link IMonomer} (intended * e.g. for HETATMs). * * @param oAtom The {@link IPDBAtom} to add */ @Override public void addAtom(IPDBAtom oAtom) { super.addAtom(oAtom); }
@Test public void testBioPolymer() { IBioPolymer oBioPolymer = new BioPolymer(); Assert.assertNotNull(oBioPolymer); Assert.assertEquals(oBioPolymer.getMonomerCount(), 0);
/** *{@inheritDoc} */ @Override public IPDBPolymer clone() throws CloneNotSupportedException { return (IPDBPolymer) super.clone(); }
/** * Removes a particular strand, specified by its name. * * @param name name of the strand to remove */ @Override public void removeStrand(String name) { if (strands.containsKey(name)) { Strand strand = (Strand) strands.get(name); this.remove(strand); strands.remove(name); } }
/** * Adds the atom oAtom to a specified Monomer. Additionally, it keeps * record of the iCode. * * @param oAtom The IPDBAtom to add * @param oMonomer The monomer the atom belongs to */ public void addAtom(IPDBAtom oAtom, IMonomer oMonomer) { super.addAtom(oAtom, oMonomer); if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName())) sequentialListOfMonomers.add(oMonomer.getMonomerName()); }
/** * Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand. * Additionally, it keeps record of the iCode. * * @param oAtom The IPDBAtom to add * @param oMonomer The monomer the atom belongs to */ @Override public void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand) { super.addAtom(oAtom, oMonomer, oStrand); if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName())) sequentialListOfMonomers.add(oMonomer.getMonomerName()); }
/** * Adds the atom oAtom to a specified Monomer. Additionally, it keeps * record of the iCode. * * @param oAtom The IPDBAtom to add * @param oMonomer The monomer the atom belongs to */ public void addAtom(IPDBAtom oAtom, IMonomer oMonomer) { super.addAtom(oAtom, oMonomer); if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName())) sequentialListOfMonomers.add(oMonomer.getMonomerName()); }
/** * Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand. * Additionally, it keeps record of the iCode. * * @param oAtom The IPDBAtom to add * @param oMonomer The monomer the atom belongs to */ @Override public void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand) { super.addAtom(oAtom, oMonomer, oStrand); if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName())) sequentialListOfMonomers.add(oMonomer.getMonomerName()); }