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java.lang.Object chemaxon.marvin.plugin.CalculatorPlugin chemaxon.marvin.calculations.IonChargePlugin
Plugin class for charge calculation on ionized microspecies.
Field Summary |
Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin |
ATOM, CHART, MOLECULE, NAN, SUBRESULT |
Constructor Summary | |
IonChargePlugin()
Constructor. |
Method Summary | |
void |
checkMolecule(Molecule mol)
Checks the input molecule. |
java.lang.String |
getErrorMessage()
Returns the calculation error information message if run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter). |
protected java.lang.String |
getLicenseKey()
Returns the built-in license key for the given plugin class. |
java.lang.Object |
getResult(java.lang.Object type,
int index)
Returns the result item for the specified type and index. |
java.lang.String |
getResultAsString(java.lang.Object type,
int index,
java.lang.Object result)
Returns the specified result in String format. |
int |
getResultCount(java.lang.Object type)
Returns the number of result items for the given result key. |
int |
getResultDomain(java.lang.Object type)
Returns the calculation domain CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE . |
java.lang.Object[] |
getResultTypes()
Returns the result types (possible type: "charge"). |
boolean |
run()
Runs the charge calculation on the microspecies with sufficiently large distribution on the given pH. |
protected void |
setInputMolecule(Molecule mol)
Sets the input molecule. |
void |
setParameters(java.util.Properties params)
Sets the input parameters for the plugin. |
protected void |
standardize(Molecule mol)
Standardizes the molecule. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public IonChargePlugin()
Method Detail |
protected final java.lang.String getLicenseKey()
getLicenseKey
in class CalculatorPlugin
CalculatorPlugin.checkLicense()
public void setParameters(java.util.Properties params) throws PluginException
setParameters
in class CalculatorPlugin
params
- is the parameter table
PluginException
- on errorpublic void checkMolecule(Molecule mol) throws PluginException
checkMolecule
in class CalculatorPlugin
mol
- is the input molecule
PluginException
- with error message for the user if the molecule is refusedprotected void setInputMolecule(Molecule mol) throws PluginException
setInputMolecule
in class CalculatorPlugin
mol
- is the input molecule
PluginException
- on errorpublic boolean run() throws PluginException
run
in class CalculatorPlugin
PluginException
- on errorCalculatorPlugin.getErrorMessage()
public java.lang.String getErrorMessage()
run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter).
getErrorMessage
in class CalculatorPlugin
public java.lang.Object[] getResultTypes()
getResultTypes
in class CalculatorPlugin
public int getResultDomain(java.lang.Object type)
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
pKa always returns CalculatorPlugin.ATOM
.
getResultDomain
in class CalculatorPlugin
type
- is the result type
CalculatorPlugin.ATOM
getResultTypes()
public int getResultCount(java.lang.Object type)
getResultCount
in class CalculatorPlugin
type
- is the result type
getResultTypes()
public java.lang.Object getResult(java.lang.Object type, int index) throws PluginException
getResult
in class CalculatorPlugin
type
- is the result typeindex
- is the result index
PluginException
- if the result cannot be returnedCalculatorPlugin.getResultTypes()
public java.lang.String getResultAsString(java.lang.Object type, int index, java.lang.Object result) throws PluginException
getResultAsString
in class CalculatorPlugin
type
- is the result typeindex
- is the result indexresult
- is the result item
PluginException
- if an invalid result item is givenprotected void standardize(Molecule mol)
standardize
in class CalculatorPlugin
mol
- is the molecule to be standardized
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