private void initIOSettings() { optimize = addSetting(new BooleanIOSetting("Optimize", IOSetting.Importance.MEDIUM, "Should the structure be optimized?", "true")); mopacCommands = addSetting(new StringIOSetting("Commands", IOSetting.Importance.LOW, "What Mopac commands should be used (overwrites other choices)?", "PM3 NOINTER NOMM BONDS MULLIK PRECISE")); }
private void writeAtomContainer(IAtomContainer molecule) throws Exception { writer.write("{"); writer.write('\n'); writer.write(" IChemObjectBuilder builder = "); writer.write(builder.getSetting()); writer.write(".getInstance();"); writer.write('\n'); writer.write(" IAtomContainer mol = builder.newInstance(IAtomContainer.class);"); writer.write('\n'); IDCreator.createIDs(molecule); writeAtoms(molecule); writeBonds(molecule); writer.write("}"); writer.write('\n'); }
private void customizeJob() { fireIOSettingQuestion(optimize); try { if (optimize.isSet()) { mopacCommands.setSetting("PM3 NOINTER NOMM BONDS MULLIK PRECISE"); } else { mopacCommands.setSetting("PM3 NOINTER NOMM BONDS MULLIK XYZ 1SCF"); } } catch (CDKException exception) { throw new IllegalArgumentException(exception); } fireIOSettingQuestion(mopacCommands); }
private void initIOSettings() { optimize = addSetting(new BooleanIOSetting("Optimize", IOSetting.Importance.MEDIUM, "Should the structure be optimized?", "true")); mopacCommands = addSetting(new StringIOSetting("Commands", IOSetting.Importance.LOW, "What Mopac commands should be used (overwrites other choices)?", "PM3 NOINTER NOMM BONDS MULLIK PRECISE")); }
private void writeAtomContainer(IAtomContainer molecule) throws Exception { writer.write("{"); writer.write('\n'); writer.write(" IChemObjectBuilder builder = "); writer.write(builder.getSetting()); writer.write(".getInstance();"); writer.write('\n'); writer.write(" IAtomContainer mol = builder.newInstance(IAtomContainer.class);"); writer.write('\n'); IDCreator.createIDs(molecule); writeAtoms(molecule); writeBonds(molecule); writer.write("}"); writer.write('\n'); }
private void customizeJob() { fireIOSettingQuestion(optimize); try { if (optimize.isSet()) { mopacCommands.setSetting("PM3 NOINTER NOMM BONDS MULLIK PRECISE"); } else { mopacCommands.setSetting("PM3 NOINTER NOMM BONDS MULLIK XYZ 1SCF"); } } catch (CDKException exception) { throw new IllegalArgumentException(exception); } fireIOSettingQuestion(mopacCommands); }
"What kind of job do you want to perform?", commandOptions, "energy calculation")); comment = addSetting(new StringIOSetting("Comment", IOSetting.Importance.LOW, "What comment should be put in the file?", "Created with CDK (http://cdk.sf.net/)")); memory = addSetting(new StringIOSetting("Memory", IOSetting.Importance.LOW, "How much memory do you want to use?", "unset"));
try { IAtomContainer container = (IAtomContainer) arg0; writer.write(mopacCommands.getSetting()); int formalCharge = AtomContainerManipulator.getTotalFormalCharge(container); if (formalCharge != 0) writer.write(" CHARGE=" + formalCharge);
"What kind of job do you want to perform?", commandOptions, "energy calculation")); comment = addSetting(new StringIOSetting("Comment", IOSetting.Importance.LOW, "What comment should be put in the file?", "Created with CDK (http://cdk.sf.net/)")); memory = addSetting(new StringIOSetting("Memory", IOSetting.Importance.LOW, "How much memory do you want to use?", "unset"));
try { IAtomContainer container = (IAtomContainer) arg0; writer.write(mopacCommands.getSetting()); int formalCharge = AtomContainerManipulator.getTotalFormalCharge(container); if (formalCharge != 0) writer.write(" CHARGE=" + formalCharge);
private void initIOSettings() { write2DCoordinates = addSetting(new BooleanIOSetting("write2DCoordinates", IOSetting.Importance.LOW, "Should 2D coordinates be added?", "true")); write3DCoordinates = addSetting(new BooleanIOSetting("write3DCoordinates", IOSetting.Importance.LOW, "Should 3D coordinates be added?", "true")); builder = addSetting(new StringIOSetting("builder", IOSetting.Importance.LOW, "Which IChemObjectBuilder should be used?", "DefaultChemObjectBuilder")); }
(namespacePrefix.getSetting().length() > 0) ? namespacePrefix.getSetting() : null); root.addNamespaceDeclaration("xsi", "http://www.w3.org/2001/XMLSchema-instance"); root.addAttribute(new Attribute("xsi:schemaLocation=", "http://www.w3.org/2001/XMLSchema-instance", "http://www.xml-cml.org/schema/cml2/core " + instanceLocation.getSetting()));
private void initIOSettings() { write2DCoordinates = addSetting(new BooleanIOSetting("write2DCoordinates", IOSetting.Importance.LOW, "Should 2D coordinates be added?", "true")); write3DCoordinates = addSetting(new BooleanIOSetting("write3DCoordinates", IOSetting.Importance.LOW, "Should 3D coordinates be added?", "true")); builder = addSetting(new StringIOSetting("builder", IOSetting.Importance.LOW, "Which IChemObjectBuilder should be used?", "DefaultChemObjectBuilder")); }
(namespacePrefix.getSetting().length() > 0) ? namespacePrefix.getSetting() : null); root.addNamespaceDeclaration("xsi", "http://www.w3.org/2001/XMLSchema-instance"); root.addAttribute(new Attribute("xsi:schemaLocation=", "http://www.w3.org/2001/XMLSchema-instance", "http://www.xml-cml.org/schema/cml2/core " + instanceLocation.getSetting()));
private void initIOSettings() { cmlIds = addSetting(new BooleanIOSetting("CMLIDs", IOSetting.Importance.LOW, "Should the output use CML identifiers?", "true")); namespacedOutput = addSetting(new BooleanIOSetting("NamespacedOutput", IOSetting.Importance.LOW, "Should the output use namespaced output?", "true")); namespacePrefix = addSetting(new StringIOSetting("NamespacePrefix", IOSetting.Importance.LOW, "What should the namespace prefix be? [empty is no prefix]", "")); schemaInstanceOutput = addSetting(new BooleanIOSetting("SchemaInstance", IOSetting.Importance.LOW, "Should the output use the Schema-Instance attribute?", "false")); instanceLocation = addSetting(new StringIOSetting("InstanceLocation", IOSetting.Importance.LOW, "Where is the schema found?", "")); indent = addSetting(new BooleanIOSetting("Indenting", IOSetting.Importance.LOW, "Should the output be indented?", "true")); xmlDeclaration = addSetting(new BooleanIOSetting("XMLDeclaration", IOSetting.Importance.LOW, "Should the output contain an XML declaration?", "true")); }
private void initIOSettings() { cmlIds = addSetting(new BooleanIOSetting("CMLIDs", IOSetting.Importance.LOW, "Should the output use CML identifiers?", "true")); namespacedOutput = addSetting(new BooleanIOSetting("NamespacedOutput", IOSetting.Importance.LOW, "Should the output use namespaced output?", "true")); namespacePrefix = addSetting(new StringIOSetting("NamespacePrefix", IOSetting.Importance.LOW, "What should the namespace prefix be? [empty is no prefix]", "")); schemaInstanceOutput = addSetting(new BooleanIOSetting("SchemaInstance", IOSetting.Importance.LOW, "Should the output use the Schema-Instance attribute?", "false")); instanceLocation = addSetting(new StringIOSetting("InstanceLocation", IOSetting.Importance.LOW, "Where is the schema found?", "")); indent = addSetting(new BooleanIOSetting("Indenting", IOSetting.Importance.LOW, "Should the output be indented?", "true")); xmlDeclaration = addSetting(new BooleanIOSetting("XMLDeclaration", IOSetting.Importance.LOW, "Should the output contain an XML declaration?", "true")); }