Package chemaxon.struc
Interface Smolecule
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- 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
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Field Summary
Fields Modifier and Type Field 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).
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method 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, 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
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Field Detail
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A_BOND
static final int A_BOND
Use arrays to store bonds.- See Also:
- Constant Field Values
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A_CHARGE
static final int A_CHARGE
Use charge array.- See Also:
- Constant Field Values
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A_RADICAL
static final int A_RADICAL
Use radical array.- See Also:
- Constant Field Values
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A_HYBRIDIZATION
static final int A_HYBRIDIZATION
Use hybridization state array.- See Also:
- Constant Field Values
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A_MASSNO
static final int A_MASSNO
Use mass number array.- See Also:
- Constant Field Values
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A_IMPLH
static final int A_IMPLH
Use implicit Hydrogen count array.- See Also:
- Constant Field Values
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A_EXPLH
static final int A_EXPLH
Use explicit Hydrogen count array.- See Also:
- Constant Field Values
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A_VALENCE
static final int A_VALENCE
Use valence array.- See Also:
- Constant Field Values
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A_ATOMMAP
static final int A_ATOMMAP
Use atom type array.- See Also:
- Constant Field Values
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A_RGROUP
static final int A_RGROUP
Use R-group ID array.- See Also:
- Constant Field Values
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A_PARITY
static final int A_PARITY
Atom parity.- See Also:
A_ASTEREO
, Constant Field Values
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A_CHIRALITY
static final int A_CHIRALITY
Chirality.- See Also:
A_ASTEREO
, Constant Field Values
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A_ASTEREO
static final int A_ASTEREO
Use atom stereo properties arrays, equals
.A_PARITY
|A_CHIRALITY
- See Also:
- Constant Field Values
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A_ALL
static final int A_ALL
Use all atom and bond property arrays.- See Also:
- Constant Field Values
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RGROUP_MAX
static final int RGROUP_MAX
Maximum R-group index (32767).- See Also:
getRgroupId(int)
, Constant Field Values
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Method Detail
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getArrayFlags
int getArrayFlags()
Gets info about the used arrays.- Returns:
- the array info
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getAtomType
int getAtomType(int atom)
Gets the type of an atom.- Parameters:
atom
- the atom index- Returns:
- the atom type
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getCharge
int getCharge(int atom)
Gets the charge of an ion.- Parameters:
atom
- the atom index- Returns:
- the charge
- See Also:
A_CHARGE
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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
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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
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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
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getQPropAsInt
int getQPropAsInt(int atom, String name)
Gets a query property as an integer.- Parameters:
atom
- the atom indexname
- the property name- Returns:
- the property's value
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inAtomList
boolean inAtomList(int atom, int atno)
Tests whether the specified element is in the atom list.- Parameters:
atom
- the atom indexatno
- the atomic number of the element to check- Returns:
true
if the atom list contains the element,false
otherwise
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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
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getImplicitHcount
int getImplicitHcount()
Gets the total number of implicit Hydrogens.- Returns:
- the number of implicit Hydrogens
- See Also:
A_IMPLH
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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
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getHcount
int getHcount(int atom)
Gets the total number of hydrogens of an atom. This method should returngetImplicitHcount(atom)
|getExplicitHcount(atom)
- Parameters:
atom
- the atom index- Returns:
- sum of the number of implicit and explicit Hydrogens
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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
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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
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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
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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
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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
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getAtomStereo
int getAtomStereo(int atom)
Gets atom stereo properties as an integer.- Returns:
getParity(atom)
|getChirality(atom)
- See Also:
A_ASTEREO
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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
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getNeighbor
int getNeighbor(int atom, int i)
Gets the index of a neighbor of an atom.- Parameters:
atom
- the atom indexi
- the neighbor index- Returns:
- the atom index of the i-th neighbor of atom k
- See Also:
A_BOND
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areNeighbors
boolean areNeighbors(int atom1, int atom2)
Tests whether two atoms are connected.- Parameters:
atom1
- first atom indexatom2
- second atom index- Returns:
true
if they are connected,false
otherwise- See Also:
A_BOND
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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
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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
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gearch
chemaxon.struc.Gearch gearch()
Gets graph search algorithms.- Returns:
- graph searches
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getBondIndex
int getBondIndex(int atom1, int atom2)
Gets the index of the bond between the specified atoms.- Parameters:
atom1
- first atom indexatom2
- second atom index- Returns:
- the bond index or -1
- See Also:
A_BOND
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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
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getBondType
int getBondType(int atom1, int atom2)
Gets the type of a bond between the two specified atoms.- Parameters:
atom1
- first atom indexatom2
- 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
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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
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