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java.lang.Object chemaxon.marvin.plugin.CalculatorPlugin chemaxon.marvin.calculations.logDPlugin
Plugin class for logD calculation.
API usage example:
// instantiate and validate plugin logDPlugin plugin = new logDPlugin(); plugin.validate(<logD license>); // set parameters plugin.setCloridIonConcentration(0.2); plugin.setNaKIonConcentration(0.2); plugin.setpHLower(3.0); plugin.setpHUpper(6.0); plugin.setpHStep(1.0); MolImporter importer = new MolImporter("targets.sdf"); Molecule mol = null; while ((mol = importer.read()) != null) { // set molecule and run calculation plugin.setMolecule(mol); plugin.run(); double[] pHs = plugin.getpHs(); double[] logDs = plugin.getlogDs(); // get and print logD values for (int i=0; i < pHs.length; ++i) { double pH = pHs[i]; double logD = logDs[i]; System.out.println(pH+", "+logD); } } importer.close();
Another example showing logD calculation at a single pH value:
// instantiate and validate plugin logDPlugin plugin = new logDPlugin(); plugin.validate(<logD license>); // set pH plugin.setpH(3.0); // run the calculation plugin.run(); // get result double logD = plugin.getlogD(); // print result System.out.println("logD at pH 3.0: "+logD);
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 | |
logDPlugin()
Constructor. |
Method Summary | |
double |
calclogD(double pH)
Returns the logD value at fixed pH. |
void |
checkMolecule(Molecule mol)
Checks the input molecule. |
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. |
double |
getlogD()
Returns the logD value for the pH specified in setpH(double) . |
double[] |
getlogDs()
Returns the logD array. |
java.lang.String |
getOutputClassName()
Returns the output provider class name for the command line interface. |
double[] |
getpHs()
Returns the pH array. |
double[] |
getReflogDs()
Returns the reference logD array. |
double[] |
getRefpHs()
Returns the reference pH array. |
java.lang.Object |
getResult(java.lang.Object type,
int index)
Returns the result item for the specified type and index. |
java.lang.Object |
getResult(java.lang.Object type,
java.lang.String arg)
Returns the result item for the specified pH. |
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. |
java.lang.String |
getXAxisLabel(java.lang.Object type)
Returns the X axis label to be displayed in case of chart data. |
java.lang.String[] |
getXLabels()
Returns the X label array (pH array as String[] ). |
java.lang.String |
getYAxisLabel(java.lang.Object type)
Returns the Y axis label to be displayed. |
boolean |
run()
Runs the logD calculation. |
void |
setCloridIonConcentration(double c)
Sets the Cl- concentration (default: 0.1 ). |
protected void |
setInputMolecule(Molecule mol)
Sets the input molecule. |
void |
setNaKIonConcentration(double c)
Sets the Na+, K+ concentration (default: 0.1 ). |
void |
setParameters(java.util.Properties params)
Sets the input parameters for the plugin. |
void |
setpH(double pH)
Sets a single pH value for the logD calculation. |
void |
setpHLower(double lower)
Sets pH lower limit (default: 0.0 ). |
void |
setpHStep(double step)
Sets pH step to be taken between the pH lower and upper limits (default: 1.0 ). |
void |
setpHUpper(double upper)
Sets pH upper limit (default: 14.0 ). |
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 logDPlugin()
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 setCloridIonConcentration(double c)
Cl-
concentration (default: 0.1
).
c
- is the concentrationpublic void setNaKIonConcentration(double c)
Na+, K+
concentration (default: 0.1
).
c
- is the concentrationpublic void setpHLower(double lower)
0.0
).
lower
- is the pH lower limitpublic void setpHUpper(double upper)
14.0
).
upper
- is the pH upper limitpublic void setpHStep(double step)
1.0
).
step
- is the pH steppublic void setpH(double pH)
pH
- is the pH valuepublic void checkMolecule(Molecule mol) throws PluginException
RxnMolecule
,
if the molecule contains R-groups or if the molecule consists of
more than one fragments.
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 (standardized) 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): hydrogen valence error.
getErrorMessage
in class CalculatorPlugin
public double calclogD(double pH) throws PluginException
pH
- is the pH value
PluginException
- on errorpublic java.lang.Object[] getResultTypes()
getResultTypes
in class CalculatorPlugin
public double[] getRefpHs()
public double[] getReflogDs()
public double getlogD()
setpH(double)
.
public double[] getpHs()
public double[] getlogDs()
public java.lang.String getXAxisLabel(java.lang.Object type)
getXAxisLabel
in class CalculatorPlugin
type
- is the result typepublic java.lang.String getYAxisLabel(java.lang.Object type)
getYAxisLabel
in class CalculatorPlugin
type
- is the result typepublic int getResultDomain(java.lang.Object type)
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
Can be combined with CalculatorPlugin.CHART
to denote chart-type data.
logD returns CalculatorPlugin.MOLECULE
combined with
CalculatorPlugin.CHART
for type "logD",
CalculatorPlugin.MOLECULE
combined with
CalculatorPlugin.SUBRESULT
for type "reflogD".
getResultDomain
in class CalculatorPlugin
type
- is the result type
CalculatorPlugin.MOLECULE
CalculatorPlugin.getResultTypes()
public int getResultCount(java.lang.Object type)
1
.
getResultCount
in class CalculatorPlugin
type
- is the result type
CalculatorPlugin.getResultTypes()
public java.lang.Object getResult(java.lang.Object type, int index) throws PluginException
(pH, logD)
arrays as
a double[2][]
with the 0-th element being the pH
array and the 1-st element being the logD
array.
getResult
in class CalculatorPlugin
type
- is the result type: "logD" or "reflogD"index
- is the result index
PluginException
- if the result cannot be returnedCalculatorPlugin.getResultTypes()
public java.lang.Object getResult(java.lang.Object type, java.lang.String arg) throws PluginException
getResult
in class CalculatorPlugin
type
- is the result type (not used)arg
- is the pH as string
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
(pH, logD)
value pairs in string format:
the values are rounded using the 'precision' input parameter
that determines the number of fractional digits displayed,
pH and logD are separated by a tab character.
getResultAsString
in class CalculatorPlugin
type
- is the result typeindex
- is the result indexresult
- is the result item
PluginException
- if an invalid result item is givenpublic java.lang.String[] getXLabels()
String[]
).
getXLabels
in class CalculatorPlugin
public java.lang.String getOutputClassName()
getOutputClassName
in class CalculatorPlugin
protected void standardize(Molecule mol)
standardize
in class CalculatorPlugin
mol
- is the molecule to be standardized
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