String hybridization = attrValue.substring(attrValue.indexOf('#') + 1); if ("sp3".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3); } else if ("sp2".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP2); } else if ("sp1".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP1); } else if ("s".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.S); } else if ("planar".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.PLANAR3); } else if ("sp3d1".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D1); } else if ("sp3d2".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D2); } else if ("sp3d3".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D3); } else if ("sp3d4".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D4); } else if ("sp3d5".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D5);
String hybridization = attrValue.substring(attrValue.indexOf('#') + 1); if ("sp3".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3); } else if ("sp2".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP2); } else if ("sp1".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP1); } else if ("s".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.S); } else if ("planar".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.PLANAR3); } else if ("sp3d1".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D1); } else if ("sp3d2".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D2); } else if ("sp3d3".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D3); } else if ("sp3d4".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D4); } else if ("sp3d5".equals(hybridization)) { currentAtomType.setHybridization(IAtomType.Hybridization.SP3D5);
} else if (scalarType == SCALAR_HYBRIDIZATION) { if ("sp1".equals(currentChars)) { atomType.setHybridization(Hybridization.SP1); } else if ("sp2".equals(currentChars)) { atomType.setHybridization(Hybridization.SP2); } else if ("sp3".equals(currentChars)) { atomType.setHybridization(Hybridization.SP3); } else if ("planar".equals(currentChars)) { atomType.setHybridization(Hybridization.PLANAR3); } else { logger.warn("Unrecognized hybridization in config file: ", currentChars);
} else if (scalarType == SCALAR_HYBRIDIZATION) { if ("sp1".equals(currentChars)) { atomType.setHybridization(Hybridization.SP1); } else if ("sp2".equals(currentChars)) { atomType.setHybridization(Hybridization.SP2); } else if ("sp3".equals(currentChars)) { atomType.setHybridization(Hybridization.SP3); } else if ("planar".equals(currentChars)) { atomType.setHybridization(Hybridization.PLANAR3); } else { logger.warn("Unrecognized hybridization in config file: ", currentChars);
/** * Method to test the clone() method */ @Test public void testClone_Hybridization() throws Exception { IAtomType at = (IAtomType) newChemObject(); at.setHybridization(Hybridization.PLANAR3); IAtomType clone = (IAtomType) at.clone(); at.setHybridization(Hybridization.SP1); Assert.assertEquals(Hybridization.PLANAR3, clone.getHybridization()); }
@Test public void testSetHybridization_Null() { Hybridization hybridization = Hybridization.SP1; IAtomType atom = (IAtomType) newChemObject(); atom.setHybridization(hybridization); Assert.assertEquals(hybridization, atom.getHybridization()); atom.setHybridization(null); Assert.assertNull(atom.getHybridization()); }
@Test public void testSetHybridization_IAtomType_Hybridization() { Hybridization hybridization = Hybridization.SP1; IAtomType atom = (IAtomType) newChemObject(); atom.setHybridization(hybridization); Assert.assertEquals(hybridization, atom.getHybridization()); }
private static void deserializeAtomTypeFields(Resource rdfObject, IAtomType element) { deserializeIsotopeFields(rdfObject, element); Statement hybrid = rdfObject.getProperty(CDK.HASHYBRIDIZATION); if (hybrid != null) { Resource rdfHybrid = (Resource) hybrid.getObject(); if (RESOURCE_TO_HYBRID.containsKey(rdfHybrid)) { element.setHybridization(RESOURCE_TO_HYBRID.get(rdfHybrid)); } } Statement name = rdfObject.getProperty(CDK.HASATOMTYPENAME); if (name != null) { element.setAtomTypeName(name.getString()); } Statement order = rdfObject.getProperty(CDK.HASMAXBONDORDER); if (order != null) { Resource maxOrder = (Resource) order.getResource(); element.setMaxBondOrder(resource2Order(maxOrder)); } Statement formalCharge = rdfObject.getProperty(CDK.HASFORMALCHARGE); if (formalCharge != null) element.setFormalCharge(formalCharge.getInt()); }
private static void deserializeAtomTypeFields(Resource rdfObject, IAtomType element) { deserializeIsotopeFields(rdfObject, element); Statement hybrid = rdfObject.getProperty(CDK.HASHYBRIDIZATION); if (hybrid != null) { Resource rdfHybrid = (Resource) hybrid.getObject(); if (RESOURCE_TO_HYBRID.containsKey(rdfHybrid)) { element.setHybridization(RESOURCE_TO_HYBRID.get(rdfHybrid)); } } Statement name = rdfObject.getProperty(CDK.HASATOMTYPENAME); if (name != null) { element.setAtomTypeName(name.getString()); } Statement order = rdfObject.getProperty(CDK.HASMAXBONDORDER); if (order != null) { Resource maxOrder = (Resource) order.getResource(); element.setMaxBondOrder(resource2Order(maxOrder)); } Statement formalCharge = rdfObject.getProperty(CDK.HASFORMALCHARGE); if (formalCharge != null) element.setFormalCharge(formalCharge.getInt()); }