|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectjavax.vecmath.Tuple3f
javax.vecmath.Point3f
org.jmol.smiles.SmilesAtom
public class SmilesAtom
This class represents an atom in a SmilesMolecule
.
Field Summary | |
---|---|
private short |
atomicMass
|
(package private) java.lang.String |
atomName
|
(package private) int |
atomSite
|
(package private) SmilesAtom[] |
atomsOr
|
(package private) char |
bioType
|
(package private) int |
bondCount
|
(package private) SmilesBond[] |
bonds
|
private int |
charge
|
private int |
chiralClass
|
private int |
chiralOrder
|
(package private) int |
component
|
(package private) int |
connectivity
|
private int |
covalentHydrogenCount
|
(package private) int |
degree
|
(package private) short |
elementNumber
|
(package private) boolean |
hasSymbol
|
(package private) int |
implicitHydrogenCount
|
(package private) int |
index
|
(package private) int |
iNested
|
private boolean |
isAromatic
|
(package private) boolean |
isBioAtom
|
(package private) boolean |
isFirst
|
(package private) boolean |
isLeadAtom
|
(package private) int |
jmolIndex
|
private int |
matchingAtom
|
(package private) int |
missingHydrogenCount
|
(package private) int |
nAtomsOr
|
(package private) int |
nonhydrogenDegree
|
(package private) boolean |
not
|
(package private) int |
notBondedIndex
|
(package private) boolean |
notCrossLinked
|
(package private) int |
nPrimitives
|
(package private) SmilesAtom |
parent
|
(package private) SmilesAtom[] |
primitives
|
(package private) java.lang.String |
residueChar
|
(package private) java.lang.String |
residueName
|
(package private) int |
ringConnectivity
|
(package private) int |
ringMembership
|
(package private) int |
ringSize
|
(package private) boolean |
selected
|
(package private) static int |
STEREOCHEMISTRY_ALLENE
|
(package private) static int |
STEREOCHEMISTRY_DEFAULT
|
(package private) static int |
STEREOCHEMISTRY_OCTAHEDRAL
|
(package private) static int |
STEREOCHEMISTRY_SQUARE_PLANAR
|
(package private) static int |
STEREOCHEMISTRY_TETRAHEDRAL
|
(package private) static int |
STEREOCHEMISTRY_TRIGONAL_BIPYRAMIDAL
|
(package private) static java.lang.String |
UNBRACKETED_SET
|
(package private) int |
valence
|
Fields inherited from class javax.vecmath.Tuple3f |
---|
x, y, z |
Constructor Summary | |
---|---|
SmilesAtom(int index)
Constructs a SmilesAtom . |
|
SmilesAtom(int iComponent,
int ptAtom,
int flags,
short atomicNumber,
int charge)
|
Method Summary | |
---|---|
SmilesAtom |
addAtomOr()
|
(package private) void |
addBond(SmilesBond bond)
Add a bond to the atom. |
SmilesAtom |
addPrimitive()
|
(package private) static boolean |
allowSmilesUnbracketed(java.lang.String xx)
|
short |
getAtomicAndIsotopeNumber()
|
short |
getAtomicMass()
Returns the atomic mass of the atom. |
(package private) static java.lang.String |
getAtomLabel(int atomicNumber,
int isotopeNumber,
int valence,
int charge,
int nH,
boolean isAromatic,
java.lang.String stereo)
|
java.lang.String |
getAtomName()
|
int |
getAtomSite()
|
SmilesBond |
getBond(int number)
Returns the bond at index number . |
int |
getBondCount()
|
int |
getBondedAtomIndex(int j)
|
(package private) SmilesBond |
getBondNotTo(SmilesAtom atom,
boolean allowH)
|
(package private) SmilesBond |
getBondTo(SmilesAtom atom)
if atom is null, return bond TO this atom (bond.getAtom2() == this) otherwise, return bond connecting this atom with that atom |
char |
getChainID()
|
int |
getCharge()
Returns the charge of the atom. |
int |
getChiralClass()
Returns the chiral class of the atom. |
(package private) static int |
getChiralityClass(java.lang.String xx)
|
int |
getChiralOrder()
Returns the chiral order of the atom. |
int |
getCovalentBondCount()
Returns the number of bonds of this atom. |
int |
getCovalentHydrogenCount()
|
boolean |
getCrossLinkLeadAtomIndexes(java.util.List vLinks)
|
(package private) static int |
getDefaultCount(int elementNumber,
boolean isAromatic)
|
JmolEdge[] |
getEdges()
|
short |
getElementNumber()
Returns the atomic number of the element or 0 |
int |
getExplicitHydrogenCount()
|
int |
getFormalCharge()
|
java.lang.String |
getGroup1(char c0)
|
java.lang.String |
getGroup3(boolean allowNull)
|
java.lang.String |
getGroupType()
|
int |
getImplicitHydrogenCount()
|
int |
getIndex()
Returns the atom index of the atom. |
short |
getIsotopeNumber()
|
int |
getMatchingAtom()
Returns the number of a matching atom in a molecule. |
int |
getMatchingBondedAtom(int i)
|
int |
getModelIndex()
|
int |
getOffsetResidueAtom(java.lang.String name,
int offset)
|
int |
getResno()
|
int |
getValence()
|
boolean |
isAromatic()
|
boolean |
isCrossLinked(JmolNode node)
|
boolean |
isDeleted()
|
boolean |
isDna()
|
boolean |
isLeadAtom()
|
boolean |
isNucleic()
|
boolean |
isProtein()
|
boolean |
isPurine()
|
boolean |
isPyrimidine()
|
boolean |
isRna()
|
void |
setAtomicMass(int mass)
Sets the atomic mass of the atom. |
(package private) void |
setAtomName(java.lang.String name)
|
(package private) void |
setBioAtom(char bioType)
|
void |
setBondArray()
|
void |
setBonds(SmilesBond[] bonds)
|
void |
setCharge(int charge)
Sets the charge of the atom. |
void |
setChiralClass(int chiralClass)
Sets the chiral class of the atom. |
void |
setChiralOrder(int chiralOrder)
Sets the chiral order of the atom. |
void |
setConnectivity(int connectivity)
|
void |
setDegree(int degree)
|
void |
setExplicitHydrogenCount(int count)
Sets the number of explicit hydrogen atoms bonded with this atom. |
void |
setGroupBits(java.util.BitSet bs)
|
boolean |
setHydrogenCount(SmilesSearch molecule)
Finalizes the hydrogen count hydrogens in a SmilesMolecule . |
void |
setImplicitHydrogenCount(int count)
Sets the number of implicit hydrogen atoms bonded with this atom. |
void |
setMatchingAtom(int atom)
Sets the number of a matching atom in a molecule. |
void |
setNonhydrogenDegree(int degree)
|
void |
setRingConnectivity(int rc)
|
void |
setRingMembership(int rm)
|
void |
setRingSize(int rs)
|
boolean |
setSymbol(java.lang.String symbol)
Sets the symbol of the atm. |
void |
setValence(int valence)
|
java.lang.String |
toString()
|
Methods inherited from class javax.vecmath.Point3f |
---|
distance, distanceL1, distanceLinf, distanceSquared, project |
Methods inherited from class javax.vecmath.Tuple3f |
---|
absolute, absolute, add, add, clamp, clamp, clampMax, clampMax, clampMin, clampMin, clone, epsilonEquals, equals, equals, get, get, getX, getY, getZ, hashCode, interpolate, interpolate, negate, negate, scale, scale, scaleAdd, scaleAdd, set, set, set, set, setX, setY, setZ, sub, sub |
Methods inherited from class java.lang.Object |
---|
finalize, getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.jmol.api.JmolNode |
---|
set |
Field Detail |
---|
static final int STEREOCHEMISTRY_DEFAULT
static final int STEREOCHEMISTRY_ALLENE
static final int STEREOCHEMISTRY_TETRAHEDRAL
static final int STEREOCHEMISTRY_TRIGONAL_BIPYRAMIDAL
static final int STEREOCHEMISTRY_OCTAHEDRAL
static final int STEREOCHEMISTRY_SQUARE_PLANAR
static final java.lang.String UNBRACKETED_SET
int index
java.lang.String atomName
java.lang.String residueName
java.lang.String residueChar
boolean isBioAtom
char bioType
boolean isLeadAtom
int notBondedIndex
boolean notCrossLinked
boolean not
boolean selected
boolean hasSymbol
boolean isFirst
int jmolIndex
short elementNumber
private short atomicMass
private int charge
int missingHydrogenCount
int implicitHydrogenCount
private int matchingAtom
private int chiralClass
private int chiralOrder
private boolean isAromatic
SmilesAtom parent
SmilesBond[] bonds
int bondCount
int iNested
SmilesAtom[] atomsOr
int nAtomsOr
SmilesAtom[] primitives
int nPrimitives
int component
int atomSite
int degree
int nonhydrogenDegree
int valence
int connectivity
int ringMembership
int ringSize
int ringConnectivity
private int covalentHydrogenCount
Constructor Detail |
---|
public SmilesAtom(int index)
SmilesAtom
.
index
- Atom number in the molecule.public SmilesAtom(int iComponent, int ptAtom, int flags, short atomicNumber, int charge)
Method Detail |
---|
static int getChiralityClass(java.lang.String xx)
static boolean allowSmilesUnbracketed(java.lang.String xx)
void setBioAtom(char bioType)
void setAtomName(java.lang.String name)
public void setBonds(SmilesBond[] bonds)
public SmilesAtom addAtomOr()
public SmilesAtom addPrimitive()
public java.lang.String toString()
toString
in class javax.vecmath.Tuple3f
public boolean setHydrogenCount(SmilesSearch molecule)
SmilesMolecule
.
"missing" here means the number of atoms not present in the SMILES string
for unbracketed atoms or the number of hydrogen atoms "CC" being really CH3CH3
or explicitly mentioned in the bracketed atom, "[CH2]". These hydrogen atoms
are not part of the topological model constructed and need to be accounted for.
molecule
- Molecule containing the atom.
static int getDefaultCount(int elementNumber, boolean isAromatic)
public int getIndex()
getIndex
in interface JmolNode
public boolean isAromatic()
public boolean setSymbol(java.lang.String symbol)
symbol
- Atom symbol.
public short getElementNumber()
getElementNumber
in interface JmolNode
public short getAtomicMass()
public void setAtomicMass(int mass)
mass
- Atomic mass.public int getCharge()
public void setCharge(int charge)
charge
- Charge.public int getMatchingAtom()
public void setMatchingAtom(int atom)
atom
- Temporary: number of a matching atom in a molecule.public int getChiralClass()
CHIRALITY_...
constants)
public void setChiralClass(int chiralClass)
CHIRALITY_...
constants)
chiralClass
- Chiral class.public int getChiralOrder()
public void setChiralOrder(int chiralOrder)
chiralOrder
- Chiral order.public void setExplicitHydrogenCount(int count)
count
- Number of hydrogen atoms.public void setImplicitHydrogenCount(int count)
count
- Number of hydrogen atoms.public void setDegree(int degree)
public void setNonhydrogenDegree(int degree)
public void setValence(int valence)
public void setConnectivity(int connectivity)
public void setRingMembership(int rm)
public void setRingSize(int rs)
public void setRingConnectivity(int rc)
public int getModelIndex()
getModelIndex
in interface JmolNode
public int getAtomSite()
getAtomSite
in interface JmolNode
public int getImplicitHydrogenCount()
getImplicitHydrogenCount
in interface JmolNode
public int getExplicitHydrogenCount()
public int getFormalCharge()
getFormalCharge
in interface JmolNode
public short getIsotopeNumber()
getIsotopeNumber
in interface JmolNode
public short getAtomicAndIsotopeNumber()
getAtomicAndIsotopeNumber
in interface JmolNode
public java.lang.String getAtomName()
getAtomName
in interface JmolNode
public java.lang.String getGroup3(boolean allowNull)
getGroup3
in interface JmolNode
public java.lang.String getGroup1(char c0)
getGroup1
in interface JmolNode
void addBond(SmilesBond bond)
bond
- Bond to add.public void setBondArray()
public JmolEdge[] getEdges()
getEdges
in interface JmolNode
public SmilesBond getBond(int number)
number
.
number
- Bond number.
public int getCovalentBondCount()
getCovalentBondCount
in interface JmolNode
public int getBondCount()
public int getMatchingBondedAtom(int i)
public int getBondedAtomIndex(int j)
getBondedAtomIndex
in interface JmolNode
public int getCovalentHydrogenCount()
getCovalentHydrogenCount
in interface JmolNode
public int getValence()
getValence
in interface JmolNode
SmilesBond getBondTo(SmilesAtom atom)
atom
-
SmilesBond getBondNotTo(SmilesAtom atom, boolean allowH)
public boolean isLeadAtom()
isLeadAtom
in interface JmolNode
public int getOffsetResidueAtom(java.lang.String name, int offset)
getOffsetResidueAtom
in interface JmolNode
public void setGroupBits(java.util.BitSet bs)
setGroupBits
in interface JmolNode
public boolean isCrossLinked(JmolNode node)
isCrossLinked
in interface JmolNode
public boolean getCrossLinkLeadAtomIndexes(java.util.List vLinks)
getCrossLinkLeadAtomIndexes
in interface JmolNode
public java.lang.String getGroupType()
getGroupType
in interface JmolNode
public int getResno()
getResno
in interface JmolNode
public char getChainID()
getChainID
in interface JmolNode
static java.lang.String getAtomLabel(int atomicNumber, int isotopeNumber, int valence, int charge, int nH, boolean isAromatic, java.lang.String stereo)
public boolean isDna()
isDna
in interface JmolNode
public boolean isRna()
isRna
in interface JmolNode
public boolean isNucleic()
isNucleic
in interface JmolNode
public boolean isProtein()
isProtein
in interface JmolNode
public boolean isPurine()
isPurine
in interface JmolNode
public boolean isPyrimidine()
isPyrimidine
in interface JmolNode
public boolean isDeleted()
isDeleted
in interface JmolNode
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |