Exception handling has been added to many more PPChem SDK (Java, Python, DotNet) methods in the 2022 release. PPChem SDK API headers and signatures are backwards compatible and there is no need to change existing code that calls these methods. However, the updated Java PPChem SDK methods now throw exceptions, and as a result, applications that call these Java methods need to handle or re-throw exceptions if it was not already in place. For example, getChirality() method of the Atom class now throws exceptions:
public Chirality getChirality() throws Exception;
And the following code snippet shows how to handle exceptions thrown by this method:
import com.accelrys.chem.*;
import java.io.FileOutputStream;
import java.io.PrintWriter;
public class Example_GetChirality {
static void runExample() {
MolIO molIO = null;
Molecule mol = null;
try {
molIO = PPChemSDKFactory.createMolIO();
mol = PPChemSDKFactory.createMolecule();
String inputSmiles = “[C@@H](Cl)c1ccccc1";
molIO.readMolecule(inputSmiles, MolIO.FormatType.SMILES_String, mol);
for (int i = 0; i < mol.getNumAtoms(); ++i) {
mol.getAtom(i).getChirality();
}
} catch (Exception e) {
System.out.println("Caught Exception: " + e.getMessage());
e.printStackTrace();
} finally {
if (mol != null)
mol.close();
if (molIO != null)
molIO.close();
}
}
}
If getChirality() is not inside a try-catch block and runExample() does not re-throw exceptions, there will be an error “unreported exception Exception; must be caught or declared to be thrown”.
Here is a list of Java methods that didn’t use to but now throw exceptions:
Atom class
appendLabel
setType
setNonStandardType
getSumBondOrder
getChirality
getHybridization
setHybridization
setCharge
setRadical
setWeight
setStereo
getValence
isLegalValence
getNumHydrogens
getNumExplicitHydrogens
getNumExplicitHydrogens
setNumImplicitHydrogens
estimateNumImplicitHydrogens
getNumLonePairs
getNumLonePairsForDraw
getNumPiElectrons
invertStereo
clearStereo
getStereoFromCoordinates
canHaveStereo
hasStereo
hasPseudoStereo
hasUnknownPseudoStereo
hasMesoStereo
is
getSymmetryClass
getCanonicalIndex
getProperties
Bond class
setType
setStereo
invertStereo
getStereoFromCoordinates
hasStereo
is
getProperties
CalcPicture class
setCaptionProperty
setChiralityLabels
setChiralityLabelMode
setRAndSLabels
CustomData class
getOwnerType
getOwnerSgroupType
getOwnerIndex
setName
setValue
setVariable
setQueryType
setQueryOp
SetFieldType
setUnits
setDisplay
setPlacement
setDisplayUnits
setNumDisplayChars
GenGroup class
getInternalAtoms
getInternalBonds
getLinkBonds
getInternalAtom
getInternalBond
getLinkBond
getBracketX1
getBracketX2
getBracketY1
getBracketY2
addAutoBrackets
MarkushBond class
getBasisAtom
Mixture class
getAtom
getBond
addAutoBrackets
setBracketCoordinates
MixtureComponent class
getAtom
getBond
addAutoBrackets
setBracketCoordinates
Molecule class
setHydrogenFill
getNumFragments
getNumComplexedFragments
getNumRings
getNumChains
getNumBridges
getRingSize
getSmallestRingOnAtom
getSmallestRingOnBond
isBridgeRing
isAromaticRing
getRingBonds
getRingAtoms
getChainBonds
getChainAtoms
getBridgeAtoms
getBridgeBonds
getRingBonds
getRingAtoms
getChainBonds
getChainAtoms
getComplexedFragmentBonds
getComplexedFragmentAtoms
getFragmentBonds
getFragmentAtoms
getFragmentRings
getFragmentChains
getFragmentBridges
getRingsOnAtom
getRingsOnBond
getNumRingAssemblies
getRingAssemblyBonds
getRingAssemblyAtoms
getRingAssemblyRings
getFragmentRingAssemblies
getNumRingsOnlyCovalentBonds
getNumRingsWithCoordinationBonds
getNumRingsWithHydrogenBonds
getNumRingAssembliesOnlyCovalentBonds
getNumRingAssembliesWithCoordinationBonds
getNumRingAssembliesWithHydrogenBonds
getNumFragmentsOnlyCovalentBonds
getNumFragmentsWithCoordinationBonds
getNumFragmentsWithHydrogenBonds
ringHasCoordinationBonds
ringHasHydrogenBonds
ringAssemblyHasOnlyCovalentBonds
ringAssemblyHasCoordinationBonds
ringAssemblyHasHydrogenBonds
fragmentHasOnlyCovalentBonds
fragmentHasCoordinationBonds
fragmentHasHydrogenBonds
getNumAtomSymmetryClasses
getNumAlleneCenters
getAlleneEndpoint1
getAlleneEndpoint2
getAlleneDistance
getAlleneAtoms
getAlleneBonds
getAlleneStereoParity
setAlleneStereoParity
getNumAtropisomerCenters
getAtropisomerBond
getAtropisomerStereoParity
setAtropisomerStereoParity
getNumSquarePlanarCenters
getNumTrigonalBipyramidalCenters
getNumOctahedralCenters
getSquarePlanarCenterAtom
getTrigonalBipyramidalCenterAtom
getOctahedralCenterAtom
getCustomDataContainingAtom
MolIO class
addPDBReferenceFile
clearPDBReferenceFiles
verifyMolecularFormat
Monomer class
getAtom
getBond
getBracketX1
getBracketX2
getBracketY1
getBracketY2
addAutoBrackets
setBracketCoordinates
MulGroup class
getInternalAtom
getUniqueAtom
getInternalBond
getLinkBond
getBracketX1
getBracketX2
getBracketY1
getBracketY2
addAutoBrackets
setBracketCoordinates
PiSystem class
getAtom
getBond
getCentroidX
getCentroidY
getCentroidZ
Polymer class
getLinkBond
getInternalAtom
getBracketX1
getBracketX2
getBracketY1
getBracketY2
addAutoBrackets
setBracketCoordinates
PropertyCollection class
hasProperty
Reaction class
getReactant
getProduct
getReagent
getPropertyNameByIndex
getPropertyStringValueByIndex
getPropertySizeByIndex
getPropertyIthValueByIndex
removePropertyByIndex
getReactantAtomStatusFlags
getReactantBondStatusFlags
getProductAtomStatusFlags
getProductBondStatusFlags
getProductAtomMappedFromReactantAtom
getReactantAtomMappedFromProductAtom
RepeatUnit class
getInternalAtom
getInternalBond
getLinkBond
getBracketX1
getBracketX2
getBracketY1
getBracketY2
addAutoBrackets
setBracketCoordinates
SCSRSeqAtom class
getAttachmentAtom
getAtomLabel
getTemplateClass
getAttachmentLabel
addAttachment
setAttachmentAtom
setAttachmentLabel
deleteAttachment
SCSRTemplate class
getTemplateClass
getName
getAltName
SGMappingEngine class
getSearchOptions
setDefaultOptions
getQueryMolecule
SuperAtom class
getAtom
getLinkBond
getAttachmentPointApoAtom
getAttachmentPointLeavingAtom
getAttachmentPointLabel
getCrossingBondCStateBond
getCrossingBondCStateX
getCrossingBondCStateY
getBondVectorBond
getBondVectorX
getBondVectorY
setClassName
setLabel
