chemaxon.struc
Interface Smolecule

All Superinterfaces:

Incomplecule

All Known Subinterfaces:

WSmolecule

public interface Smolecule
extends Incomplecule

Array-based abstract molecule class.

PLEASE DO NOT IMPLEMENT THIS INTERFACE! It may get more abstract methods in later versions.

Since:

Marvin 5.2.2, 04/24/2009

Version:

5.3, 06/03/2009

Author:

Peter Csizmadia

Field Summary

static int	A_ALL Use all atom and bond property arrays.
static int	A_ASTEREO Use atom stereo properties arrays, equals A_PARITY|A_CHIRALITY.
static int	A_ATOMMAP Use atom type array.
static int	A_BOND Use arrays to store bonds.
static int	A_CHARGE Use charge array.
static int	A_CHIRALITY Chirality.
static int	A_EXPLH Use explicit Hydrogen count array.
static int	A_HYBRIDIZATION Use hybridization state array.
static int	A_IMPLH Use implicit Hydrogen count array.
static int	A_MASSNO Use mass number array.
static int	A_PARITY Atom parity.
static int	A_RADICAL Use radical array.
static int	A_RGROUP Use R-group ID array.
static int	A_VALENCE Use valence array.
static int	RGROUP_MAX Maximum R-group index (32767).

Method Summary

boolean	areNeighbors(int atom1, int atom2) Tests whether two atoms are connected.
chemaxon.struc.Gearch	gearch() Gets graph search algorithms.
int	getArrayFlags() Gets info about the used arrays.
int	getAtom1(int i) Gets the index of the first atom of the specified bond.
int	getAtom2(int i) Gets the index of the second atom of the specified bond.
int	getAtomMap(int atom) Gets the atom-atom mapping number.
int	getAtomStereo(int atom) Gets atom stereo properties as an integer.
int	getAtomType(int atom) Gets the type of an atom.
int	getBondFlags(int i) Gets the bond descriptor flags.
int	getBondIndex(int atom1, int atom2) Gets the index of the bond between the specified atoms.
int	getBondType(int i) Gets the type of a bond.
int	getBondType(int atom1, int atom2) Gets the type of a bond between the two specified atoms.
int	getCharge(int atom) Gets the charge of an ion.
int	getChirality(int atom) Gets the chirality of an atom.
int	getExplicitHcount(int atom) Gets the number of explicit hydrogen atom neighbors of the given atom.
int	getHcount(int atom) Gets the total number of hydrogens of an atom.
int	getHybridizationState(int atom) Gets the hybridization state of an atom.
int	getImplicitHcount() Gets the total number of implicit Hydrogens.
int	getImplicitHcount(int atom) Gets the number of implicit Hydrogens of an atom.
int	getMassno(int atom) Gets the mass number of an atom.
int	getNeighbor(int atom, int i) Gets the index of a neighbor of an atom.
int	getNeighborCount(int atom) Gets the number of neighbors of an atom.
int	getParity(int atom) Gets the parity of an atom.
int	getQPropAsInt(int atom, java.lang.String name) Gets a query property as an integer.
int	getRadical(int atom) Gets the radical value of an atom.
int	getRgroupId(int atom) Gets the R-group identifier of an atom.
int	getValence(int atom) Gets the valence.
boolean	inAtomList(int atom, int atno) Tests whether the specified element is in the atom list.

Methods inherited from interface chemaxon.struc.Incomplecule

getAtomCount, getBondCount, getName, properties

Field Detail

A_BOND

static final int A_BOND

Use arrays to store bonds.

See Also:

Constant Field Values

A_CHARGE

static final int A_CHARGE

Use charge array.

See Also:

Constant Field Values

A_RADICAL

static final int A_RADICAL

Use radical array.

See Also:

Constant Field Values

A_HYBRIDIZATION

static final int A_HYBRIDIZATION

Use hybridization state array.

See Also:

Constant Field Values

A_MASSNO

static final int A_MASSNO

Use mass number array.

See Also:

Constant Field Values

A_IMPLH

static final int A_IMPLH

Use implicit Hydrogen count array.

See Also:

Constant Field Values

A_EXPLH

static final int A_EXPLH

Use explicit Hydrogen count array.

See Also:

Constant Field Values

A_VALENCE

static final int A_VALENCE

Use valence array.

See Also:

Constant Field Values

A_ATOMMAP

static final int A_ATOMMAP

Use atom type array.

See Also:

Constant Field Values

A_RGROUP

static final int A_RGROUP

Use R-group ID array.

See Also:

Constant Field Values

A_PARITY

static final int A_PARITY

Atom parity.

See Also:

A_ASTEREO, Constant Field Values

A_CHIRALITY

static final int A_CHIRALITY

Chirality.

See Also:

A_ASTEREO, Constant Field Values

A_ASTEREO

static final int A_ASTEREO

Use atom stereo properties arrays, equals A_PARITY|A_CHIRALITY.

See Also:

Constant Field Values

A_ALL

static final int A_ALL

Use all atom and bond property arrays.

See Also:

Constant Field Values

RGROUP_MAX

static final int RGROUP_MAX

Maximum R-group index (32767).

See Also:

getRgroupId(int), Constant Field Values

Method Detail

getArrayFlags

int getArrayFlags()

Gets info about the used arrays.

Returns:

the array info

getAtomType

int getAtomType(int atom)

Gets the type of an atom.

Parameters:

atom - the atom index

Returns:

the atom type

getCharge

int getCharge(int atom)

Gets the charge of an ion.

Parameters:

atom - the atom index

Returns:

the charge

See Also:

A_CHARGE

getRadical

int getRadical(int atom)

Gets the radical value of an atom.

Parameters:

atom - the atom index

Returns:

the radical value

See Also:

A_RADICAL

getMassno

int getMassno(int atom)

Gets the mass number of an atom. In the case of an element it returns 0, because it is a mix of isotopes having different mass numbers.

Parameters:

atom - the atom index

Returns:

the mass number, or zero if not specified

See Also:

A_MASSNO

getHybridizationState

int getHybridizationState(int atom)

Gets the hybridization state of an atom.

Parameters:

atom - the atom index

Returns:

the hybridization state

See Also:

HybridizationStateConsts, A_HYBRIDIZATION

getQPropAsInt

int getQPropAsInt(int atom,
                  java.lang.String name)

Gets a query property as an integer.

Parameters:

atom - the atom index

name - the property name

Returns:

the property's value

inAtomList

boolean inAtomList(int atom,
                   int atno)

Tests whether the specified element is in the atom list.

Parameters:

atom - the atom index

atno - the atomic number of the element to check

Returns:

true if the atom list contains the element, false otherwise

getImplicitHcount

int getImplicitHcount(int atom)

Gets the number of implicit Hydrogens of an atom.

Parameters:

atom - the atom index

Returns:

the number of Hydrogens

See Also:

A_IMPLH

getImplicitHcount

int getImplicitHcount()

Gets the total number of implicit Hydrogens.

Returns:

the number of implicit Hydrogens

See Also:

A_IMPLH

getExplicitHcount

int getExplicitHcount(int atom)

Gets the number of explicit hydrogen atom neighbors of the given atom.

Parameters:

atom - the atom index

Returns:

the number of Hydrogens

See Also:

A_EXPLH

getHcount

int getHcount(int atom)

Gets the total number of hydrogens of an atom. This method should return getImplicitHcount(atom)|getExplicitHcount(atom)

Parameters:

atom - the atom index

Returns:

sum of the number of implicit and explicit Hydrogens

getValence

int getValence(int atom)

Gets the valence. If valence is set as a property, returns that. Otherwise the valence is the sum of bond orders plus the number of implicit hydrogens or query hydrogen atoms.

Parameters:

atom - the atom index

Returns:

the valence

See Also:

A_VALENCE

getAtomMap

int getAtomMap(int atom)

Gets the atom-atom mapping number.

Parameters:

atom - the atom index

Returns:

the map value (positive integer) or 0

See Also:

A_ATOMMAP

getRgroupId

int getRgroupId(int atom)

Gets the R-group identifier of an atom.

Parameters:

atom - the atom index

Returns:

the R-group identifier (between 0 and RGROUP_MAX) or 0 for normal atoms

See Also:

A_RGROUP

getParity

int getParity(int atom)

Gets the parity of an atom.

Parameters:

atom - the atom index

Returns:

the parity or 0

See Also:

A_PARITY, StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, StereoConstants.PARITY_UNSPEC, StereoConstants.PARITY_EITHER

getChirality

int getChirality(int atom)

Gets the chirality of an atom.

Parameters:

atom - the atom index

Returns:

the chirality or 0 if the atom is not chiral

See Also:

A_CHIRALITY, StereoConstants.CHIRALITY_R, StereoConstants.CHIRALITY_S

getAtomStereo

int getAtomStereo(int atom)

Gets atom stereo properties as an integer.

Returns:

getParity(atom)|getChirality(atom)

See Also:

A_ASTEREO

getNeighborCount

int getNeighborCount(int atom)

Gets the number of neighbors of an atom.

Parameters:

atom - the atom index

Returns:

the number of neighbors

See Also:

A_BOND

getNeighbor

int getNeighbor(int atom,
                int i)

Gets the index of a neighbor of an atom.

Parameters:

atom - the atom index

i - the neighbor index

Returns:

the atom index of the i-th neighbor of atom k

See Also:

A_BOND

areNeighbors

boolean areNeighbors(int atom1,
                     int atom2)

Tests whether two atoms are connected.

Parameters:

atom1 - first atom index

atom2 - second atom index

Returns:

true if they are connected, false otherwise

See Also:

A_BOND

getAtom1

int getAtom1(int i)

Gets the index of the first atom of the specified bond.

Parameters:

i - the bond index

Returns:

an atom index

See Also:

A_BOND

getAtom2

int getAtom2(int i)

Gets the index of the second atom of the specified bond.

Parameters:

i - the bond index

Returns:

an atom index

See Also:

A_BOND

gearch

chemaxon.struc.Gearch gearch()

Gets graph search algorithms.

Returns:

graph searches

getBondIndex

int getBondIndex(int atom1,
                 int atom2)

Gets the index of the bond between the specified atoms.

Parameters:

atom1 - first atom index

atom2 - second atom index

Returns:

the bond index or -1

See Also:

A_BOND

getBondType

int getBondType(int i)

Gets the type of a bond.

Parameters:

i - the bond index

Returns:

the bond type

See Also:

A_BOND, MolBond.ANY, MolBond.AROMATIC, MolBond.SINGLE_OR_DOUBLE, MolBond.SINGLE_OR_AROMATIC, MolBond.DOUBLE_OR_AROMATIC, MolBond.CONJUGATED, MolBond.COORDINATE

getBondType

int getBondType(int atom1,
                int atom2)

Gets the type of a bond between the two specified atoms.

Parameters:

atom1 - first atom index

atom2 - second atom index

Returns:

the bond type

See Also:

A_BOND, MolBond.ANY, MolBond.AROMATIC, MolBond.SINGLE_OR_DOUBLE, MolBond.SINGLE_OR_AROMATIC, MolBond.DOUBLE_OR_AROMATIC, MolBond.CONJUGATED, MolBond.COORDINATE

getBondFlags

int getBondFlags(int i)

Gets the bond descriptor flags.

Parameters:

i - the bond index

Returns:

getBondType(i) | stereo1 | stereo2 | topology | reacting_center

See Also:

A_BOND