Package chemaxon.struc
Interface Smolecule
Array-based molecule interface.
PLEASE DO NOT IMPLEMENT THIS INTERFACE! It may get more abstract methods in later versions.
- Since:
- Marvin 5.2.2, 04/24/2009
-
Field Summary
Modifier and TypeFieldDescriptionstatic final int
Use all atom and bond property arrays.static final int
Use atom stereo properties arrays, equals
.A_PARITY
|A_CHIRALITY
static final int
Use atom type array.static final int
Use arrays to store bonds.static final int
Use charge array.static final int
Chirality.static final int
Use explicit Hydrogen count array.static final int
Use hybridization state array.static final int
Use implicit Hydrogen count array.static final int
Use mass number array.static final int
Atom parity.static final int
Use radical array.static final int
Use R-group ID array.static final int
Use valence array.static final int
Maximum R-group index (32767). -
Method Summary
Modifier and TypeMethodDescriptionboolean
areNeighbors
(int atom1, int atom2) Tests whether two atoms are connected.chemaxon.struc.Gearch
gearch()
Gets graph search algorithms.int
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
Gets the number of atoms.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
Gets the number of bonds.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
getHybridizationState
(int atom) Gets the hybridization state of an atom.int
getImplicitHcount
(int atom) Gets the number of implicit Hydrogens of an atom.int
getMassno
(int atom) Gets the mass number of an atom.getName()
Gets the molecule title/name.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.default int
getRadical
(int atom) Deprecated, for removal: This API element is subject to removal in a future version.getRadicalValue
(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.Gets the property container.
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Field Details
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A_BOND
static final int A_BONDUse arrays to store bonds.- See Also:
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A_CHARGE
static final int A_CHARGEUse charge array.- See Also:
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A_RADICAL
static final int A_RADICALUse radical array.- See Also:
-
A_HYBRIDIZATION
static final int A_HYBRIDIZATIONUse hybridization state array.- See Also:
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A_MASSNO
static final int A_MASSNOUse mass number array.- See Also:
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A_IMPLH
static final int A_IMPLHUse implicit Hydrogen count array.- See Also:
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A_EXPLH
static final int A_EXPLHUse explicit Hydrogen count array.- See Also:
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A_VALENCE
static final int A_VALENCEUse valence array.- See Also:
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A_ATOMMAP
static final int A_ATOMMAPUse atom type array.- See Also:
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A_RGROUP
static final int A_RGROUPUse R-group ID array.- See Also:
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A_PARITY
static final int A_PARITYAtom parity.- See Also:
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A_CHIRALITY
static final int A_CHIRALITYChirality.- See Also:
-
A_ASTEREO
static final int A_ASTEREOUse atom stereo properties arrays, equals
.A_PARITY
|A_CHIRALITY
- See Also:
-
A_ALL
static final int A_ALLUse all atom and bond property arrays.- See Also:
-
RGROUP_MAX
static final int RGROUP_MAXMaximum R-group index (32767).- See Also:
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Method Details
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getName
String getName()Gets the molecule title/name.- Returns:
- the molecule name or an empty string
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getAtomCount
int getAtomCount()Gets the number of atoms.- Returns:
- the number of atoms
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getBondCount
int getBondCount()Gets the number of bonds.- Returns:
- the number of bonds
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properties
MPropertyContainer properties()Gets the property container.- Returns:
- the property container
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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:
-
getRadical
Deprecated, for removal: This API element is subject to removal in a future version.UsegetRadicalValue(int)
instead.Gets the radical value of an atom.- Parameters:
atom
- the atom index- Returns:
- the radical value
- See Also:
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getRadicalValue
Gets the radical value of an atom.- Parameters:
atom
- the atom index- Returns:
- the radical value
- See Also:
-
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:
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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:
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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:
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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:
-
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:
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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:
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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:
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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:
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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:
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getAtomStereo
int getAtomStereo(int atom) Gets atom stereo properties as an integer.- Returns:
getParity(atom)
|getChirality(atom)
- See Also:
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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:
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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:
-
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:
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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:
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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:
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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:
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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:
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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:
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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:
-
getRadicalValue(int)
instead.