public class OrbitalElectronegativityPlugin extends MajorMicrospeciesAccessorPlugin
References:
API usage example:
// create plugin
OrbitalElectronegativityPlugin plugin = new OrbitalElectronegativityPlugin();
// read target molecule
MolImporter mi = new MolImporter(new ByteArrayInputStream("Clc1cc(Cl)c(Cl)cc1".getBytes()));
Molecule mol = mi.read();
mi.close();
// optional: take major microspecies at pH=7.4
// skip this if you want to calculate orbital electronegativity for the input molecule as it is
plugin.setpH(7.4);
// set target molecule
plugin.setMolecule(mol);
// run the calculation
plugin.run();
// get orbital electronegativity values for each atom
int count = mol.getAtomCount();
for (int i=0; i < count; ++i) {
double sigmaoen = plugin.getSigmaOen(i);
if (!Double.isNaN(sigmaoen)) {
System.out.println("sigma orbital electronegativity for atom "+(i+1)+": "+sigmaoen);
}
}
For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.
CalculatorPlugin.HydrogenDataionizerATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, explicitHydrogens, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, KEEP_HYDROGENS, keepHydrogens, licenseEnvironment, MOLECULE, MOLECULES, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED, TRUE| Constructor and Description |
|---|
OrbitalElectronegativityPlugin()
Constructor.
|
| Modifier and Type | Method and Description |
|---|---|
String |
getErrorMessage()
Returns the calculation error information message if
run()
returned false (calculation error): hydrogen valence error. |
double |
getPiOEN(int index)
Returns the pi orbital electronegativity of a specified atom.
|
String |
getProductName()
Returns the product identifier of the plugin as given by
LicenseManager. |
Object |
getResult(Object type,
int index)
Returns the result item for the specified type and index.
|
String |
getResultAsString(Object type,
int index,
Object result)
Returns the specified result in String format.
|
int |
getResultCount(Object type)
Returns the number of result items for the given result type.
|
int |
getResultDomain(Object type)
Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE. |
Molecule |
getResultMolecule()
Returns the result molecule for display.
|
Object[] |
getResultTypes()
Returns the result types (possible types: "sigma", "pi").
|
double |
getSigmaOEN(int index)
Returns the sigma orbital electronegativity of a specified atom.
|
String |
getTypeString(Object type)
Returns a string representation of the given type.
|
boolean |
isLicensed()
Returns
true if the plugin is licensed. |
boolean |
run()
Runs the orbital electornegativity calculation.
|
protected void |
setInputMolecule(Molecule mol)
Sets the input molecule.
|
void |
setParameters(Properties params)
Sets the input parameters for the plugin.
|
void |
setTakeResonantStructures(boolean resonance)
Sets calculation with resonant structures.
|
checkMolecule, createModifiedInputMolecule, getIonizerErrorMessage, getpH, setpH, standardizearrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, setProgressMonitor, standardizeIonicGroups, standardizeNeutralGroupspublic OrbitalElectronegativityPlugin()
public boolean isLicensed()
true if the plugin is licensed. The license checking
is based on the product name, returned by getProductName().isLicensed in interface chemaxon.license.LicensableisLicensed in class MajorMicrospeciesAccessorPlugintrue if the plugin is licensedpublic String getProductName()
LicenseManager.getProductName in class CalculatorPluginLicenseManager.CHARGE_PLUGIN_GROUPpublic void setParameters(Properties params) throws PluginException
setParameters in class MajorMicrospeciesAccessorPluginparams - is the parameter tablePluginException - on errorpublic void setTakeResonantStructures(boolean resonance)
false.resonance - is true if orbital electornegativity
should be calculated with resonant structuresprotected void setInputMolecule(Molecule mol) throws PluginException
setInputMolecule in class CalculatorPluginmol - is the input moleculePluginException - on errorpublic boolean run()
throws PluginException
run in class CalculatorPluginPluginException - on errorCalculatorPlugin.getErrorMessage()public String getErrorMessage()
run()
returned false (calculation error): hydrogen valence error.getErrorMessage in class MajorMicrospeciesAccessorPluginpublic double getSigmaOEN(int index)
index - is the atom indexpublic double getPiOEN(int index)
index - is the atom indexpublic Object[] getResultTypes()
getResultTypes in class CalculatorPluginpublic int getResultDomain(Object type)
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE. Orbital electornegativity plugin
always returns CalculatorPlugin.ATOM.getResultDomain in class CalculatorPlugintype - is the result typeCalculatorPlugin.ATOMgetResultTypes()public int getResultCount(Object type)
getResultCount in class CalculatorPlugintype - is the result typegetResultTypes()public String getTypeString(Object type)
getTypeString in class CalculatorPlugintype - is the type objectpublic Object getResult(Object type, int index) throws PluginException
getResult in class CalculatorPlugintype - is the result type ("sigma" or "pi")index - is the atom indexPluginException - if the result cannot be returnedgetResultTypes()public String getResultAsString(Object type, int index, Object result) throws PluginException
getResultAsString in class CalculatorPlugintype - is the result typeindex - is the result indexresult - is the result itemPluginException - if an invalid result item is givenpublic Molecule getResultMolecule() throws PluginException
MolAtom.getExtraLabel()).
Molecular results are stored in molecule properties
with keys being the result types
(Molecule.getProperty(String)).getResultMolecule in class CalculatorPluginPluginException - on error