chemaxon.checkers

Class StructureCheckerHelper

java.lang.Object

chemaxon.checkers.StructureCheckerHelper

public class StructureCheckerHelper
extends Object

This helper class contains utility functions used by StructureChecker instances providing constants and utility functions.

Since:

Marvin 5.4

Version:

5.7

Author:

Attila Szabo

Field Summary

Fields

Modifier and Type	Field and Description
static double	MAXIMAL_DISTANCE_LIMIT This constant represents the the upper bound of bond length for ChemAxon built-in StructureChecker implementations
static double	MINIMAL_ATOM_DISTANCE_LIMIT This constant represents the minimal allowed atom distance (distance here means euclidean distance) between two atoms for ChemAxon built-in StructureChecker implementations
static double	MINIMAL_DISTANCE_LIMIT This constant represents the minimal allowed bond distance (distance here means euclidean distance) between two bonds and the lower bound of bond length for ChemAxon built-in StructureChecker implementations

Constructor Summary

Constructors

Constructor and Description
StructureCheckerHelper()

Method Summary

Methods

Modifier and Type	Method and Description
static double	calculateCosAFromScalarMul(MolBond bond1, MolBond bond2) Calculate the cosines value of the angle between the bonds from the scalar multiplication of the bonds.
static List<MolBond>	createNeighbourBonds(Molecule molecule, MolBond bond, boolean ignoreRingBonds) This method returns a List of MolBond which contains all bonds which are in isNeighbour relation with the MolBond instance represented by parameter bond
static double	distance(MolAtom atom1, MolAtom atom2) Calculates the distance of two atoms.
static chemaxon.util.abbrevgroup.AbbrevGroupStorage	getDefaultAbbrevgroups() Imports default and user abbreviations and returns them in a AbbrevGroupStorage.
static boolean	isAbsoluteStereoRelevant(Molecule mol) Determines if molecule contains a stereo center with no enhanced stereo property.
static boolean	isAromatic(int[] is, Molecule mol) Determines if a ring in the molecule is aromatic or not
static boolean	isChiral(Molecule mol) Determines if the molecule contains an atom with R or S stereo configuration.
static boolean	isDaylightFormatWithoutOptions(String format) Returns true if daylight format with options supported, false otherwise
static boolean	isTerminal(MolBond molBond) This method returns true if the MolBond represented by molBond parameter is terminal in a Molecule structure, false otherwise
static boolean	ringHasOnlyOneNeighbour(int[] is, Molecule mol, MolAtom atom) This function determines if the ring (indexed with idx parameter) has only one neighbour (and this neighbour is the the atom parameter) or not.

Methods inherited from class java.lang.Object

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

Field Detail

MINIMAL_ATOM_DISTANCE_LIMIT

public static final double MINIMAL_ATOM_DISTANCE_LIMIT

This constant represents the minimal allowed atom distance (distance here means euclidean distance) between two atoms for ChemAxon built-in StructureChecker implementations

See Also:

Constant Field Values

MINIMAL_DISTANCE_LIMIT

public static final double MINIMAL_DISTANCE_LIMIT

This constant represents the minimal allowed bond distance (distance here means euclidean distance) between two bonds and the lower bound of bond length for ChemAxon built-in StructureChecker implementations

See Also:

Constant Field Values

MAXIMAL_DISTANCE_LIMIT

public static final double MAXIMAL_DISTANCE_LIMIT

This constant represents the the upper bound of bond length for ChemAxon built-in StructureChecker implementations

See Also:

Constant Field Values

Constructor Detail

StructureCheckerHelper

public StructureCheckerHelper()

Method Detail

distance

public static double distance(MolAtom atom1,
              MolAtom atom2)

Calculates the distance of two atoms. (Distance here is the euclidean distance)

Parameters:

atom1 - is a MolAtom instance

atom2 - is a MolAtom instance

Returns:

the distance of the two atoms

createNeighbourBonds

public static List<MolBond> createNeighbourBonds(Molecule molecule,
                                 MolBond bond,
                                 boolean ignoreRingBonds)

This method returns a List of MolBond which contains all bonds which are in isNeighbour relation with the MolBond instance represented by parameter bond

Parameters:

molecule - is a Molecule instance which contains the bonds

bond - is a MolBond instance. The method will return the neighbors of this bond.

ignoreRingBonds - is a boolean parameter. If this parameter is true no ring bonds will treated as neighbor

Returns:

a List of MolBond which contains all bonds which are in isNeighbour relation with the MolBond instance represented by parameter bond

getDefaultAbbrevgroups

public static chemaxon.util.abbrevgroup.AbbrevGroupStorage getDefaultAbbrevgroups()

Imports default and user abbreviations and returns them in a AbbrevGroupStorage.

Returns:

default and user abbreviations in a AbbrevGroupStorage

isTerminal

public static boolean isTerminal(MolBond molBond)

This method returns true if the MolBond represented by molBond parameter is terminal in a Molecule structure, false otherwise

Parameters:

molBond - a MolBond instance

Returns:

true if the MolBond represented by molBond parameter is terminal in a Molecule structure, false otherwise

isAbsoluteStereoRelevant

public static boolean isAbsoluteStereoRelevant(Molecule mol)

Determines if molecule contains a stereo center with no enhanced stereo property. Absolute stereo makes sense only if this method returns true.

Parameters:

mol - is the molecule

Returns:

true if molecule contains a stereo center with no enhanced stereo property

isChiral

public static boolean isChiral(Molecule mol)

Determines if the molecule contains an atom with R or S stereo configuration.

Parameters:

mol - is the Molecule instance

Returns:

true if the molecule is chiral.

isAromatic

public static boolean isAromatic(int[] is,
                 Molecule mol)

Determines if a ring in the molecule is aromatic or not

Parameters:

is - an index array containing the indices of the ring in the molecule

mol - a Molecule instance which contains the ring

Returns:

true if the ring is aromatic false otherwise

ringHasOnlyOneNeighbour

public static boolean ringHasOnlyOneNeighbour(int[] is,
                              Molecule mol,
                              MolAtom atom)

This function determines if the ring (indexed with idx parameter) has only one neighbour (and this neighbour is the the atom parameter) or not.

Parameters:

is - an index array containing the indices of the ring in the molecule

mol - is a Molecule instance which contains the ring and the atom

atom - is a MolAtom instance

Returns:

true if the atom is the only neighbour of the ring false otherwise

calculateCosAFromScalarMul

public static double calculateCosAFromScalarMul(MolBond bond1,
                                MolBond bond2)

Calculate the cosines value of the angle between the bonds from the scalar multiplication of the bonds.

Parameters:

bond1 - the first bond

bond2 - the second bond

Returns:

the cosines value of the angle between the bonds

isDaylightFormatWithoutOptions

public static boolean isDaylightFormatWithoutOptions(String format)

Returns true if daylight format with options supported, false otherwise

Parameters:

format - the molecule format represented as a String object

Returns:

true if daylight format with options supported, false otherwise