@PublicAPI public class logPPlugin extends CalculatorPlugin
Reference:
API usage example:
// fill parameters Properties params = new Properties(); params.put("type", "logP"); // create plugin logPPlugin plugin = new logPPlugin(); // set logP calculation method plugin.setlogPMethod(logPPlugin.METHOD_WEIGHTED); // set method weights plugin.setWeightOfMethods(1, 2, 1, 0); // set parameters plugin.setCloridIonConcentration(0.2); plugin.setNaKIonConcentration(0.2); // set result types plugin.setUserTypes("logPTrue,logPMicro"); // for each input molecule run the calculation and display the results System.out.println("molecule\tlogP"); MolImporter mi = new MolImporter("targets.sdf"))); Molecule target = null; while ((target = mi.read()) != null) { // set the input molecule plugin.setMolecule(target); // run the calculation plugin.run(); // get the overal logP value double logp = plugin.getlogPTrue(); double logpm = plugin.getlogPMicro(); System.out.println("True logP : "+logp); System.out.println("Micro logP: "+logpm); System.out.println(); } mi.close();
For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.
CalculatorPlugin.HydrogenData
Modifier and Type | Field and Description |
---|---|
static int |
METHOD_KLOP
Deprecated.
This field will not be available from May 2016. Use
LogPMethod instead. |
static int |
METHOD_PHYS
Deprecated.
This field will not be available from May 2016. Use
LogPMethod instead. |
static int |
METHOD_USER_DEFINED
Deprecated.
Use
LogPMethod.USER_DEFINED instead. |
static int |
METHOD_VG
Deprecated.
Use
LogPMethod.CHEMAXON instead. |
static int |
METHOD_WEIGHTED
Deprecated.
Use
LogPMethod.CONSENSUS instead. |
ATOM, 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 |
---|
logPPlugin()
Constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
checkMolecule(Molecule mol)
Checks the input molecule.
|
protected Molecule |
createModifiedInputMolecule(Molecule mol)
Returns the major tautomeric form of the molecule.
|
double |
getAtomlogPHIncrement(int index)
Deprecated.
Increments of implicit H-s are not calculated. Returns the same value as
getAtomlogPIncrement(int) |
double |
getAtomlogPIncrement(int index)
Returns the logP increment for the specified atom.
|
java.lang.String |
getErrorMessage()
Returns the calculation error information message if
run()
returned false (calculation error): hydrogen valence error. |
double |
getlogDpI()
Returns the logD value at pI.
|
double |
getlogPMicro()
Returns the micro logP value.
|
double |
getlogPNonionic()
Returns the logP value for the non-ionic form.
|
double |
getlogPTrue()
Returns the most typical logP among logD at pI, micro logP and nonionic logP.
|
java.lang.String |
getProductName()
Returns the product identifier of the plugin as given by
LicenseManager . |
java.lang.Object |
getResult(java.lang.Object type,
int index)
Returns the result item for the specified key 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 . |
Molecule |
getResultMolecule()
Returns the result molecule for display.
|
java.lang.Object[] |
getResultTypes()
Returns the result types.
|
double |
getStandardError(java.lang.Object type,
int index) |
double |
getStructurallogPIncrement()
Returns the structural logP increment.
|
static java.lang.String[] |
getTrainingIds()
Returns the id's of available logP trainings.
|
java.lang.String |
getTypeString(java.lang.Object type)
Returns a string representation of the given type.
|
java.lang.Object[] |
getUserTypes()
Returns the user defined result types.
|
java.lang.String |
getWarningMessage()
Returns the calculation warning message.
|
boolean |
needError() |
boolean |
run()
Runs the logP calculation.
|
void |
setCloridIonConcentration(double c)
Sets the
Cl- concentration (default: 0.1 ). |
void |
setConsiderTautomerization(boolean considerTautomerization)
Sets to consider tautomerization.
|
protected void |
setInputMolecule(Molecule mol)
Sets the input molecule.
|
void |
setlogPMethod(int method)
Deprecated.
Use
setlogPMethod(LogPMethod) instead. |
void |
setlogPMethod(chemaxon.marvin.calculations.LogPMethod method)
Sets the logP calculation method.
|
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 |
setTakeMajorTatomericForm(boolean takeMajorTautomericForm)
Deprecated.
|
void |
setTraining(java.lang.String trainingId)
Sets the user defined training.
|
void |
setTrainingResults(java.io.InputStream trainingResultStream)
Sets the user defined training from a stream.
|
void |
setUserTypes(java.lang.String chtypes)
Sets user types.
|
void |
setWeightOfMethods(double wVG,
double wKLOP,
double wPHYS,
double wUSER)
Deprecated.
This function will not be available from May 2016. Use
setlogPMethod(LogPMethod) instead. |
void |
standardize(Molecule mol)
Standardizes the molecule.
|
arrangeHydrogenIncerments, 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, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, setProgressMonitor, standardizeIonicGroups, standardizeNeutralGroups
@Deprecated public static final int METHOD_VG
LogPMethod.CHEMAXON
instead.setlogPMethod(LogPMethod)
,
Constant Field Values@Deprecated public static final int METHOD_KLOP
LogPMethod
instead.setlogPMethod(LogPMethod)
,
Constant Field Values@Deprecated public static final int METHOD_PHYS
LogPMethod
instead.setlogPMethod(LogPMethod)
,
Constant Field Values@Deprecated public static final int METHOD_USER_DEFINED
LogPMethod.USER_DEFINED
instead.setlogPMethod(LogPMethod)
,
Constant Field Values@Deprecated public static final int METHOD_WEIGHTED
LogPMethod.CONSENSUS
instead.setlogPMethod(LogPMethod)
,
Constant Field Valuespublic java.lang.String getProductName()
LicenseManager
.getProductName
in class CalculatorPlugin
LicenseManager.PARTITIONING_PLUGIN_GROUP
public void setParameters(java.util.Properties params) throws PluginException
setParameters
in class CalculatorPlugin
params
- is the parameter tablePluginException
- 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 setConsiderTautomerization(boolean considerTautomerization)
false
.considerTautomerization
- the calculation will consider tautomerization and resonance if set (true
)@Deprecated public void setTakeMajorTatomericForm(boolean takeMajorTautomericForm)
setConsiderTautomerization(boolean)
false
.takeMajorTautomericForm
- the calculation will be performed on the major
tutomeric form of the input molecule if set (true
)protected final Molecule createModifiedInputMolecule(Molecule mol) throws PluginException
createModifiedInputMolecule
in class CalculatorPlugin
mol
- is the input moleculePluginException
- on errorpublic void setUserTypes(java.lang.String chtypes) throws PluginException
chtypes
- is the type stringPluginException
- for invalid typepublic 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 moleculePluginException
- 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 moleculePluginException
- on errorpublic void setlogPMethod(chemaxon.marvin.calculations.LogPMethod method)
LogPMethod.CONSENSUS
LogPMethod.CHEMAXON
LogPMethod.USER_DEFINED
LogPMethod.CONSENSUS
.method
- is the logP calculation method@Deprecated public void setlogPMethod(int method)
setlogPMethod(LogPMethod)
instead.METHOD_WEIGHTED
.method
- is the logP calculation methodsetWeightOfMethods(double, double, double, double)
@Deprecated public void setWeightOfMethods(double wVG, double wKLOP, double wPHYS, double wUSER)
setlogPMethod(LogPMethod)
instead.METHOD_VG
method = 1
METHOD_KLOP
method = 1
METHOD_PHYS
method = 1
METHOD_USER_DEFINED
method = 0
METHOD_WEIGHTED
method.wVG
- weight of METHOD_VG
methodwKLOP
- weight of METHOD_KLOP
methodwPHYS
- weight of METHOD_PHYS
methodwUSER
- weight of METHOD_USER_DEFINED
methodsetlogPMethod(int)
public static java.lang.String[] getTrainingIds()
public void setTraining(java.lang.String trainingId) throws PluginException
trainingId
- the training idPluginException
- if training id is invalid, or parameter file for training cannot be loadedpublic void setTrainingResults(java.io.InputStream trainingResultStream) throws PluginException
PluginException
- for I/O problems.public 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 java.lang.String getWarningMessage()
getWarningMessage
in class CalculatorPlugin
CalculatorPlugin.getWarningMessage()
public double getlogPMicro()
run()
.public double getlogPNonionic()
run()
.public double getlogDpI()
run()
.public double getlogPTrue()
public double getAtomlogPIncrement(int index)
index
- is the atom index@Deprecated public double getAtomlogPHIncrement(int index)
getAtomlogPIncrement(int)
index
- is the atom indexpublic double getStructurallogPIncrement()
public java.lang.Object[] getResultTypes()
getResultTypes
in class CalculatorPlugin
public java.lang.Object[] getUserTypes()
public java.lang.String getTypeString(java.lang.Object type)
getTypeString
in class CalculatorPlugin
type
- is the type objectpublic int getResultDomain(java.lang.Object type)
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
Returns CalculatorPlugin.ATOM
for type "increments" and
CalculatorPlugin.MOLECULE
otherwise.getResultDomain
in class CalculatorPlugin
type
- is the result typeCalculatorPlugin.MOLECULE
or CalculatorPlugin.ATOM
getResultTypes()
public int getResultCount(java.lang.Object type)
1
otherwise.getResultCount
in class CalculatorPlugin
type
- is the result typegetResultTypes()
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 indexPluginException
- if the result cannot be returnedgetResultTypes()
public double getStandardError(java.lang.Object type, int index)
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 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 CalculatorPlugin
PluginException
- on errorpublic void standardize(Molecule mol)
standardize
in class CalculatorPlugin
mol
- is the molecule to be standardizedpublic boolean needError()