public String perceiveCDKAtomTypes(IMolecule mol)
throws InvocationTargetException {
ICDKMolecule cdkmol;
try {
cdkmol = cdk.asCDKMolecule(mol);
}
catch ( BioclipseException e ) {
e.printStackTrace();
throw new InvocationTargetException(
e, "Error while creating a ICDKMolecule" );
}
IAtomContainer ac = cdkmol.getAtomContainer();
CDKAtomTypeMatcher cdkMatcher
= CDKAtomTypeMatcher.getInstance(ac.getBuilder());
StringBuffer result = new StringBuffer();
int i = 1;
for (IAtom atom : ac.atoms()) {
IAtomType type = null;
try {
type = cdkMatcher.findMatchingAtomType(ac, atom);
}
catch ( CDKException e ) {}
result.append(i).append(':').append(
type != null ? type.getAtomTypeName() : "null"
).append('\n'); // FIXME: should use NEWLINE here
i++;
}
return result.toString();
}
@Test
public void testConfigureUnsetProperties() {
IAtom atom = new NNAtom(Elements.CARBON);
IAtomType atomType = new NNAtomType(Elements.CARBON);
atomType.setExactMass(12.0);
AtomTypeManipulator.configureUnsetProperties(atom, atomType);
Assert.assertEquals(12.0, atom.getExactMass(), 0.1);
}
@Test
public void testGetAtomType_String() throws Exception {
IAtomType atomType = atf.getAtomType("C4");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C4", atomType.getAtomTypeName());
Assert.assertEquals(4.0, atomType.getBondOrderSum(), 0.001);
Assert.assertEquals(IBond.Order.TRIPLE, atomType.getMaxBondOrder());
}
@Test
public void testConfigure_IAtom_IAtomType() {
IAtom atom = new NNAtom(Elements.CARBON);
IAtomType atomType = new NNAtomType(Elements.CARBON);
atomType.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, true);
AtomTypeManipulator.configure(atom, atomType);
Assert.assertEquals(
atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR),
atom.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
}
@Test
public void testGetAtomTypeFromJmol() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/jmol_atomtypes.txt", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("H");
Assert.assertNotNull(atomType);
Assert.assertEquals("H", atomType.getSymbol());
Assert.assertEquals("H", atomType.getAtomTypeName());
}
/**
* Clean up chemical model ,removing duplicates empty molecules etc
*
* @param chemModel
* @param avoidOverlap
* @throws CDKException
*/
public static void cleanUpChemModel(final IChemModel chemModel,
final boolean avoidOverlap, final AbstractJChemPaintPanel panel)
throws CDKException {
JChemPaint.setReactionIDs(chemModel);
JChemPaint.replaceReferencesWithClones(chemModel);
// check the model is not completely empty
if (ChemModelManipulator.getBondCount(chemModel) == 0
&& ChemModelManipulator.getAtomCount(chemModel) == 0) {
throw new CDKException(
"Structure does not have bonds or atoms. Cannot depict structure.");
}
JChemPaint.removeDuplicateAtomContainers(chemModel);
JChemPaint.checkCoordinates(chemModel);
JChemPaint.removeEmptyAtomContainers(chemModel);
if (avoidOverlap) {
try {
ControllerHub.avoidOverlap(chemModel);
} catch (final Exception e) {
JOptionPane.showMessageDialog(panel,
GT._("Structure could not be generated"));
throw new CDKException("Cannot depict structure");
}
}
// We update implicit Hs in any case
final CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher
.getInstance(chemModel.getBuilder());
for (final IAtomContainer container : ChemModelManipulator
.getAllAtomContainers(chemModel)) {
for (final IAtom atom : container.atoms()) {
if (!(atom instanceof IPseudoAtom)) {
try {
final IAtomType type = matcher.findMatchingAtomType(
container, atom);
if (type != null
&& type.getFormalNeighbourCount() != null) {
final int connectedAtomCount = container
.getConnectedAtomsCount(atom);
atom.setImplicitHydrogenCount(type
.getFormalNeighbourCount()
- connectedAtomCount);
}
} catch (final CDKException e) {
e.printStackTrace();
}
}
}
}
}
/** Tests if the electron count matches the Hückel 4n+2 rule. */
private static boolean isHueckelValid(IAtomContainer singleRing) throws CDKException {
int electronCount = 0;
for (IAtom ringAtom : singleRing.atoms()) {
if (ringAtom.getHybridization() != CDKConstants.UNSET
&& (ringAtom.getHybridization() == Hybridization.SP2)
|| ringAtom.getHybridization() == Hybridization.PLANAR3) {
// for example, a carbon
// note: the double bond is in the ring, that has been tested earlier
// FIXME: this does assume bond orders to be resolved too, when detecting
// sprouting double bonds
if ("N.planar3".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("N.minus.planar3".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("N.amide".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("S.2".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("S.planar3".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("C.minus.planar".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("O.planar3".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("N.sp2.3".equals(ringAtom.getAtomTypeName())) {
electronCount += 1;
} else {
if (factory == null) {
factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/dict/data/cdk-atom-types.owl", ringAtom.getBuilder());
}
IAtomType type = factory.getAtomType(ringAtom.getAtomTypeName());
Object property = type.getProperty(CDKConstants.PI_BOND_COUNT);
if (property != null && property instanceof Integer) {
electronCount += ((Integer) property).intValue();
}
}
} else if (ringAtom.getHybridization() != null
&& ringAtom.getHybridization() == Hybridization.SP3
&& getLonePairCount(ringAtom) > 0) {
// for example, a nitrogen or oxygen
electronCount += 2;
}
}
return (electronCount % 4 == 2) && (electronCount > 2);
}
/**
* This method calculates the hybridization of an atom.
*
* @param atom The IAtom for which the DescriptorValue is requested
* @param container Parameter is the atom container.
* @return The hybridization
*/
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
IAtomType atomType;
try {
atomType =
CDKAtomTypeMatcher.getInstance(atom.getBuilder()).findMatchingAtomType(container, atom);
} catch (CDKException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult((int) Double.NaN), // does that work??
getDescriptorNames(),
new CDKException("Atom type was null"));
}
if (atomType == null) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult((int) Double.NaN), // does that work??
getDescriptorNames(),
new CDKException("Atom type was null"));
}
if (atomType.getHybridization() == null) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult((int) Double.NaN), // does that work??
getDescriptorNames(),
new CDKException("Hybridization was null"));
}
int hybridizationCDK = atomType.getHybridization().ordinal();
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult(hybridizationCDK),
getDescriptorNames());
}
public String perceiveSybylAtomTypes(IMolecule mol)
throws InvocationTargetException {
ICDKMolecule cdkmol;
try {
cdkmol = cdk.asCDKMolecule(mol);
}
catch (BioclipseException e) {
System.out.println("Error converting cdk10 to cdk");
e.printStackTrace();
throw new InvocationTargetException(e);
}
IAtomContainer ac = cdkmol.getAtomContainer();
CDKAtomTypeMatcher cdkMatcher
= CDKAtomTypeMatcher.getInstance(ac.getBuilder());
AtomTypeMapper mapper
= AtomTypeMapper.getInstance(
"org/openscience/cdk/dict/data/cdk-sybyl-mappings.owl" );
IAtomType[] sybylTypes = new IAtomType[ac.getAtomCount()];
int atomCounter = 0;
int a=0;
for (IAtom atom : ac.atoms()) {
IAtomType type;
try {
type = cdkMatcher.findMatchingAtomType(ac, atom);
}
catch (CDKException e) {
type = null;
}
if (type==null) {
// logger.debug("AT null for atom: " + atom);
type = atom.getBuilder().newAtomType(atom.getSymbol());
type.setAtomTypeName("X");
}
AtomTypeManipulator.configure(atom, type);
a++;
}
try {
CDKHueckelAromaticityDetector.detectAromaticity(ac);
// System.out.println("Arom: "
// + CDKHueckelAromaticityDetector.detectAromaticity(ac) );
}
catch (CDKException e) {
logger.debug("Failed to perceive aromaticity: " + e.getMessage());
}
for (IAtom atom : ac.atoms()) {
String mappedType = mapper.mapAtomType(atom.getAtomTypeName());
if ("C.2".equals(mappedType)
&& atom.getFlag(CDKConstants.ISAROMATIC)) {
mappedType = "C.ar";
}
else if ("N.pl3".equals(mappedType)
&& atom.getFlag(CDKConstants.ISAROMATIC)) {
mappedType = "N.ar";
}
try {
sybylTypes[atomCounter] = factory.getAtomType(mappedType);
}
catch (NoSuchAtomTypeException e) {
// yes, setting null's here is important
sybylTypes[atomCounter] = null;
}
atomCounter++;
}
StringBuffer result = new StringBuffer();
// now that full perception is finished, we can set atom type names:
for (int i = 0; i < sybylTypes.length; i++) {
if (sybylTypes[i] != null) {
ac.getAtom(i).setAtomTypeName(sybylTypes[i].getAtomTypeName());
}
else {
ac.getAtom(i).setAtomTypeName("X");
}
result.append(i).append(':').append(ac.getAtom(i).getAtomTypeName())
/*.append("\n")*/;
}
return result.toString();
}
/**
* Test reading from a XML config file with content like:
*
* <pre>
* <atomType id="C">
* <!-- for example in CC-->
* <atom elementType="C" formalCharge="0">
* <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
* <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
* <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
* <scalar dataType="xsd:integer" dictRef="cdk:valency">4</scalar>
* </atom>
* <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
* <scalar dataType="xsd:string" dictRef="cdk:DA">-</scalar>
* <scalar dataType="xsd:string" dictRef="cdk:sphericalMatcher">[CSP]-[0-4][-]?+;[A-Za-z\+\-&&[^=%]]{0,6}[(].*+</scalar>
* </atomType>
* </pre>
*
* @throws Exception if the atom typ info cannot be loaded
*/
@Test
public void testGetAtomTypeFromMM2() throws Exception {
AtomTypeFactory factory;
factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/mm2_atomtypes.xml", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C", atomType.getAtomTypeName());
Assert.assertEquals(
"[CSP]-[0-4][-]?+;[A-Za-z\\+\\-&&[^=%]]{0,6}[(].*+",
atomType.getProperty(CDKConstants.SPHERICAL_MATCHER));
Assert.assertEquals(Hybridization.SP3, atomType.getHybridization());
atomType = factory.getAtomType("Sthi");
Assert.assertNotNull(atomType);
Assert.assertEquals("S", atomType.getSymbol());
Assert.assertEquals("Sthi", atomType.getAtomTypeName());
Assert.assertEquals(
"S-[2];[H]{0,3}+=C.*+", atomType.getProperty(CDKConstants.SPHERICAL_MATCHER));
Assert.assertEquals(Hybridization.SP2, atomType.getHybridization());
Assert.assertTrue(atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
Assert.assertEquals(5, atomType.getProperty(CDKConstants.PART_OF_RING_OF_SIZE));
}
@Test
public void testGetAtomTypeFromOWL_Sybyl() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/dict/data/sybyl-atom-types.owl", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C.3");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C.3", atomType.getAtomTypeName());
Assert.assertEquals(4, atomType.getFormalNeighbourCount().intValue());
Assert.assertEquals(IAtomType.Hybridization.SP3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
0, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(0, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
}