Index (Sugar Removal Utility 1.4.0.0 API)

A C D E G H I L M O P R S U V W
All Classes and Interfaces|All Packages|Constant Field Values

A

ADD_PROPERTY_TO_SUGAR_CONTAINING_MOLECULES_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for whether to add a property to given atom containers to indicate that the structure contains (or contained before removal) sugar moieties (default: true).
addCircularSugarToPatternsList(String) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Allows to add an additional sugar ring (represented as a SMILES string) to the list of circular sugar structures an input molecule is scanned for in circular sugar detection.
addCircularSugarToPatternsList(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Allows to add an additional sugar ring to the list of circular sugar structures an input molecule is scanned for in circular sugar detection.
addLinearSugarToPatternsList(String) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Allows to add an additional linear sugar (represented as SMILES string) to the list of linear sugar structures an input molecule is scanned for in linear sugar detection.
addLinearSugarToPatternsList(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Allows to add an additional linear sugar to the list of linear sugar structures an input molecule is scanned for in linear sugar detection.
addUniqueIndicesToAtoms(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Adds an index as property to all atom objects of the given atom container to identify them uniquely within the atom container and its clones.
ALL - Enum constant in enum class de.unijena.cheminf.deglycosylation.SugarRemovalUtility.PreservationModeOption: Specifies that all structures should be preserved.
areAllExocyclicBondsSingle(IAtomContainer, IAtomContainer, boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Checks whether all exocyclic bonds connected to a given ring fragment of a parent atom container are of single order.
areCircularSugarsWithKetoGroupsDetected() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Specifies whether potential sugar cycles with keto groups are detected in circular sugar detection.
areLinearAcidicSugarsDetected() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Specifies whether linear acidic sugar patterns are currently included in the linear sugar structures used for initial detection of linear sugars in a given molecule.
areLinearSugarsInRingsDetected() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Specifies whether linear sugar structures that are part of a ring should be detected according to the current settings.
areOnlyCircularSugarsWithEnoughExocyclicOxygenAtomsDetected() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Specifies whether detected circular sugar candidates must have a sufficient number of attached exocyclic oxygen atoms in order to be detected as a sugar moiety.
areOnlyCircularSugarsWithOGlycosidicBondDetected() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Specifies whether only circular sugar moieties that are attached to the parent structure or other sugar moieties via an O-glycosidic bond should be detected and subsequently removed.
areOnlyTerminalSugarsRemoved() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Specifies whether only terminal sugar moieties should be removed, i.e.
arePropertiesAddedToSugarContainingMolecules() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Specifies whether a property is added to given atom containers that contain (or contained before removal) sugar moieties.
areSpiroRingsDetectedAsCircularSugars() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Specifies whether spiro rings are included in the initial set of detected rings considered for circular sugar detection.

C

checkUniqueIndicesOfAtoms(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Checks whether all atoms in the given molecule have a unique (in the given molecule) index as property.
CIRCULAR_SUGARS_SMILES - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Circular sugar structures represented as SMILES codes.
clearCircularSugarPatternsList() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Clears all the circular sugar structures an input molecule is scanned for in circular sugar detection.
clearLinearSugarPatternsList() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Clears all the linear sugar structures an input molecule is scanned for in linear sugar detection.
combineOverlappingCandidates(List<IAtomContainer>) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Combines all overlapping (i.e.
compareVersions(String, String) - Static method in class de.unijena.cheminf.deglycosylation.Main: Compares two version strings of the form "x.y.z" of variable length position by position after splitting at each "." and parsing to integers.
CONTAINS_CIRCULAR_SUGAR_PROPERTY_KEY - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Property key to indicate that the structure contains (or contained before removal) circular sugar moieties.
CONTAINS_LINEAR_SUGAR_PROPERTY_KEY - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Property key to indicate that the structure contains (or contained before removal) linear sugar moieties.
CONTAINS_SUGAR_PROPERTY_KEY - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Property key to indicate that the structure contains (or contained before removal) sugar moieties (of any kind).

D

de.unijena.cheminf.deglycosylation - package de.unijena.cheminf.deglycosylation
DETECT_CIRCULAR_SUGARS_ONLY_WITH_ENOUGH_EXOCYCLIC_OXYGEN_ATOMS_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for whether detected circular sugar candidates must have a sufficient number of attached, single-bonded exocyclic oxygen atoms in order to be detected as a sugar moiety (default: true).
DETECT_CIRCULAR_SUGARS_ONLY_WITH_O_GLYCOSIDIC_BOND_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for whether only circular sugar moieties that are attached to the parent structure or other sugar moieties via an O-glycosidic bond should be detected and subsequently removed (default: false).
DETECT_CIRCULAR_SUGARS_WITH_KETO_GROUPS_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for whether sugar-like rings that have keto groups should also be detected as circular sugars (default: false).
DETECT_LINEAR_ACIDIC_SUGARS_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for whether to include the linear acidic sugar patterns in the linear sugar structures used for initial detection of linear sugars in a given molecule (default: false).
DETECT_LINEAR_SUGARS_IN_RINGS_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for whether linear sugar structures that are part of a ring should be detected (default: false).
DETECT_SPIRO_RINGS_AS_CIRCULAR_SUGARS_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for whether to include spiro rings in the initial set of detected rings considered for circular sugar detection (default: false).
detectLinearSugarCandidatesByPatternMatching(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Initial detection of linear sugar candidates by substructure search for the linear sugar patterns in the given molecule.
detectPotentialSugarCycles(IAtomContainer, boolean, boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Detects and returns cycles of the given molecule that are isolated (spiro rings included or not according to the boolean parameter), isomorph to the circular sugar patterns, and only have exocyclic single bonds (keto groups ignored or not according to the boolean parameter).
doesRingHaveEnoughExocyclicOxygenAtoms(int, int) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Simple decision-making function for deciding whether a candidate sugar ring has enough attached, single-bonded exocyclic oxygen atoms according to the set threshold.

E

ESTER_SMARTS_PATTERN - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Daylight SMARTS pattern for matching ester bonds between linear sugars.
ETHER_SMARTS_PATTERN - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Daylight SMARTS pattern for matching ether bonds between linear sugars.
execute() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Executes the application.
EXOCYCLIC_OXYGEN_ATOMS_TO_ATOMS_IN_RING_RATIO_THRESHOLD_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for the minimum ratio of attached exocyclic, single-bonded oxygen atoms to the number of atoms in the candidate circular sugar structure to reach in order to be classified as a sugar moiety if the number of exocyclic oxygen atoms should be evaluated (default: 0.5 so at a minimum 3 connected, exocyclic oxygen atoms for a six-membered ring, for example).

G

generateSubstructureIdentifier(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Creates an identifier string for substructures of a molecule, based on the unique indices of the included atoms.
generateSubstructureIdentifiers(List<IAtomContainer>) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Creates an identifier string for every substructures in the given list, based on the unique indices of the included atoms, respectively, and returns a set of the generated ids.
getCircularSugarCandidates(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Extracts circular sugar moieties from the given molecule, according to the current settings for circular sugar detection.
getCircularSugarPatternsList() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Returns a list of (unique) SMILES strings representing the circular sugar structures an input molecule is scanned for in circular sugar detection.
getDefaultThreshold() - Method in enum class de.unijena.cheminf.deglycosylation.SugarRemovalUtility.PreservationModeOption: Returns the default threshold to preserve a structure (inclusive) for this option.
getExocyclicOxygenAtomCount(IAtomContainer, IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Returns the number of attached exocyclic oxygen atoms of a given ring in the original atom container.
getExocyclicOxygenAtomsToAtomsInRingRatioThresholdSetting() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Returns the currently set minimum ratio of attached, exocyclic, single-bonded oxygen atoms to the number of atoms in the candidate circular sugar structure to reach in order to be classified as a sugar moiety if the number of exocyclic oxygen atoms should be evaluated.
getInstance() - Static method in class org.openscience.cdk.cdkbook.SMILESFormatMatcher
getLinearSugarCandidateMaxSizeSetting() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Returns the currently set maximum number of carbon atoms a linear sugar candidate can have in order to be detected as a sugar moiety (and subsequently be removed).
getLinearSugarCandidateMinSizeSetting() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Returns the currently set minimum number of carbon atoms a linear sugar candidate must have in order to be detected as a sugar moiety (and subsequently be removed).
getLinearSugarCandidates(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Extracts linear sugar moieties from the given molecule, according to the current settings for linear sugar detection.
getLinearSugarPatternsList() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Returns a list of (unique) SMILES strings representing the linear sugar structures an input molecule is scanned for in linear sugar detection.
getNumberOfCircularAndLinearSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Detects circular and linear sugar moieties in the given molecule according to the current settings for circular and linear sugar detection and returns the number of detected moieties.
getNumberOfCircularSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Detects circular sugar moieties in the given molecule according to the current settings for circular sugar detection and returns the number of detected moieties.
getNumberOfLinearSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Detects linear sugar moieties in the given molecule according to the current settings for linear sugar detection and returns the number of detected moieties.
getPreservationModeSetting() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Returns the current setting for how to determine whether a substructure that gets disconnected from the molecule during the removal of a sugar moiety should be preserved or can get removed along with the sugar.
getPreservationModeThresholdSetting() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Returns the current threshold of e.g.

H

hasCircularOrLinearSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Detects circular and linear sugar moieties in the given molecule, according to the current settings for sugar detection.
hasCircularSugarInPatternsList(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Checks whether the given circular sugar is already present in the list of circular sugar structures an input molecule is scanned for in circular sugar detection.
hasCircularSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Detects circular sugar moieties in the given molecule, according to the current settings for circular sugar detection.
hasGlycosidicBond(IAtomContainer, IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Checks all exocyclic connections of the given ring to detect an O-glycosidic bond.
hasLinearSugarInPatternsList(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Checks whether the given linear sugar is already present in the list of linear sugar structures an input molecule is scanned for in linear sugar detection.
hasLinearSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Detects linear sugar moieties in the given molecule, according to the current settings for linear sugar detection.
HEAVY_ATOM_COUNT - Enum constant in enum class de.unijena.cheminf.deglycosylation.SugarRemovalUtility.PreservationModeOption: Specifies that whether a structure is worth preserving will be judged by its heavy atom count.

I

INDEX_PROPERTY_KEY - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Property key for index that is added to any IAtom object in a given IAtomContainer object for internal unique identification of the respective IAtom object.
IS_SPIRO_ATOM_PROPERTY_KEY - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Key for property that is added to IAtom objects that connect a spiro ring system for identification and preservation of these atoms in the removal process.
isLegalTypeOfMoietiesToRemove(int) - Static method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Checks whether the given integer number is mapped to a type of moieties to remove, i.e.
isMoleculeEmptyAfterRemovalOfThisRing(IAtomContainer, IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Checks whether the given molecule would be empty after removal of the given ring.
isQualifiedForGlycosidicBondExemption(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Tests whether the given molecule qualifies for the glycosidic bond exemption.
isTerminal(IAtomContainer, IAtomContainer, List<IAtomContainer>) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Checks whether the given substructure is terminal (i.e.
isTooSmallToPreserve(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Checks whether the given molecule or structure is too small to be kept according to the current preservation mode and threshold setting.

L

LINEAR_ACIDIC_SUGARS_SMILES - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Linear acidic sugar structures represented as SMILES codes.
LINEAR_SUGAR_CANDIDATE_MAX_SIZE_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for the maximum number of carbon atoms a linear sugar candidate can have in order to be detected as a sugar moiety (and subsequently be removed, default: 7, inclusive).
LINEAR_SUGAR_CANDIDATE_MIN_SIZE_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for the minimum number of carbon atoms a linear sugar candidate must have in order to be detected as a sugar moiety (and subsequently be removed, default: 4, inclusive).
LINEAR_SUGARS_SMILES - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Linear sugar structures represented as SMILES codes.

M

main(String[]) - Static method in class de.unijena.cheminf.deglycosylation.Main: Instantiates the SugarRemovalUtilityCmdApplication class and calls its execute() method.
Main - Class in de.unijena.cheminf.deglycosylation: Main entry point for the Sugar Removal Utility command-line application.
Main() - Constructor for class de.unijena.cheminf.deglycosylation.Main
matches(int, String) - Method in class org.openscience.cdk.cdkbook.SMILESFormatMatcher
matches(List<String>) - Method in class org.openscience.cdk.cdkbook.SMILESFormatMatcher
MOLECULAR_WEIGHT - Enum constant in enum class de.unijena.cheminf.deglycosylation.SugarRemovalUtility.PreservationModeOption: Specifies that whether a structure is worth preserving will be judged by its molecular weight.

O

org.openscience.cdk.cdkbook - package org.openscience.cdk.cdkbook

P

partitionAndSortUnconnectedFragments(IAtomContainer) - Static method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Utility method that can be used to partition the unconnected structures in an atom container, e.g.
PEROXIDE_SMARTS_PATTERN - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Daylight SMARTS pattern for matching peroxide bonds between linear sugars.
postProcessAfterRemoval(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Clears away too small structures (according to the set preservation mode) from the given molecule.
PRESERVATION_MODE_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for how to determine whether a substructure that gets disconnected from the molecule during the removal of a sugar moiety should be preserved or can get removed along with the sugar.
printAllMoleculesAsSmiles(List<IAtomContainer>) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Prints all molecules in the given list as unique SMILES representations to System.out.

R

REMOVE_ONLY_TERMINAL_SUGARS_DEFAULT - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Default setting for whether only terminal sugar moieties should be removed, i.e.
removeAndReturnCircularAndLinearSugars(IAtomContainer, boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes circular and linear sugar moieties from the given atom container and returns the resulting aglycon (at list index 0) and the removed sugar moieties.
removeAndReturnCircularSugars(IAtomContainer, boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes circular sugar moieties from the given atom container and returns the resulting aglycon (at list index 0) and the removed circular sugar moieties.
removeAndReturnLinearSugars(IAtomContainer, boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes linear sugar moieties from the given atom container and returns the resulting aglycon (at list index 0) and the removed linear sugar moieties.
removeAtomsOfCircularSugarsFromCandidates(List<IAtomContainer>, IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes all atoms belonging to possible circular sugars, as returned by the method for initial circular sugar detection, from the given linear sugar candidates.
removeCandidatesContainingCircularSugars(List<IAtomContainer>, IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Deprecated.
removeCircularAndLinearSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes circular and linear sugar moieties from the given atom container.
removeCircularAndLinearSugars(IAtomContainer, boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes circular and linear sugar moieties from the given atom container.
removeCircularSugarFromPatternsList(String) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Allows to remove a sugar ring pattern (represented as SMILES string) from the list of circular sugar structures an input molecule is scanned for in circular sugar detection.
removeCircularSugarFromPatternsList(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Allows to remove a sugar ring from the list of circular sugar structures an input molecule is scanned for in circular sugar detection.
removeCircularSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes circular sugar moieties from the given atom container.
removeCircularSugars(IAtomContainer, boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes circular sugar moieties from the given atom container.
removeCircularSugarsFromCandidates(List<IAtomContainer>, IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Deprecated.
removeCyclicAtomsFromSugarCandidates(List<IAtomContainer>, IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes all atoms that are part of a cycle from the given linear sugar candidates.
removeLinearSugarFromPatternsList(String) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Allows to remove a linear sugar pattern (represented as SMILES string) from the list of linear sugar structures an input molecule is scanned for in linear sugar detection.
removeLinearSugarFromPatternsList(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Allows to remove a linear sugar pattern from the list of linear sugar structures an input molecule is scanned for in linear sugar detection.
removeLinearSugars(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes linear sugar moieties from the given atom container.
removeLinearSugars(IAtomContainer, boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes linear sugar moieties from the given atom container.
removeSugarCandidates(IAtomContainer, List<IAtomContainer>) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes the given sugar moieties (or substructures in general) from the given molecule and returns the removed moieties (not the aglycon!).
removeSugarCandidatesWithCyclicAtoms(List<IAtomContainer>, IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Deprecated.
removeTooSmallAndTooLargeCandidates(List<IAtomContainer>) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Discards all linear sugar candidates that are too small or too big according to the current settings.
removeTooSmallDisconnectedStructures(IAtomContainer) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Removes all unconnected fragments that are too small to keep according to the current preservation mode and threshold setting.
restoreDefaultSettings() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets all settings to their default values (see public static constants or enquire via get/is methods).

S

selectBiggestUnconnectedFragment(IAtomContainer) - Static method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Utility method that can be used to select the 'biggest' (i.e.
selectHeaviestUnconnectedFragment(IAtomContainer) - Static method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Utility method that can be used to select the 'heaviest' (i.e.
setAddPropertyToSugarContainingMoleculesSetting(boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the option to add a respective property to given atom containers that contain (or contained before removal) sugar moieties.
setDetectCircularSugarsOnlyWithEnoughExocyclicOxygenAtomsSetting(boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the option to only detect (and subsequently remove) circular sugars that have a sufficient number of attached, exocyclic, single-bonded oxygen atoms.
setDetectCircularSugarsOnlyWithOGlycosidicBondSetting(boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the option to only detect (and subsequently remove) circular sugar moieties that are attached to the parent structure or other sugar moieties via an O-glycosidic bond.
setDetectCircularSugarsWithKetoGroupsSetting(boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the option to detect potential sugar cycles with keto groups as circular sugars in circular sugar detection.
setDetectLinearAcidicSugarsSetting(boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the option to include linear acidic sugar patterns in the linear sugar structures used for initial detection of linear sugars in a given molecule.
setDetectLinearSugarsInRingsSetting(boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the option to detect linear sugar structures that are part of a ring.
setDetectSpiroRingsAsCircularSugarsSetting(boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the option to include spiro rings in the initial set of detected rings considered for circular sugar detection.
setExocyclicOxygenAtomsToAtomsInRingRatioThresholdSetting(double) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the minimum ratio of attached, exocyclic, single-bonded oxygen atoms to the number of atoms in the candidate circular sugar structure to reach in order to be classified as a sugar moiety if the number of exocyclic oxygen atoms should be evaluated.
setLinearSugarCandidateMaxSizeSetting(int) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the maximum number of carbon atoms a linear sugar candidate can have in order to be detected as a sugar moiety (and subsequently be removed).
setLinearSugarCandidateMinSizeSetting(int) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the minimum number of carbon atoms a linear sugar candidate must have in order to be detected as a sugar moiety (and subsequently be removed).
setPreservationModeSetting(SugarRemovalUtility.PreservationModeOption) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the preservation mode for structures that get disconnected by sugar removal and the preservation mode threshold is set to the default value of the given enum constant.
setPreservationModeThresholdSetting(int) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the preservation mode threshold, i.e.
setRemoveOnlyTerminalSugarsSetting(boolean) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sets the option to remove only terminal sugar moieties, i.e.
SMILESFormatMatcher - Class in org.openscience.cdk.cdkbook
SMILESFormatMatcher() - Constructor for class org.openscience.cdk.cdkbook.SMILESFormatMatcher
splitEtherEsterAndPeroxideBonds(List<IAtomContainer>) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Splits all ether, ester, and peroxide bonds in the given linear sugar candidates and separates those that get disconnected in the process.
splitOverlappingCandidatesPseudoRandomly(List<IAtomContainer>) - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Deprecated.
SugarRemovalUtility - Class in de.unijena.cheminf.deglycosylation: The Sugar Removal Utility (SRU) implements a generalized algorithm for automated detection of circular and linear sugars in molecular structures and their removal, as described in "Schaub, J., Zielesny, A., Steinbeck, C., Sorokina, M.
SugarRemovalUtility(IChemObjectBuilder) - Constructor for class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: Sole constructor of this class.
SugarRemovalUtility.PreservationModeOption - Enum Class in de.unijena.cheminf.deglycosylation: Enum with options for how to determine whether a substructure that gets disconnected from the molecule during the removal of a sugar moiety should be preserved or can get removed along with the sugar.
SugarRemovalUtilityCmdApplication - Class in de.unijena.cheminf.deglycosylation: Controller of the Sugar Removal Utility command-line application.
SugarRemovalUtilityCmdApplication(String[]) - Constructor for class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Constructor that parses the command-line arguments and instantiates this class and the SugarRemovalUtility with the given settings.

U

updateLinearSugarPatterns() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtility: All linear sugar patterns represented by atom containers in the respective list are sorted, parsed into actual pattern objects and stored in the internal list for initial linear sugar detection.

V

valueOf(String) - Static method in enum class de.unijena.cheminf.deglycosylation.SugarRemovalUtility.PreservationModeOption: Returns the enum constant of this class with the specified name.
values() - Static method in enum class de.unijena.cheminf.deglycosylation.SugarRemovalUtility.PreservationModeOption: Returns an array containing the constants of this enum class, in the order they are declared.
VERSION - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Version string of this class to print out if -v --version is queried from the command-line.

W

wasHelpOrVersionQueried() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Returns true if the -h --help or -v --version options were used at the command-line.

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