@PublicAPI public class TPSAPlugin extends MajorMicrospeciesAccessorPlugin
Reference:
API usage example:
// read input molecule MolImporter mi = new MolImporter("test.mol"); Molecule mol = mi.read(); mi.close(); // create plugin TPSAPlugin plugin = new TPSAPlugin(); // optional: take major microspecies at pH=7.4 plugin.setpH(7.4); // set target molecule plugin.setMolecule(mol); // run the calculation plugin.run(); // get result double area = plugin.getSurfaceArea(); // print result System.out.println("Polar surface area (pH=7.4): "+area);
For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.
CalculatorPlugin.HydrogenData
ionizer
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 |
---|
TPSAPlugin()
Constructor.
|
Modifier and Type | Method and Description |
---|---|
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. |
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.MOLECULE . |
Molecule |
getResultMolecule()
Returns the result molecule for display.
|
java.lang.Object[] |
getResultTypes()
Returns the result types.
|
double |
getSurfaceArea()
Returns the surface area.
|
double |
getTPSA()
Deprecated.
as of Marvin 4.1, replaced by
getSurfaceArea() |
java.lang.String |
getTypeString(java.lang.Object type)
Returns a string representation of the given type.
|
boolean |
run()
Runs the surface area calculation.
|
void |
setExcludePhosphorus(boolean p)
Sets to exclude phosphorus from PSA calculation.
Default: true , phosphorus i excluded. |
void |
setExcludeSulfur(boolean s)
Sets to exclude sulfur from PSA calculation.
Default: true , sulfur i excluded. |
protected void |
setInputMolecule(Molecule mol)
Sets the input molecule.
|
void |
setParameters(java.util.Properties params)
Sets the input parameters for the plugin.
|
createModifiedInputMolecule, getIonizerErrorMessage, getpH, isLicensed, setpH, standardize
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, 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, standardizeNeutralGroups
public java.lang.String getProductName()
CalculatorPlugin
LicenseManager
.
The name is used by the CalculatorPlugin.isLicensed()
method.getProductName
in class CalculatorPlugin
public void setParameters(java.util.Properties params) throws PluginException
setParameters
in class MajorMicrospeciesAccessorPlugin
params
- is the parameter tablePluginException
- on errorpublic 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 MajorMicrospeciesAccessorPlugin
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 setExcludeSulfur(boolean s)
true
, sulfur i excluded.s
- if true
sulfur is excluded from PSA calculationpublic void setExcludePhosphorus(boolean p)
true
, phosphorus i excluded.p
- if true
phosphorus is excluded from PSA calculationpublic 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 MajorMicrospeciesAccessorPlugin
public java.lang.Object[] getResultTypes()
getResultTypes
in class CalculatorPlugin
public int getResultDomain(java.lang.Object type)
CalculatorPlugin.MOLECULE
.getResultDomain
in class CalculatorPlugin
type
- is the result typeCalculatorPlugin.MOLECULE
getResultTypes()
public int getResultCount(java.lang.Object type)
1
.getResultCount
in class CalculatorPlugin
type
- is the result typegetResultTypes()
@Deprecated public double getTPSA()
getSurfaceArea()
public double getSurfaceArea()
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 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 java.lang.String getTypeString(java.lang.Object type)
getTypeString
in class CalculatorPlugin
type
- is the type objectpublic 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 error