chemaxon.marvin.calculations

Class StructuralFrameworksPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.StructuralFrameworksPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class StructuralFrameworksPlugin
extends CalculatorPlugin

Plugin class to calculate Bemis-Murcko and other structural scaffolds of input molecules. The plugin inside executes a series of atomic (not in chemical sense) operations which are accessible to the user. The configuration which is set either by setParameters( Properties ) or by the individual setters. The operation chain is set up according to the actual configuration by getHost( boolean ).

API usage example:

    // read input molecule
    MolImporter mi = new MolImporter("test.mol");
    Molecule mol = mi.read();
    mi.close();

    // create plugin
    StructuralFrameworksPlugin plugin = new StructuralFrameworksPlugin();

    // set framework type
    plugin.setType(StructuralFrameworksPlugin.FrameworkTypes.bemismurcko );

    // process only the largest fragment
    plugin.setLfin( true );

    // set target molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get result
    Molecule result = plugin.getResultMolecule()

    // print result
    System.out.println("Bemis-Murcko framework in SMILES format: "+result.toFormat("smiles") );
 

Author:

Gabor Imre

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StructuralFrameworksPlugin.FrameworkTypes FrameworkTypes represents the available calculations
static interface	StructuralFrameworksPlugin.VerbosePrinter Verbose printer specification

Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin

CalculatorPlugin.HydrogenData

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

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 Summary

Constructors

Constructor and Description
StructuralFrameworksPlugin()

Method Summary

Modifier and Type	Method and Description
boolean	canRepeat() Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise.
void	checkMolecule(Molecule mol) Checks the input molecule.
java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
Molecule	getResult()
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) Get a calculation result (returned by getResultMolecule() after a run() call in the given format setFormat(String)
int	getResultCount() Returns the number of result items for the first result type.
int	getResultDomain(java.lang.Object type) Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.
Molecule	getResultMolecule() Get result structure
java.lang.Object[]	getResultTypes() Returns the result types.
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
boolean	handlesMultiFragmentMolecules() This plugin handles multifrag molecules.
boolean	run() Run calculation
void	setDehydrogenize(boolean b) Set dehydrogenize parameter
void	setFormat(java.lang.String f) Set output format used by CalculatorPlugin.getResultAsString(int, Object)
void	setHydrogenize(boolean b) Set hydrogenize parameter
protected void	setInputMolecule(Molecule mol) Set input molecule to process
void	setKeepSingleAtom(boolean b) Set behavior on acyclic input
void	setLfin(boolean b) Set handling option for multi fragment (disconnected) inputs
void	setLfout(boolean b) Set handling option for multi fragment (disconnected) results.
void	setOeqcheck(boolean b) Set oeqcheck parameter
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin Accepted parameters: type: [bmf|mcs|sssr|cssr|allringsystems|largestringsystem| largestring|keep] Framework calculation type bmf: Bemis-Murcko framework bmfl: Bemis-Murcko loose framework mcs: Pairwise Maximum Common Substructure sssr: SSSR cssr: CSSR allringsystems: all fused ring systems largestringsystem: largest fused ring system largestring: largest ring keep: no framework reduction; useful for testing pre/post process keepsingleatom: [true|false] If set true then a single atom will be assigned to acyclic fragments.
void	setPruneIn(boolean b) Set prunein parameter
void	setPruneOut(boolean b) Set pruneout parameter
void	setType(StructuralFrameworksPlugin.FrameworkTypes ft) Set framework type to calculate.
void	setVerbosePrinter(StructuralFrameworksPlugin.VerbosePrinter verb) Set or clear verbose printer Verbose messages will be sent to the verbose printer to ease debugging
void	standardize(Molecule mol) Standardize input molecule Standardization currently ungroups SGroups

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

arrangeHydrogenIncerments, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, setProgressMonitor, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

StructuralFrameworksPlugin

public StructuralFrameworksPlugin()

Method Detail

setVerbosePrinter

public void setVerbosePrinter(StructuralFrameworksPlugin.VerbosePrinter verb)

Set or clear verbose printer Verbose messages will be sent to the verbose printer to ease debugging

Parameters:

verb - Verbose printer. Use null to clear verbose.

checkMolecule

public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule. Throws exception if the molecule is not accepted as input molecule, otherwise does nothing (simply returns). In addition to the default implementation (which refuses query molecules, molecules with SRU S-groups, molecules with multicenter S-groups and molecules with coordinate bonds) this method will check if Frameworks can be executed on the structure.

Currently the following cases (in addition to the default behavior) fail:

• mcs Framework calculation needs at least two disconnected fragments. If the molecule contains no atoms or consists of one connected fragment exception is thrown.

Overrides:

checkMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - with error message for the user if the molecule is refused

setInputMolecule

protected void setInputMolecule(Molecule mol)
                         throws PluginException

Set input molecule to process

Specified by:

setInputMolecule in class CalculatorPlugin

Parameters:

mol - Input molecule

Throws:

PluginException

canRepeat

public boolean canRepeat()

Description copied from class: CalculatorPlugin

Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise. For internal use.

Overrides:

canRepeat in class CalculatorPlugin

Returns:

true if allowed, false otherwise

standardize

public void standardize(Molecule mol)

Standardize input molecule
Standardization currently ungroups SGroups

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - Input molecule to standardize

run

public boolean run()
            throws PluginException

Run calculation

Specified by:

run in class CalculatorPlugin

Returns:

true if success

Throws:

PluginException

See Also:

CalculatorPlugin.getErrorMessage()

getResultMolecule

public Molecule getResultMolecule()
                           throws PluginException

Get result structure

Overrides:

getResultMolecule in class CalculatorPlugin

Returns:

The calculated framework

Throws:

PluginException

handlesMultiFragmentMolecules

public boolean handlesMultiFragmentMolecules()

This plugin handles multifrag molecules.

Overrides:

handlesMultiFragmentMolecules in class CalculatorPlugin

Returns:

true

setKeepSingleAtom

public void setKeepSingleAtom(boolean b)

Set behavior on acyclic input

Parameters:

b - If set true then a single atom will be assigned to acyclic fragments. If false then acyclic fragments will be projected to empty structures

setFormat

public void setFormat(java.lang.String f)

Set output format used by CalculatorPlugin.getResultAsString(int, Object)

Parameters:

f - Output format to use

setLfin

public void setLfin(boolean b)

Set handling option for multi fragment (disconnected) inputs

Parameters:

b - If set true then the calculation will run only on the largest input fragment. Note that this necessarily yields the largest scaffold

setLfout

public void setLfout(boolean b)

Set handling option for multi fragment (disconnected) results. Note that disconnected result can be caused by disconnected input or by further modifications of the scaffold generation algorithm

Parameters:

b - If set true then only the largest calculated scaffold will be returned. Note that the returned scaffold not necessarily calculated from the largest fragment.

setType

public void setType(StructuralFrameworksPlugin.FrameworkTypes ft)

Set framework type to calculate.

Note that default framework type is Bemis-Murcko

Parameters:

ft - Framework to calculate

setPruneIn

public void setPruneIn(boolean b)

Set prunein parameter

Parameters:

b - If true then input will be generalizes

setPruneOut

public void setPruneOut(boolean b)

Set pruneout parameter

Parameters:

b - If true then result will be generalized

setHydrogenize

public void setHydrogenize(boolean b)

Set hydrogenize parameter

Parameters:

b - If true then input will be hydrogenized

setDehydrogenize

public void setDehydrogenize(boolean b)

Set dehydrogenize parameter

Parameters:

b - If true then explicit hydrogens will be removed from the input

setOeqcheck

public void setOeqcheck(boolean b)

Set oeqcheck parameter

Parameters:

b - If true then eqivalent result fragments will be filtered

setParameters

public void setParameters(java.util.Properties params)
                   throws PluginException

Sets the input parameters for the plugin Accepted parameters:

• type: [bmf|mcs|sssr|cssr|allringsystems|largestringsystem| largestring|keep] Framework calculation type
  • bmf: Bemis-Murcko framework
  • bmfl: Bemis-Murcko loose framework
  • mcs: Pairwise Maximum Common Substructure
  • sssr: SSSR
  • cssr: CSSR
  • allringsystems: all fused ring systems
  • largestringsystem: largest fused ring system
  • largestring: largest ring
  • keep: no framework reduction; useful for testing pre/post process
• keepsingleatom: [true|false] If set true then a single atom will be assigned to acyclic fragments. If false then acyclic fragments will be projected to empty structures
• lfin: [true|false] If set true then the calculation will run only on the largest input fragment. Note that this necessarily yields the largest scaffold
• lfout: [true|false] If set true then only the largest calculated scaffold will be returned. Note that the returned scaffold not necessarily calculated from the largest fragment.
• prunein: [true|false] Generalize input
• pruneout: [true|false] Generalize output
• hydrogenize: [true|false] Add explicit hydrogens
• dehydrogenize: [true|false] Remove explicit hydrogens
• oeqcheck: [true|false] Remove equivalent output fragments
• format: format to use for string export

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - parameter table

Throws:

PluginException

getProductName

public java.lang.String getProductName()

Description copied from class: CalculatorPlugin

Returns the product identifier of the plugin as given by LicenseManager. The name is used by the CalculatorPlugin.isLicensed() method.

Specified by:

getProductName in class CalculatorPlugin

Returns:

product identifier or a default string

getResultDomain

public int getResultDomain(java.lang.Object type)

Description copied from class: CalculatorPlugin

Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES. The default implementation returns CalculatorPlugin.MOLECULE.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the calculation domain

See Also:

CalculatorPlugin.getResultTypes()

getResultTypes

public java.lang.Object[] getResultTypes()

Description copied from class: CalculatorPlugin

Returns the result types. The default implementation returns null.

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultCount

public int getResultCount()

Description copied from class: CalculatorPlugin

Returns the number of result items for the first result type.

Overrides:

getResultCount in class CalculatorPlugin

Returns:

the number of result items

See Also:

CalculatorPlugin.getResultTypes()

getResult

public Molecule getResult()
                   throws PluginException

Throws:

PluginException

getResult

public java.lang.Object getResult(java.lang.Object type,
                                  int index)
                           throws PluginException

Description copied from class: CalculatorPlugin

Returns the result item for the specified type and index. The default implementation returns null.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the result item for the specified type and index

Throws:

PluginException - if the result cannot be returned

See Also:

CalculatorPlugin.getResultTypes()

getResultAsString

public java.lang.String getResultAsString(java.lang.Object type,
                                          int index,
                                          java.lang.Object result)
                                   throws PluginException

Get a calculation result (returned by getResultMolecule() after a run() call in the given format setFormat(String)

Overrides:

getResultAsString in class CalculatorPlugin

Parameters:

type - this parameter is ignored

index - this patameter is ignored

result - result given by getResultMolecule()

Returns:

String representatin in the given format

Throws:

PluginException

getTypeString

public java.lang.String getTypeString(java.lang.Object type)

Returns a string representation of the given type.

Overrides:

getTypeString in class CalculatorPlugin

Parameters:

type - is the type object

Returns:

the type string