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void org::openscience::cdk::tools::LoggingTool::error ( Object  object  )  [inline]

Shows ERROR output for the Object. It uses the toString() method.

Parameters:
object Object to apply toString() too and output

Definition at line 385 of file LoggingTool.java.

Referenced by org::openscience::cdk::templates::AminoAcids::aaBondInfo(), org::openscience::cdk::applications::jchempaint::action::ZoomAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::WebLinkAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ValidateAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ShowChemObjectDumpAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::SaveAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::PreferencesAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::PerceiveAtomTypesAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::OpenAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ExportCompChemAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ExportAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CreateSmilesAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CreateReactionAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CreateInChIAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ConvertToRadicalAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ConvertToPseudoAtomAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ConvertToAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ChangeIsotopeAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ChangeAtomSymbolAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::AdjustBondOrdersAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::AddHydrogenAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::JChemPaintPanel::addFilePopUpMenu(), org::openscience::cdk::applications::jchempaint::action::AddHydrogenAction::addHydrogenToAllMolecules(), org::openscience::cdk::applications::jchempaint::action::AddHydrogenAction::addHydrogenToOneAtom(), org::openscience::cdk::tools::AtomTypeTools::assignAtomTypePropertiesToAtom(), org::openscience::cdk::protein::ProteinPocketFinder::assignVdWRadiiToProtein(), org::openscience::cdk::debug::DebugStrand::clone(), org::openscience::cdk::debug::DebugSingleElectron::clone(), org::openscience::cdk::debug::DebugRing::clone(), org::openscience::cdk::debug::DebugReactionSet::clone(), org::openscience::cdk::debug::DebugReaction::clone(), org::openscience::cdk::debug::DebugPseudoAtom::clone(), org::openscience::cdk::debug::DebugPolymer::clone(), org::openscience::cdk::debug::DebugMonomer::clone(), org::openscience::cdk::debug::DebugMoleculeSet::clone(), org::openscience::cdk::debug::DebugMolecule::clone(), org::openscience::cdk::debug::DebugMapping::clone(), org::openscience::cdk::debug::DebugLonePair::clone(), org::openscience::cdk::debug::DebugIsotope::clone(), org::openscience::cdk::debug::DebugElement::clone(), org::openscience::cdk::debug::DebugElectronContainer::clone(), org::openscience::cdk::debug::DebugCrystal::clone(), org::openscience::cdk::debug::DebugChemSequence::clone(), org::openscience::cdk::debug::DebugChemObject::clone(), org::openscience::cdk::debug::DebugChemModel::clone(), org::openscience::cdk::debug::DebugChemFile::clone(), org::openscience::cdk::debug::DebugBond::clone(), org::openscience::cdk::debug::DebugBioPolymer::clone(), org::openscience::cdk::debug::DebugAtomType::clone(), org::openscience::cdk::debug::DebugAtomParity::clone(), org::openscience::cdk::debug::DebugAtomContainerSet::clone(), org::openscience::cdk::debug::DebugAtomContainer::clone(), org::openscience::cdk::debug::DebugAtom::clone(), org::openscience::cdk::debug::DebugAminoAcid::clone(), configureLog4j(), org::openscience::cdk::templates::AminoAcids::createAAs(), org::openscience::cdk::applications::jchempaint::JChemPaintPopupMenu::createMenuItem(), org::openscience::cdk::applications::jchempaint::JChemPaintMenuBar::createMenuItem(), org::openscience::cdk::io::ReaderFactory::createReader(), org::openscience::cdk::applications::jchempaint::ToolBarMaker::createToolbar(), org::openscience::cdk::applications::jchempaint::ToolBarMaker::createToolbarButton(), org::openscience::cdk::io::WriterFactory::createWriter(), org::openscience::cdk::config::ElementPTFactory::ElementPTFactory(), org::openscience::cdk::io::cml::MDMoleculeConvention::endElement(), org::openscience::cdk::io::iterator::event::EventCMLHandler::endObject(), org::openscience::cdk::tools::StructureResonanceGenerator::existAC(), org::openscience::cdk::atomtype::ValencyMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::StructGenMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::MMFF94AtomTypeMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::MM2AtomTypeMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::HybridizationStateATMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::HybridizationMatcher::findMatchingAtomType(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::generate3DCoordinates(), org::openscience::cdk::applications::jchempaint::action::JCPAction::getAction(), org::openscience::cdk::config::AtomTypeFactory::getAllAtomTypes(), org::openscience::cdk::tools::StructureResonanceGenerator::getAllStructures(), org::openscience::cdk::config::AtomTypeFactory::getAtomTypes(), org::openscience::cdk::structgen::deterministic::GENMDeterministicGenerator::getBasicUnit(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::getBondCoordinates(), org::openscience::cdk::geometry::GeometryTools::getBondCoordinates(), org::openscience::cdk::io::cml::CMLResolver::getCMLType(), org::openscience::cdk::qsar::DescriptorEngine::getDescriptorClassNameByInterface(), org::openscience::cdk::qsar::DescriptorEngine::getDescriptorClassNameByPackage(), org::openscience::cdk::qsar::DescriptorEngine::getDictionaryClass(), org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel::getDictionaryDatabase(), org::openscience::cdk::dict::DictionaryDatabase::getDictionaryEntries(), org::openscience::cdk::config::ElementPTFactory::getElement(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getGUIDefinition(), org::openscience::cdk::config::IsotopeFactory::getIsotopes(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getJChemPaintDir(), org::openscience::cdk::tools::GenerateFragments::getLinkerFragmentsAsSmileArray(), org::openscience::cdk::config::IsotopeFactory::getMajorIsotope(), org::openscience::cdk::tools::GenerateFragments::getMurckoFrameworksAsSmileArray(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getResource(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getResources(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getResourceString(), org::openscience::cdk::tools::GenerateFragments::getRingFragmentsAsSmileArray(), org::openscience::cdk::applications::jchempaint::action::JCPAction::getSource(), org::openscience::cdk::applications::swing::ChemObjectTree::getTree(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getUserHome(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getUserPropsFile(), org::openscience::cdk::io::ReaderFactory::guessFormat(), org::openscience::cdk::io::iterator::IteratingMDLReader::hasNext(), org::openscience::cdk::tools::HydrogenAdder::HydrogenAdder(), org::openscience::cdk::io::INChIReader::init(), org::openscience::cdk::config::IsotopeFactory::IsotopeFactory(), org::openscience::cdk::tools::SmilesValencyChecker::isSaturated(), org::openscience::cdk::applications::plugin::PluginClassLoader::loadClass(), org::openscience::cdk::applications::plugin::CDKPluginManager::loadPlugins(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::mapAtomsOfAlignedStructures(), org::openscience::cdk::isomorphism::matchers::smarts::RecursiveSmartsAtom::matches(), org::openscience::cdk::io::CIFReader::parseIntoDouble(), org::openscience::cdk::smiles::SmilesParser::parseString(), org::openscience::cdk::applications::swing::PeriodicTablePanel::PeriodicTablePanel(), org::openscience::cdk::atomtype::StructGenAtomTypeGuesser::possbibleAtomTypes(), org::openscience::cdk::ringsearch::FiguerasSSSRFinder::prepareRing(), org::openscience::cdk::io::cml::CMLErrorHandler::print(), org::openscience::cdk::qsar::DescriptorEngine::process(), org::openscience::cdk::io::iterator::event::EventCMLReader::process(), org::openscience::cdk::applications::demo::EventCMLDemo::process(), org::openscience::cdk::io::inchi::INChIContentProcessorTool::processConnections(), org::openscience::cdk::io::inchi::INChIContentProcessorTool::processFormula(), org::openscience::cdk::structgen::RandomGenerator::proposeStructure(), org::openscience::cdk::io::VASPReader::read(), org::openscience::cdk::io::ShelXReader::read(), org::openscience::cdk::io::MACiEReader::read(), org::openscience::cdk::io::CIFReader::read(), org::openscience::cdk::io::PDBReader::readAtom(), org::openscience::cdk::io::MDLV3000Reader::readAtomBlock(), org::openscience::cdk::config::CDKBasedAtomTypeConfigurator::readAtomTypes(), org::openscience::cdk::config::atomtypes::AtomTypeReader::readAtomTypes(), org::openscience::cdk::protein::ProteinPocketFinder::readBioPolymer(), org::openscience::cdk::io::MDLV3000Reader::readBondBlock(), org::openscience::cdk::io::XYZReader::readChemFile(), org::openscience::cdk::io::PMPReader::readChemFile(), org::openscience::cdk::io::PDBReader::readChemFile(), org::openscience::cdk::io::MDLV2000Reader::readChemFile(), org::openscience::cdk::io::MDLReader::readChemFile(), org::openscience::cdk::io::INChIReader::readChemFile(), org::openscience::cdk::config::AtomTypeFactory::readConfiguration(), org::openscience::cdk::dict::DictionaryDatabase::readDictionary(), org::openscience::cdk::config::elements::ElementPTReader::readElements(), org::openscience::cdk::config::isotopes::IsotopeReader::readIsotopes(), org::openscience::cdk::io::Mol2Reader::readMolecule(), org::openscience::cdk::io::MDLV2000Reader::readMolecule(), org::openscience::cdk::io::MDLReader::readMolecule(), org::openscience::cdk::internet::WWMMatrixReader::readMolecule(), org::openscience::cdk::internet::DADMLReader::readMolecule(), org::openscience::cdk::io::SMILESReader::readMoleculeSet(), org::openscience::cdk::io::MACiEReader::readReactions(), org::openscience::cdk::io::MDLV3000Reader::readSGroup(), org::openscience::cdk::internet::DADMLReader::resolveLinks(), org::openscience::cdk::applications::jchempaint::JChemPaintPanel::runScript(), org::openscience::cdk::structgen::VicinitySampler::sample(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::searchAndPlaceBranches(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::setForceField(), org::openscience::cdk::layout::StructureDiagramGenerator::setMolecule(), org::openscience::cdk::io::iterator::event::EventCMLHandler::setObjectProperty(), org::openscience::cdk::internet::DADMLReader::setQuery(), org::openscience::cdk::applications::jchempaint::JChemPaintPanel::showChemFile(), org::openscience::cdk::protein::ProteinPocketFinder::sitefinder(), org::openscience::cdk::smiles::SmilesParser::SmilesParser(), org::openscience::cdk::io::cml::MDMoleculeConvention::startElement(), org::openscience::cdk::controller::AbstractController2D::updateAtom(), org::openscience::cdk::io::MDLWriter::write(), org::openscience::cdk::io::CDKSourceCodeWriter::write(), org::openscience::cdk::io::SVGWriter::writeAtomContainer(), org::openscience::cdk::io::XYZWriter::writeMolecule(), org::openscience::cdk::io::SMILESWriter::writeMolecule(), org::openscience::cdk::io::MDLRXNWriter::writeMoleculeSet(), and org::openscience::cdk::io::MDLRXNWriter::writeReaction().

                                     {
        if (doDebug) {
            errorString("" + object);
        }
    }


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