Smolecule (Marvin API documentation (c) 1998-2019 ChemAxon Ltd.)

All Superinterfaces:

Incomplecule

All Known Subinterfaces:

WSmolecule
```
@PublicAPI
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

Fields
Modifier and Type	Field and Description
`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

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`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

Interface Smolecule

Field Summary

Method Summary

Methods inherited from interface chemaxon.struc.Incomplecule

Field Detail

A_BOND

A_CHARGE

A_RADICAL

A_HYBRIDIZATION

A_MASSNO

A_IMPLH

A_EXPLH

A_VALENCE

A_ATOMMAP

A_RGROUP

A_PARITY

A_CHIRALITY

A_ASTEREO

A_ALL

RGROUP_MAX

Method Detail

getArrayFlags

getAtomType

getCharge

getRadical

getMassno

getHybridizationState

getQPropAsInt

inAtomList

getImplicitHcount

getImplicitHcount

getExplicitHcount

getHcount

getValence

getAtomMap

getRgroupId

getParity

getChirality

getAtomStereo

getNeighborCount

getNeighbor

areNeighbors

getAtom1

getAtom2

gearch

getBondIndex

getBondType

getBondType

getBondFlags