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java.lang.Objectchemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.MajorMicrospeciesPlugin
chemaxon.marvin.calculations.ChargePlugin
Plugin class for charge calculation. Sigma, pi and total charge values can be calculated by this plugin.
References:
API usage example:
// create plugin ChargePlugin plugin = new ChargePlugin(); plugin.validate(<charge license>); // read target molecule MolImporter mi = new MolImporter(new ByteArrayInputStream("Clc1cc(Cl)c(Cl)cc1".getBytes())); Molecule mol = mi.read(); // optional: take major microspecies at pH=7.4 // skip this if you want to calculate charge for the input molecule as it is plugin.setpH(7.4); // set target molecule plugin.setMolecule(mol); // run the calculation plugin.run(); // get charge values for each atom int count = mol.getAtomCount(); for (int i=0; i < count; ++i) { double charge = plugin.getTotalCharge(i); if (!Double.isNaN(charge)) { System.out.println("total charge for atom "+(i+1)+": "+charge); } }
Field Summary |
Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin |
ATOM, BLUE, CALCRGB_OFF, CHART, HYDROGEN_VALENCE_ERROR_MSG, MOLECULE, NAN, RED, SUBRESULT |
Constructor Summary | |
ChargePlugin()
Constructor. |
Method Summary | |
double |
getAromaticRingCharge(int index)
Returns the total partial charge of the smallest aromatic ring containing the specified atom. |
double |
getAromaticSystemCharge(int index)
Returns the total partial charge of the aromatic system containing the specified atom. |
java.lang.String |
getErrorMessage()
Returns the calculation error information message if run()
returned false (calculation error): hydrogen valence error. |
protected java.lang.String |
getLicenseKey()
Returns the built-in license key for the given plugin class. |
java.lang.String |
getOutputClassName()
Returns the output provider class name for the command line interface. |
double |
getPiCharge(int index)
Returns the pi charge of a specified atom. |
java.lang.Object |
getResult(java.lang.Object type,
int index)
Returns the result item for the specified type and index. |
double |
getResultantImplicitHCharge(int index)
Returns sum of implicit H charge around a central atom |
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 type. |
int |
getResultDomain(java.lang.Object type)
Returns the calculation domain CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE . |
java.lang.Object[] |
getResultTypes()
Returns the result types (possible types: "sigma", "pi", "total"). |
double |
getSigmaCharge(int index)
Returns the sigma charge of a specified atom. |
double |
getTotalCharge(int index)
Returns the total charge of a specified atom. |
boolean |
run()
Runs the charge calculation. |
protected void |
setInputMolecule(Molecule mol)
Sets the input molecule. |
void |
setParameters(java.util.Properties params)
Sets the input parameters for the plugin. |
Methods inherited from class chemaxon.marvin.calculations.MajorMicrospeciesPlugin |
checkMolecule, getMainMolecule, getMajorMicrospecies, getMolText, getpH, getReferenceMolecule, getSuffix, isMajorMs, setpH, standardize |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public ChargePlugin()
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 MajorMicrospeciesPlugin
params
- is the parameter table
PluginException
- on errorprotected void setInputMolecule(Molecule mol) throws PluginException
setInputMolecule
in class MajorMicrospeciesPlugin
mol
- is the input molecule
PluginException
- on errorpublic boolean run() throws PluginException
run
in class MajorMicrospeciesPlugin
PluginException
- on errorpublic java.lang.String getErrorMessage()
run()
returned false (calculation error): hydrogen valence error.
getErrorMessage
in class MajorMicrospeciesPlugin
public double getTotalCharge(int index)
index
- is the atom index
Double.NaN
for implicit H-spublic double getSigmaCharge(int index)
index
- is the atom index
Double.NaN
for implicit H-spublic double getPiCharge(int index)
index
- is the atom index
Double.NaN
for implicit H-spublic double getResultantImplicitHCharge(int index)
index
- is the central atom index
public double getAromaticSystemCharge(int index)
index
- is the atom index
public double getAromaticRingCharge(int index)
index
- is the atom index
public java.lang.Object[] getResultTypes()
getResultTypes
in class MajorMicrospeciesPlugin
public int getResultDomain(java.lang.Object type)
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
Charge always returns CalculatorPlugin.ATOM
.
getResultDomain
in class MajorMicrospeciesPlugin
type
- is the result type
CalculatorPlugin.ATOM
getResultTypes()
public int getResultCount(java.lang.Object type)
getResultCount
in class MajorMicrospeciesPlugin
type
- is the result type
getResultTypes()
public java.lang.Object getResult(java.lang.Object type, int index) throws PluginException
getResult
in class MajorMicrospeciesPlugin
type
- is the result type ("total", "pi", "sigma" or "implh")index
- is the atom index
PluginException
- if the result cannot be returnedgetResultTypes()
public java.lang.String getOutputClassName()
getOutputClassName
in class MajorMicrospeciesPlugin
public java.lang.String getResultAsString(java.lang.Object type, int index, java.lang.Object result) throws PluginException
getResultAsString
in class MajorMicrospeciesPlugin
type
- is the result typeindex
- is the result indexresult
- is the result item
PluginException
- if an invalid result item is given
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