TopologyAnalyser (Marvin API documentation (c) 1998-2012 ChemAxon Ltd.)

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chemaxon.calculations
Class TopologyAnalyser

java.lang.Object
  chemaxon.calculations.TopologyAnalyser

All Implemented Interfaces:: chemaxon.license.Licensable

public class TopologyAnalyser
extends java.lang.Object
implements chemaxon.license.Licensable
extends java.lang.Object
implements chemaxon.license.Licensable

Central class for accessing functions analysing the topology of a molecule.

Since:: Marvin 3.5
Version:: Marvin 5.4, 01/09/2010
Author:: Gyorgy Pirok

Constructor Summary
`TopologyAnalyser()`

Method Summary
`int`	`aliphaticAtomCount()` Deprecated. as of release 5.5, replaced by `Ring.aliphaticAtomCount()`
`int`	`aliphaticBondCount()` Deprecated. as of release 5.5, replaced by `Ring.aliphaticBondCount()`
`int`	`aliphaticRingCount()` Deprecated. as of release 5.5, replaced by `Ring.aliphaticRingCount()`
`int`	`aliphaticRingCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.aliphaticRingCount(int)`
`int[][]`	`aliphaticRings()` Deprecated. as of release 5.5, replaced by `Ring.aliphaticRings()`
`int[][]`	`aliphaticRings(int size)` Deprecated. as of release 5.5, replaced by `Ring.aliphaticRings(int)`
`int`	`aromaticAtomCount()` Deprecated. as of release 5.5, replaced by `Ring.aromaticAtomCount()`
`int`	`aromaticBondCount()` Deprecated. as of release 5.5, replaced by `Ring.aromaticBondCount()`
`int`	`aromaticRingCount()` Deprecated. as of release 5.5, replaced by `Ring.aromaticRingCount()`
`int`	`aromaticRingCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.aromaticRingCount(int)`
`int[][]`	`aromaticRings()` Deprecated. as of release 5.5, replaced by `Ring.aromaticRings()`
`int[][]`	`aromaticRings(int size)` Deprecated. as of release 5.5, replaced by `Ring.aromaticRings(int)`
`int`	`asymmetricAtomCount()` Deprecated. as of release 5.5, replaced by `Stereochemistry.asymmetricAtomCount()`
`int[]`	`asymmetricAtoms()` Deprecated. as of release 5.5, replaced by `Stereochemistry.asymmetricAtoms()`
`int`	`atomCount()` Calculates the number of atoms in the molecule including implicit hydrogens.
`double`	`balabanIndex()` Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
`int`	`bondCount()` Calculates the number of bonds in the molecule including bonds of implicit hydrogens.
`int`	`bondType(int b)` Determines the type of a bond (aromatic bonds are automatically recognized)
`int`	`carboaliphaticRingCount()` Deprecated. as of release 5.5, replaced by `Ring.carboaliphaticRingCount()`
`int`	`carboaromaticRingCount()` Deprecated. as of release 5.5, replaced by `Ring.carboaromaticRingCount()`
`int`	`carboRingCount()` Deprecated. as of release 5.5, replaced by `Ring.carboRingCount()`
`int`	`carboRingCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.carboRingCount(int)`
`int[][]`	`carboRings()` Deprecated. as of release 5.5, replaced by `Ring.carboRings()`
`int[][]`	`carboRings(int size)` Deprecated. as of release 5.5, replaced by `Ring.carboRings(int)`
`int`	`chainAtomCount()` Deprecated. as of release 5.5, replaced by `Ring.chainAtomCount()`
`int`	`chainBondCount()` Deprecated. as of release 5.5, replaced by `Ring.chainBondCount()`
`int`	`chiralCenterCount()` Deprecated. as of release 5.5, replaced by `Stereochemistry.chiralCenterCount()`
`int[]`	`chiralCenters()` Deprecated. as of release 5.5, replaced by `Stereochemistry.chiralCenters()`
`int`	`cyclomaticNumber()` Calculates the smallest number of graph edges which must be removed such that no circuit remains.
`int`	`distanceCount(int a, int d)` Counts the given value in a row of the distance matrix.
`int`	`distanceDegree(int a)` Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
`int`	`eccentricity(int a)` Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
`int`	`fragmentCount()` Calculates the number of fragments (disconnected parts) of the molecule.
`int`	`fusedAliphaticRingCount()` Deprecated. as of release 5.5, replaced by `Ring.fusedAliphaticRingCount()`
`int`	`fusedAliphaticRingCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.fusedAliphaticRingCount(int)`
`int[][]`	`fusedAliphaticRings()` Deprecated. as of release 5.5, replaced by `Ring.fusedAliphaticRings()`
`int[][]`	`fusedAliphaticRings(int size)` Deprecated. as of release 5.5, replaced by `Ring.fusedAliphaticRings(int)`
`int`	`fusedAromaticRingCount()` Deprecated. as of release 5.5, replaced by `Ring.fusedAromaticRingCount()`
`int`	`fusedAromaticRingCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.fusedAromaticRingCount(int)`
`int[][]`	`fusedAromaticRings()` Deprecated. as of release 5.5, replaced by `Ring.fusedAromaticRings()`
`int[][]`	`fusedAromaticRings(int size)` Deprecated. as of release 5.5, replaced by `Ring.fusedAromaticRings(int)`
`int`	`fusedRingCount()` Deprecated. as of release 5.5, replaced by `Ring.fusedRingCount()`
`MoleculeGraph`	`getMolecule()` Retrieves the input molecule
`int[]`	`graphInvariant()`
`double`	`hararyIndex()` Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.
`int`	`heteroaliphaticRingCount()` Deprecated. as of release 5.5, replaced by `Ring.heteroaliphaticRingCount()`
`int`	`heteroaliphaticRingCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.heteroaliphaticRingCount(int)`
`int[][]`	`heteroaliphaticRings()` Deprecated. as of release 5.5, replaced by `Ring.heteroaliphaticRings()`
`int[][]`	`heteroaliphaticRings(int size)` Deprecated. as of release 5.5, replaced by `Ring.heteroaliphaticRings(int)`
`int`	`heteroaromaticRingCount()` Deprecated. as of release 5.5, replaced by `Ring.heteroaromaticRingCount()`
`int`	`heteroaromaticRingCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.heteroaromaticRingCount(int)`
`int[][]`	`heteroaromaticRings()` Deprecated. as of release 5.5, replaced by `Ring.heteroaromaticRings()`
`int[][]`	`heteroaromaticRings(int size)` Deprecated. as of release 5.5, replaced by `Ring.heteroaromaticRings(int)`
`int`	`heteroRingCount()` Deprecated. as of release 5.5, replaced by `Ring.heteroRingCount()`
`int`	`heteroRingCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.heteroRingCount(int)`
`int[][]`	`heteroRings()` Deprecated. as of release 5.5, replaced by `Ring.heteroRings()`
`int[][]`	`heteroRings(int size)` Deprecated. as of release 5.5, replaced by `Ring.heteroRings(int)`
`int`	`hyperWienerIndex()` Calculates the hyper Wiener index of the molecule.
`boolean`	`isAliphaticAtom(int a)` Deprecated. as of release 5.5, replaced by `Ring.isAliphaticAtom(int)`
`boolean`	`isAromaticAtom(int a)` Deprecated. as of release 5.5, replaced by `Ring.isAromaticAtom(int)`
`boolean`	`isAsymmetricAtom(int a)` Deprecated. as of release 5.5, replaced by `Stereochemistry.isAsymmetricAtom(int)`
`boolean`	`isBarredAtom(int a)` Determines if an atom is is part of a certain functional group with high rotational barrier (amides, thioamides, sulphonamides).
`boolean`	`isChainAtom(int a)` Deprecated. as of release 5.5, replaced by `Ring.isChainAtom(int)`
`boolean`	`isChainBond(int b)` Deprecated. as of release 5.5, replaced by `Ring.isChainBond(int)`
`boolean`	`isChiral()` Deprecated. as of release 5.5, replaced by `Stereochemistry.isChiral()`
`boolean`	`isChiralCenter(int a)` Deprecated. as of release 5.5, replaced by `Stereochemistry.isChiralCenter(int)`
`boolean`	`isConnected()` Determines if the molecule is a connected graph or not.
`boolean`	`isConnected(int atom1, int atom2)` Determines if two atoms are members of a connected graph or not.
`boolean`	`isHinderedBiarylBridgeBond(int b)` Determines if a bond bridges two aryl systems having more than two ortho substituents.
`boolean`	`isLicensed()` Returns information about the licensing of the product.
`boolean`	`isRingAtom(int a)` Deprecated. as of release 5.5, replaced by `Ring.isRingAtom(int)`
`boolean`	`isRingBond(int b)` Deprecated. as of release 5.5, replaced by `Ring.isRingBond(int)`
`boolean`	`isRotatableBond(int b)` Determines if a bond is a rotatable or not
`int[]`	`largestRing()` Deprecated. as of release 5.5, replaced by `Ring.largestRing()`
`int`	`largestRingSize()` Deprecated. as of release 5.5, replaced by `Ring.largestRingSize()`
`int`	`largestRingSizeOfAtom(int a)` Deprecated. as of release 5.5, replaced by `Ring.largestRingSizeOfAtom(int)`
`int[]`	`largestRingSystem()` Deprecated. as of release 5.5, replaced by `Ring.largestRingSystem()`
`int`	`largestRingSystemSize()` Deprecated. as of release 5.5, replaced by `Ring.largestRingSystemSize()`
`int`	`plattIndex()` Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.
`double`	`randicIndex()` Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.
`int`	`ringAtomCount()` Deprecated. as of release 5.5, replaced by `Ring.ringAtomCount()`
`int`	`ringBondCount()` Deprecated. as of release 5.5, replaced by `Ring.ringBondCount()`
`int`	`ringCount()` Deprecated. as of release 5.5, replaced by `Ring.ringCount()`
`int`	`ringCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.ringCount(int)`
`int`	`ringCountOfAtom(int a)` Deprecated. as of release 5.5, replaced by `Ring.ringCountOfAtom(int)`
`int[][]`	`rings()` Deprecated. as of release 5.5, replaced by `Ring.rings(int)`
`int[][]`	`rings(int size)` Deprecated. as of release 5.5, replaced by `Ring.rings(int)`
`int`	`ringSystemCount()` Deprecated. as of release 5.5, replaced by `Ring.ringSystemCount()`
`int`	`ringSystemCount(int size)` Deprecated. as of release 5.5, replaced by `Ring.ringSystemCount(int)`
`int[][]`	`ringSystems()` Deprecated. as of release 5.5, replaced by `Ring.ringSystems()`
`int[][]`	`ringSystems(int size)` Deprecated. as of release 5.5, replaced by `Ring.ringSystems(int)`
`int`	`rotatableBondCount()` Calculates the number of rotatable bonds in the molecule.
`void`	`setLicenseEnvironment(java.lang.String env)` Every license can have a modifier environment that's typically an integration environment.
`void`	`setMolecule(MoleculeGraph mol)` Specifies a molecule to calculate with.
`void`	`setMolecule(MoleculeGraph mol, int aromatizationMode)` Specifies a molecule to calculate with.
`int`	`shortestPath(int atom1, int atom2)` Calculates the shortest topological path (number of bonds) between two atoms.
`int[]`	`smallestRing()` Deprecated. as of release 5.5, replaced by `Ring.smallestRing()`
`int`	`smallestRingSize()` Deprecated. as of release 5.5, replaced by `Ring.smallestRingSize()`
`int`	`smallestRingSizeOfAtom(int a)` Deprecated. as of release 5.5, replaced by `Ring.smallestRingSizeOfAtom(int)`
`int[]`	`smallestRingSystem()` Deprecated. as of release 5.5, replaced by `Ring.smallestRingSystem()`
`int`	`smallestRingSystemSize()` Deprecated. as of release 5.5, replaced by `Ring.smallestRingSystemSize()`
`java.lang.String`	`stereo(int a)` Deprecated. as of release 5.5, replaced by `Stereochemistry.stereo(int)`
`java.lang.String`	`stereo(int a1, int a2)` Deprecated. as of release 5.5, replaced by `Stereochemistry.stereo(int, int)`
`int`	`stereoDoubleBondCount()` Deprecated. as of release 5.5, replaced by `Stereochemistry.stereoDoubleBondCount()`
`double`	`stericEffectIndex(int a)` Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances.
`int`	`szegedIndex()` Calculates the Szeged index of the molecule.
`int`	`wienerIndex()` Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.
`int`	`wienerPolarity()` Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

TopologyAnalyser

public TopologyAnalyser()

Method Detail

getMolecule

public MoleculeGraph getMolecule()

Retrieves the input molecule

Returns:: the molecule to calculate with

setMolecule

public void setMolecule(MoleculeGraph mol)

Specifies a molecule to calculate with.

Parameters:: mol - the molecule to calculate with

setMolecule

public void setMolecule(MoleculeGraph mol,
                        int aromatizationMode)

Specifies a molecule to calculate with.

Parameters:

mol - the molecule to calculate with

aromatizationMode - specifies the algorithm for aromatization. Possible values:

AROM_BASIC - Basic aromatization
AROM_GENERAL - General (Daylight compatible) aromatization
AROM_LOOSE - Loose aromatization

aliphaticAtomCount

@Deprecated
public int aliphaticAtomCount()

Deprecated. as of release 5.5, replaced by Ring.aliphaticAtomCount()

Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.

Returns:: number of aliphatic atoms in the molecule

aliphaticBondCount

@Deprecated
public int aliphaticBondCount()

Deprecated. as of release 5.5, replaced by Ring.aliphaticBondCount()

Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.

Returns:: number of aliphatic bonds in the molecule

aliphaticRingCount

@Deprecated
public int aliphaticRingCount()

Deprecated. as of release 5.5, replaced by Ring.aliphaticRingCount()

Calculates the number of aliphatic ring systems of the molecule. Any ring containing an aliphatic atom/bond is considered aliphatic. Thus, aliphatic rings can contain some aromatic bonds too.

Returns:: number of aliphatic rings in the molecule

aliphaticRingCount

@Deprecated
public int aliphaticRingCount(int size)

Deprecated. as of release 5.5, replaced by Ring.aliphaticRingCount(int)

Calculates the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.

Parameters:: size - size of the ring to count
Returns:: number of aliphatic rings with the specified size in the molecule
Since:: version 5.1

aliphaticRings

@Deprecated
public int[][] aliphaticRings()

Deprecated. as of release 5.5, replaced by Ring.aliphaticRings()

Identifies the aliphatic rings in the molecule.

Returns:: aliphatic rings of the molecule (null if the molecule does not contain aliphatic rings)
Since:: version 5.2

aliphaticRings

@Deprecated
public int[][] aliphaticRings(int size)

Deprecated. as of release 5.5, replaced by Ring.aliphaticRings(int)

Indentifies aliphatic rings in the molecule having a given size (number of atoms).

Parameters:: size - size of the aliphatic rings to return
Returns:: aliphatic rings in the molecule having the given size (null if the molecule does not contain aliphatic rings)
Since:: version 5.2

aromaticAtomCount

@Deprecated
public int aromaticAtomCount()

Deprecated. as of release 5.5, replaced by Ring.aromaticAtomCount()

Calculates the number of all aromatic atoms in the molecule.

Returns:: number of aromatic atoms in the molecule

aromaticBondCount

@Deprecated
public int aromaticBondCount()

Deprecated. as of release 5.5, replaced by Ring.aromaticBondCount()

Calculates the number of all aromatic bonds in the molecule.

Returns:: number of aromatic bonds in the molecule

aromaticRingCount

@Deprecated
public int aromaticRingCount()

Deprecated. as of release 5.5, replaced by Ring.aromaticRingCount()

Calculates the number of all aromatic ring systems in the molecule (SSSR). Sometimes, aromatic rings are not part of the standard SSSR ring set. Thus, the sum of the aliphatic and aromatic rings can be greater than the number of rings.

Returns:: number of aromatic rings in the molecule

aromaticRingCount

@Deprecated
public int aromaticRingCount(int size)

Deprecated. as of release 5.5, replaced by Ring.aromaticRingCount(int)

Calculates the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.

Parameters:: size - size of the ring to count
Returns:: number of aromatic rings with the specified size in the molecule
Since:: version 5.1

aromaticRings

@Deprecated
public int[][] aromaticRings()

Deprecated. as of release 5.5, replaced by Ring.aromaticRings()

Identifies the aromatic rings in the molecule.

Returns:: aromatic rings of the molecule (null if the molecule is aliphatic)
Since:: version 5.2

aromaticRings

@Deprecated
public int[][] aromaticRings(int size)

Deprecated. as of release 5.5, replaced by Ring.aromaticRings(int)

Indentifies aromatic rings in the molecule having a given size (number of rings).

Parameters:: size - size of the aromatic rings to return
Returns:: aromatic rings in the molecule having the given size (null if the molecule is aliphatic or contains different sized aromatic rings only)
Since:: version 5.2

asymmetricAtomCount

@Deprecated
public int asymmetricAtomCount()

Deprecated. as of release 5.5, replaced by Stereochemistry.asymmetricAtomCount()

Calculates the number of asymmetric atoms.

Returns:: number of asymmetric atoms

asymmetricAtoms

@Deprecated
public int[] asymmetricAtoms()

Deprecated. as of release 5.5, replaced by Stereochemistry.asymmetricAtoms()

Determines the asymmetric atoms.

Returns:: indexes of asymmetric atoms
Since:: Marvin 5.3

atomCount

public int atomCount()

Calculates the number of atoms in the molecule including implicit hydrogens.

Returns:: number of atoms in the molecule

balabanIndex

public double balabanIndex()

Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.

Returns:: the Balaban index (Integer.MAX_VALUE for disconnected graphs)

bondCount

public int bondCount()

Calculates the number of bonds in the molecule including bonds of implicit hydrogens.

Returns:: number of bonds in the molecule

bondType

public int bondType(int b)

Determines the type of a bond (aromatic bonds are automatically recognized)

Parameters:: b - index of the bond
Returns:: type of the bond Possible values: 1 (single), 2 (double), 3 (triple), coordinate, conjugated and query bond types.

carboaliphaticRingCount

@Deprecated
public int carboaliphaticRingCount()

Deprecated. as of release 5.5, replaced by Ring.carboaliphaticRingCount()

Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).

Returns:: number of carboaliphatic rings

carboaromaticRingCount

@Deprecated
public int carboaromaticRingCount()

Deprecated. as of release 5.5, replaced by Ring.carboaromaticRingCount()

Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).

Returns:: number of carboaromatic rings

carboRingCount

@Deprecated
public int carboRingCount()

Deprecated. as of release 5.5, replaced by Ring.carboRingCount()

Calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only).

Returns:: number of carbocyclic rings

carboRingCount

@Deprecated
public int carboRingCount(int size)

Deprecated. as of release 5.5, replaced by Ring.carboRingCount(int)

Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).

Parameters:: size - size of the rings to count
Returns:: number of carbocyclic rings with the given size
Since:: version 5.2

carboRings

@Deprecated
public int[][] carboRings()

Deprecated. as of release 5.5, replaced by Ring.carboRings()

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).

Returns:: carbocyclic rings (null if no carbocyclic ring found in the molecule.
Since:: version 5.2

carboRings

@Deprecated
public int[][] carboRings(int size)

Deprecated. as of release 5.5, replaced by Ring.carboRings(int)

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.

Parameters:: size - size of the rings to count
Returns:: carbocyclic rings with the given size (null if no carbocyclic ring found in the molecule.
Since:: version 5.2

chainAtomCount

@Deprecated
public int chainAtomCount()

Deprecated. as of release 5.5, replaced by Ring.chainAtomCount()

Calculates the number of chain atoms in the molecule excluding hydrogens.

Returns:: number of chain atoms in the molecule

chainBondCount

@Deprecated
public int chainBondCount()

Deprecated. as of release 5.5, replaced by Ring.chainBondCount()

Calculates the number of chain bonds in the molecule excluding bonds of hydrogen atoms.

Returns:: number of chain bonds in the molecule

chiralCenterCount

@Deprecated
public int chiralCenterCount()

Deprecated. as of release 5.5, replaced by Stereochemistry.chiralCenterCount()

Calculates the number of chiral centers.

Returns:: number of chiral center atoms

chiralCenters

@Deprecated
public int[] chiralCenters()

Deprecated. as of release 5.5, replaced by Stereochemistry.chiralCenters()

Determines the chiral center atoms.

Returns:: indexes of chiral center atoms
Since:: Marvin 5.3

cyclomaticNumber

public int cyclomaticNumber()

Calculates the smallest number of graph edges which must be removed such that no circuit remains. Also known as circuit rank.

Returns:: cyclomatic number of the molecule

distanceCount

public int distanceCount(int a,
                         int d)

Counts the given value in a row of the distance matrix.

Parameters:: a - atom index; d - the distance value to count
Returns:: the distance count of a value for the atom

distanceDegree

public int distanceDegree(int a)

Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.

Parameters:: a - atom index
Returns:: the distance degree of the atom (Integer.MAX_VALUE for disconnected graphs)

eccentricity

public int eccentricity(int a)

Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.

Parameters:: a - atom index
Returns:: the eccentricity value of the atom (Integer.MAX_VALUE for disconnected graphs)

fragmentCount

public int fragmentCount()

Calculates the number of fragments (disconnected parts) of the molecule.

Returns:: number of fragments in the molecule

fusedAliphaticRingCount

@Deprecated
public int fusedAliphaticRingCount()

Deprecated. as of release 5.5, replaced by Ring.fusedAliphaticRingCount()

Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.

Returns:: number of fused aliphatic rings in the molecule

fusedAliphaticRingCount

@Deprecated
public int fusedAliphaticRingCount(int size)

Deprecated. as of release 5.5, replaced by Ring.fusedAliphaticRingCount(int)

Calculates the number of fused aliphatic rings in the molecule (rings s).

Parameters:: size - size of the fused aliphatic rings to count
Returns:: number of fused aliphatic rings having the given size
Since:: version 5.2

fusedAliphaticRings

@Deprecated
public int[][] fusedAliphaticRings()

Deprecated. as of release 5.5, replaced by Ring.fusedAliphaticRings()

Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.

Returns:: atom indexes of the fused aliphatic rings in the molecule
Since:: version 5.2

fusedAliphaticRings

@Deprecated
public int[][] fusedAliphaticRings(int size)

Deprecated. as of release 5.5, replaced by Ring.fusedAliphaticRings(int)

Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).

Parameters:: size - size of the fused aliphatic rings to count
Returns:: atom indexes of the fused aliphatic rings in the molecule having the given number of atoms
Since:: version 5.2

fusedAromaticRingCount

@Deprecated
public int fusedAromaticRingCount()

Deprecated. as of release 5.5, replaced by Ring.fusedAromaticRingCount()

Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.

Returns:: number of fused aromatic rings in the molecule

fusedAromaticRingCount

@Deprecated
public int fusedAromaticRingCount(int size)

Deprecated. as of release 5.5, replaced by Ring.fusedAromaticRingCount(int)

Calculates the number of fused aromatic rings in the molecule (rings s).

Parameters:: size - size of the fused aromatic rings to count
Returns:: number of fused aromatic rings having the given size
Since:: version 5.2

fusedAromaticRings

@Deprecated
public int[][] fusedAromaticRings()

Deprecated. as of release 5.5, replaced by Ring.fusedAromaticRings()

Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.

Returns:: atom indexes of the fused aromatic rings in the molecule
Since:: version 5.2

fusedAromaticRings

@Deprecated
public int[][] fusedAromaticRings(int size)

Deprecated. as of release 5.5, replaced by Ring.fusedAromaticRings(int)

Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).

Parameters:: size - size of the fused aromatic rings to count
Returns:: atom indexes of the fused aromatic rings in the molecule
Since:: version 5.2

fusedRingCount

@Deprecated
public int fusedRingCount()

Deprecated. as of release 5.5, replaced by Ring.fusedRingCount()

Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.

Returns:: number of fused rings in the molecule

graphInvariant

public int[] graphInvariant()

hararyIndex

public double hararyIndex()

Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.

Returns:: the Harary index (Integer.MAX_VALUE for disconnected graphs)

heteroaliphaticRingCount

@Deprecated
public int heteroaliphaticRingCount()

Deprecated. as of release 5.5, replaced by Ring.heteroaliphaticRingCount()

Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).

Returns:: number of heteroaliphatic rings
Since:: version 5.2

heteroaliphaticRingCount

@Deprecated
public int heteroaliphaticRingCount(int size)

Deprecated. as of release 5.5, replaced by Ring.heteroaliphaticRingCount(int)

Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).

Parameters:: size - size of the heteroaliphatc rings to count
Returns:: number of heteroaliphatic rings having the given size
Since:: version 5.2

heteroaliphaticRings

@Deprecated
public int[][] heteroaliphaticRings()

Deprecated. as of release 5.5, replaced by Ring.heteroaliphaticRings()

Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).

Returns:: atom indexes of heteroaliphatic rings
Since:: version 5.2

heteroaliphaticRings

@Deprecated
public int[][] heteroaliphaticRings(int size)

Deprecated. as of release 5.5, replaced by Ring.heteroaliphaticRings(int)

Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).

Parameters:: size - size of the heteroaliphatic rings to count
Returns:: heteroaliphatic rings having the given size
Since:: version 5.2

heteroaromaticRingCount

@Deprecated
public int heteroaromaticRingCount()

Deprecated. as of release 5.5, replaced by Ring.heteroaromaticRingCount()

Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing non-carbon atoms).

Returns:: number of aromatic heterocyclic rings

heteroaromaticRingCount

@Deprecated
public int heteroaromaticRingCount(int size)

Deprecated. as of release 5.5, replaced by Ring.heteroaromaticRingCount(int)

Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).

Parameters:: size - size of the heteroaromatic rings to count
Returns:: number of heteroaromatic rings having the given size
Since:: version 5.2

heteroaromaticRings

@Deprecated
public int[][] heteroaromaticRings()

Deprecated. as of release 5.5, replaced by Ring.heteroaromaticRings()

Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).

Returns:: heteroaromatic rings
Since:: version 5.2

heteroaromaticRings

@Deprecated
public int[][] heteroaromaticRings(int size)

Deprecated. as of release 5.5, replaced by Ring.heteroaromaticRings(int)

Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).

Parameters:: size - size of the heteroaromatic rings to count
Returns:: heteroaromatic rings having the given size
Since:: version 5.2

heteroRingCount

@Deprecated
public int heteroRingCount()

Deprecated. as of release 5.5, replaced by Ring.heteroRingCount()

Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).

Returns:: number of heterocyclic rings

heteroRingCount

@Deprecated
public int heteroRingCount(int size)

Deprecated. as of release 5.5, replaced by Ring.heteroRingCount(int)

Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).

Parameters:: size - size of the rings to count
Returns:: number of heterocyclic rings
Since:: version 5.2

heteroRings

@Deprecated
public int[][] heteroRings()

Deprecated. as of release 5.5, replaced by Ring.heteroRings()

Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).

Returns:: heterocyclic rings (null of no heterocyclic ring found in the molecule.
Since:: version 5.2

heteroRings

@Deprecated
public int[][] heteroRings(int size)

Deprecated. as of release 5.5, replaced by Ring.heteroRings(int)

Indentifies hetero rings in the molecule having a given size (number of atoms).

Parameters:: size - size of the hetero rings to return (zero returns all)
Returns:: hetero rings in the molecule having the given size (null if the molecule does not contain hetero rings)
Since:: version 5.2

hyperWienerIndex

public int hyperWienerIndex()

Calculates the hyper Wiener index of the molecule.

Returns:: the hyper Wiener index (Integer.MAX_VALUE for disconnected graphs)

isAliphaticAtom

@Deprecated
public boolean isAliphaticAtom(int a)

Deprecated. as of release 5.5, replaced by Ring.isAliphaticAtom(int)

Determines if an atom is a member of an aromatic ring or not.

Parameters:: a - index of the atom
Returns:: true if the atom is aliphatic.

isAromaticAtom

@Deprecated
public boolean isAromaticAtom(int a)

Deprecated. as of release 5.5, replaced by Ring.isAromaticAtom(int)

Determines if an atom is a member of an aromatic ring or not.

Parameters:: a - index of the atom
Returns:: true if the atom is aromatic.

isAsymmetricAtom

@Deprecated
public boolean isAsymmetricAtom(int a)

Deprecated. as of release 5.5, replaced by Stereochemistry.isAsymmetricAtom(int)

Determines if an atom is asymmetric or not. Asymmetric atoms have four different ligands.

Parameters:: a - index of the atom
Returns:: true if the atom is asymmetric.

isBarredAtom

public boolean isBarredAtom(int a)

Determines if an atom is is part of a certain functional group with high rotational barrier (amides, thioamides, sulphonamides).

Parameters:: a - index of the atom
Returns:: true if the atom is a barred atom.

isChainAtom

@Deprecated
public boolean isChainAtom(int a)

Deprecated. as of release 5.5, replaced by Ring.isChainAtom(int)

Determines if an atom a ring bond or a chain bond.

Parameters:: a - index of the atom
Returns:: true if the atom is a chain atom (has no ring bonds).

isChainBond

@Deprecated
public boolean isChainBond(int b)

Deprecated. as of release 5.5, replaced by Ring.isChainBond(int)

Determines if a bond is a ring bond or a chain bond.

Parameters:: b - index of the bond
Returns:: true if the bond is a chain bond, false if ring bond

isChiral

@Deprecated
public boolean isChiral()

Deprecated. as of release 5.5, replaced by Stereochemistry.isChiral()

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

Returns:: true if the molecule is chiral.

isChiralCenter

@Deprecated
public boolean isChiralCenter(int a)

Deprecated. as of release 5.5, replaced by Stereochemistry.isChiralCenter(int)

Determines if an atom can be a tetrahedral stereogenic center.

Parameters:: a - index of the atom
Returns:: true if the atom is stereogenic.

isConnected

public boolean isConnected()

Determines if the molecule is a connected graph or not. There is a path from any node to any other node in the graph.

Returns:: true if the graph is connected, false if the graph is disconnected.

isConnected

public boolean isConnected(int atom1,
                           int atom2)

Determines if two atoms are members of a connected graph or not.

Parameters:: atom1 - index of the first atom; atom2 - index of the second atom
Returns:: True if the two atoms are located on a connected graphs, false if the atoms are disconnected.

isHinderedBiarylBridgeBond

public boolean isHinderedBiarylBridgeBond(int b)

Determines if a bond bridges two aryl systems having more than two ortho substituents.

Parameters:: b - index of the bond
Returns:: true if the bond is a hindered biaryl bridge bond, false if not

isRingAtom

@Deprecated
public boolean isRingAtom(int a)

Deprecated. as of release 5.5, replaced by Ring.isRingAtom(int)

Determines if an atom a ring bond or a chain bond.

Parameters:: a - index of the atom
Returns:: true if the atom is a ring atom (has no ring bonds).

isRingBond

@Deprecated
public boolean isRingBond(int b)

Deprecated. as of release 5.5, replaced by Ring.isRingBond(int)

Determines if a bond is a ring bond or a chain bond.

Parameters:: b - index of the bond
Returns:: true if the bond is a ring bond, false if chain bond

isRotatableBond

public boolean isRotatableBond(int b)

Determines if a bond is a rotatable or not

Parameters:: b - index of the bond
Returns:: true if the bond is a rotatable bond, false otherwise

largestRing

@Deprecated
public int[] largestRing()

Deprecated. as of release 5.5, replaced by Ring.largestRing()

Identifies the atoms of the largest ring (number of atoms) in the molecule.

Returns:: atom indexes of the largest ring in the molecule (null when acyclic)
Since:: version 5.2

largestRingSize

@Deprecated
public int largestRingSize()

Deprecated. as of release 5.5, replaced by Ring.largestRingSize()

Calculates the size of the largest ring in the molecule (SSSR based).

Returns:: size of the largest ring in the molecule (0 when acyclic)

largestRingSizeOfAtom

@Deprecated
public int largestRingSizeOfAtom(int a)

Deprecated. as of release 5.5, replaced by Ring.largestRingSizeOfAtom(int)

Calculates the size of the largest ring an atom is a member of (SSSR based).

Returns:: size of the largest ring (0 when atom is not a member of a ring)

largestRingSystem

@Deprecated
public int[] largestRingSystem()

Deprecated. as of release 5.5, replaced by Ring.largestRingSystem()

Identifies the atoms of the largest ring system (number of rings) in the molecule.

Returns:: atom indexes of the largest ring system in the molecule (null when acyclic)
Since:: version 5.2

largestRingSystemSize

@Deprecated
public int largestRingSystemSize()

Deprecated. as of release 5.5, replaced by Ring.largestRingSystemSize()

Calculates the size of the largest ring system (number of rings) in the molecule.

Returns:: size of the largest ring system in the molecule (0 when acyclic)
Since:: version 5.1

plattIndex

public int plattIndex()

Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.

Returns:: the Platt index

randicIndex

public double randicIndex()

Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.

Returns:: the Randic index

ringAtomCount

@Deprecated
public int ringAtomCount()

Deprecated. as of release 5.5, replaced by Ring.ringAtomCount()

Calculates the number of ring atoms in the molecule.

Returns:: number of ring atoms in the molecule

ringBondCount

@Deprecated
public int ringBondCount()

Deprecated. as of release 5.5, replaced by Ring.ringBondCount()

Calculates the number of ring bonds in the molecule.

Returns:: number of ring bonds in the molecule

ringCount

@Deprecated
public int ringCount()

Deprecated. as of release 5.5, replaced by Ring.ringCount()

Calculates the number of rings (SSSR smallest set of smallest rings) in the molecule.

Returns:: number of rings in the molecule

ringCount

@Deprecated
public int ringCount(int size)

Deprecated. as of release 5.5, replaced by Ring.ringCount(int)

Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.

Parameters:: size - size of the ring to count
Returns:: number of rings having the spedified size

ringCountOfAtom

@Deprecated
public int ringCountOfAtom(int a)

Deprecated. as of release 5.5, replaced by Ring.ringCountOfAtom(int)

Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.

Parameters:: a - index of the atom
Returns:: number of rings the atom is a member of

rings

@Deprecated
public int[][] rings()

Deprecated. as of release 5.5, replaced by Ring.rings(int)

Identifies the rings in the molecule.

Returns:: rings of the molecule (null if the molecule is acyclic)
Since:: version 5.2

rings

@Deprecated
public int[][] rings(int size)

Deprecated. as of release 5.5, replaced by Ring.rings(int)

Identifies rings in the molecule having a given size.

Parameters:: size - size of the ring systems to return
Returns:: rings of the molecule having the given size (null if the molecule is acyclic or contains different rings only)
Since:: version 5.2

ringSystemCount

@Deprecated
public int ringSystemCount()

Deprecated. as of release 5.5, replaced by Ring.ringSystemCount()

Calculates the number of ring systems. Fused and spiro rings belong to one ring system.

Returns:: number of ring systems in the molecule
Since:: version 5.1

ringSystemCount

@Deprecated
public int ringSystemCount(int size)

Deprecated. as of release 5.5, replaced by Ring.ringSystemCount(int)

Identifies ring systems having a given size (number of rings) in the molecule. Fused and spiro rings belong to one ring system.

Parameters:: size - size of the ring to count
Returns:: number of ring systems with the specified size in the molecule
Since:: version 5.1

ringSystems

@Deprecated
public int[][] ringSystems()

Deprecated. as of release 5.5, replaced by Ring.ringSystems()

Identifies the ring systems in the molecule. Fused and spiro rings belong to one ring system.

Returns:: ring systems in the molecule (null if the molecule is acyclic)
Since:: version 5.2

ringSystems

@Deprecated
public int[][] ringSystems(int size)

Deprecated. as of release 5.5, replaced by Ring.ringSystems(int)

Indentifies the ring systems in the molecule having a given size (number of rings). Fused and spiro rings belong to one ring system.

Parameters:: size - size of the ring systems to return
Returns:: ring systems in the molecule having the given size (null if the molecule is acyclic or contains different rings only)
Since:: version 5.2

rotatableBondCount

public int rotatableBondCount()

Calculates the number of rotatable bonds in the molecule.

Returns:: number of rotatable bonds in the molecule

shortestPath

public int shortestPath(int atom1,
                        int atom2)

Calculates the shortest topological path (number of bonds) between two atoms. It returns Integer.MAX_VALUE for atoms of disconnected structures.

Parameters:: atom1 - Index of the first atom.; atom2 - Index of the second atom.
Returns:: The shortest path between two atoms.

smallestRing

@Deprecated
public int[] smallestRing()

Deprecated. as of release 5.5, replaced by Ring.smallestRing()

Identifies the smallest ring (number of atoms) in the molecule.

Returns:: atom indexes of the smallest ring in the molecule (null when acyclic)
Since:: version 5.2

smallestRingSize

@Deprecated
public int smallestRingSize()

Deprecated. as of release 5.5, replaced by Ring.smallestRingSize()

Calculates the size of the smallest ring in the molecule.

Returns:: size of the smallest ring in the molecule (0 when acyclic)

smallestRingSizeOfAtom

@Deprecated
public int smallestRingSizeOfAtom(int a)

Deprecated. as of release 5.5, replaced by Ring.smallestRingSizeOfAtom(int)

Calculates the size of the smallest ring an atom is a member of.

Returns:: size of the smallest ring (0 when atom is not a member of a ring)

smallestRingSystem

@Deprecated
public int[] smallestRingSystem()

Deprecated. as of release 5.5, replaced by Ring.smallestRingSystem()

Identifies the smallest ring system (number of rings) in the molecule.

Returns:: atom indexes of the smallest ring system in the molecule (null when acyclic)
Since:: version 5.2

smallestRingSystemSize

@Deprecated
public int smallestRingSystemSize()

Deprecated. as of release 5.5, replaced by Ring.smallestRingSystemSize()

Calculates the size of the smallest ring system (number of rings) in the molecule.

Returns:: size of the smallest ring system in the molecule (0 when acyclic)
Since:: version 5.1

stereo

@Deprecated
public java.lang.String stereo(int a)

Deprecated. as of release 5.5, replaced by Stereochemistry.stereo(int)

Calculates absolute stereo configuration of the given atom. Returns "R" or "S" correspondingly, if the atom is stereo, otherwise it returns an empty string,

Parameters:: a - index of the atom
Returns:: the absolute stereo configuration of the atom

stereo

@Deprecated
public java.lang.String stereo(int a1,
                                          int a2)

Deprecated. as of release 5.5, replaced by Stereochemistry.stereo(int, int)

Calculates absolute stereo configuration of the given double bond. Returns "E" or "Z" correspondingly, if the bond is a stereo double bond, otherwise it returns an empty string. Double bonds in small rings are not considered stereo bonds.

Parameters:: a1 - index of the atom at one end of the double bond; a2 - index of the atom at the other end of the double bond
Returns:: the absolute stereo configuration of the atom

stereoDoubleBondCount

@Deprecated
public int stereoDoubleBondCount()

Deprecated. as of release 5.5, replaced by Stereochemistry.stereoDoubleBondCount()

Calculates the number of stereo double bonds.

Returns:: number of stereo double bonds atoms

stericEffectIndex

public double stericEffectIndex(int a)

Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances. The stericEffectIndex is related to the steric hindrance of the given atom.

Parameters:: a - index of the atom
Returns:: the topological steric effect index of the atom

szegedIndex

public int szegedIndex()

Calculates the Szeged index of the molecule. The Szeged index is based on the Wiener number, which is calculated by simply counting the number of nodes on both sides of each edge (and sum these counts). The Szeged index extends the Wiener number for cyclic graphs by counting those nodes only which are nearer to the given side of the edge than to the other. Unreachable nodes (disconnected graphs) or those at equidistance position to both sides of the given edge are not taken into account.

Returns:: the Szeged index

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Description copied from interface: chemaxon.license.Licensable

Every license can have a modifier environment that's typically an integration environment. All being Licensable should be prepared to store and show a set environment to the LicenseHandler. Example implementation:

 private String licenseEnvironment = "";
 public void setLicenseEnvironment(String env) {
     licenseEnvironment = env;
 }

Specified by:: setLicenseEnvironment in interface chemaxon.license.Licensable

Parameters:: env - environment String to be stored and passed to the LicenseHandler in the isLicensed method

isLicensed

public boolean isLicensed()

Description copied from interface: chemaxon.license.Licensable

Returns information about the licensing of the product. Example implementation:


 return LicenseHandler.isLicensed( LicenseHandler.MY_IDENTIFIER, licenseEnvironment );

Specified by:: isLicensed in interface chemaxon.license.Licensable

Returns:: true if the product is correctly licensed

wienerIndex

public int wienerIndex()

Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.

Returns:: the Wiener index (Integer.MAX_VALUE for disconnected graphs)

wienerPolarity

public int wienerPolarity()

Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.

Returns:: the Wiener polarity number

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chemaxon.calculations Class TopologyAnalyser

TopologyAnalyser

getMolecule

setMolecule

setMolecule

aliphaticAtomCount

aliphaticBondCount

aliphaticRingCount

aliphaticRingCount

aliphaticRings

aliphaticRings

aromaticAtomCount

aromaticBondCount

aromaticRingCount

aromaticRingCount

aromaticRings

aromaticRings

asymmetricAtomCount

asymmetricAtoms

atomCount

balabanIndex

bondCount

bondType

carboaliphaticRingCount

carboaromaticRingCount

carboRingCount

carboRingCount

carboRings

carboRings

chainAtomCount

chainBondCount

chiralCenterCount

chiralCenters

cyclomaticNumber

distanceCount

distanceDegree

eccentricity

fragmentCount

fusedAliphaticRingCount

fusedAliphaticRingCount

fusedAliphaticRings

fusedAliphaticRings

fusedAromaticRingCount

fusedAromaticRingCount

fusedAromaticRings

fusedAromaticRings

fusedRingCount

graphInvariant

hararyIndex

heteroaliphaticRingCount

heteroaliphaticRingCount

heteroaliphaticRings

heteroaliphaticRings

heteroaromaticRingCount

heteroaromaticRingCount

heteroaromaticRings

heteroaromaticRings

heteroRingCount

heteroRingCount

heteroRings

heteroRings

hyperWienerIndex

isAliphaticAtom

isAromaticAtom

isAsymmetricAtom

isBarredAtom

isChainAtom

isChainBond

isChiral

isChiralCenter

isConnected

isConnected

isHinderedBiarylBridgeBond

isRingAtom

isRingBond

isRotatableBond

largestRing

largestRingSize

largestRingSizeOfAtom

largestRingSystem

chemaxon.calculations
Class TopologyAnalyser