public class SmilesAtom extends javajs.util.P3 implements BNode
SmilesMolecule
.Modifier and Type | Field and Description |
---|---|
(package private) boolean |
aromaticAmbiguous |
private int |
atomicMass |
(package private) java.lang.String |
atomName |
(package private) int |
atomNumber |
(package private) int |
atomSite |
(package private) SmilesAtom[] |
atomsOr |
(package private) java.lang.String |
atomType |
(package private) char |
bioType |
(package private) int |
bondCount |
(package private) SmilesBond[] |
bonds |
private int |
charge |
(package private) int |
component |
(package private) int |
connectivity |
private int |
covalentHydrogenCount |
(package private) int |
degree |
(package private) int |
elementNumber |
boolean |
hasSubpattern |
(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 |
isBioResidue |
(package private) boolean |
isFirst |
(package private) boolean |
isLeadAtom |
(package private) int |
jmolIndex |
int |
mapIndex |
private int |
matchingIndex |
private Node |
matchingNode |
(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 |
referance |
(package private) java.lang.String |
residueChar |
(package private) java.lang.String |
residueName |
(package private) int |
residueNumber |
(package private) int |
ringConnectivity |
(package private) int |
ringMembership |
(package private) int |
ringSize |
(package private) boolean |
selected |
(package private) SmilesStereo |
stereo |
(package private) static java.lang.String |
UNBRACKETED_SET |
(package private) int |
valence |
Constructor and Description |
---|
SmilesAtom() |
Modifier and Type | Method and Description |
---|---|
(package private) void |
addBond(SmilesBond bond)
Add a bond to the atom.
|
(package private) static boolean |
allowSmilesUnbracketed(java.lang.String xx) |
SmilesAtom |
appendAtomOr(SmilesAtom sAtom) |
SmilesAtom |
appendPrimitive(SmilesAtom sAtom) |
BS |
findAtomsLike(java.lang.String substring) |
int |
getAtomicAndIsotopeNumber() |
int |
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 |
getAtomNumber()
Returns the Jmol atom number
|
int |
getAtomSite() |
java.lang.String |
getAtomType() |
char |
getBioSmilesType() |
java.lang.String |
getBioStructureTypeName() |
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.atom2 == this)
otherwise, return bond connecting this atom with
that atom
|
int |
getChainID() |
java.lang.String |
getChainIDStr() |
int |
getCharge()
Returns the charge of the atom.
|
int |
getChiralClass() |
int |
getCovalentBondCount()
Returns the number of bonds of this atom.
|
int |
getCovalentHydrogenCount() |
boolean |
getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vLinks,
boolean crosslinkCovalent,
boolean crosslinkHBond) |
(package private) static int |
getDefaultCount(int elementNumber,
boolean isAromatic) |
Edge[] |
getEdges() |
int |
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) |
void |
getGroupBits(BS bs) |
int |
getImplicitHydrogenCount() |
int |
getIndex()
Returns the atom index of the atom.
|
int |
getIsotopeNumber() |
Node |
getMatchingAtom()
Returns the matching atom or null.
|
int |
getMatchingAtomIndex()
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(BNode node) |
boolean |
isDefined() |
boolean |
isDeleted() |
boolean |
isLeadAtom() |
boolean |
isNucleic() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
SmilesAtom |
setAll(int iComponent,
int ptAtom,
int atomicNumber,
int charge) |
void |
setAtomicMass(int mass)
Sets the atomic mass of the atom.
|
(package private) void |
setAtomName(java.lang.String name) |
void |
setAtomType(java.lang.String type) |
(package private) void |
setBioAtom(char bioType) |
void |
setBondArray() |
void |
setBonds(SmilesBond[] bonds) |
void |
setCharge(int charge)
Sets the charge 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.
|
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.
|
SmilesAtom |
setIndex(int index)
Constructs a
SmilesAtom . |
void |
setMatchingAtom(Node jmolAtom,
int index)
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()
Returns a string that contains the values of this Tuple3f.
|
add, add2, add3, ave, cross, distance, distanceSquared, dot, equals, floatToIntBits0, hashCode, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON
static final java.lang.String UNBRACKETED_SET
SmilesAtom[] atomsOr
int nAtomsOr
SmilesAtom[] primitives
int nPrimitives
int index
java.lang.String atomName
java.lang.String referance
java.lang.String residueName
java.lang.String residueChar
boolean isBioAtom
boolean isBioResidue
char bioType
boolean isLeadAtom
int notBondedIndex
boolean notCrossLinked
boolean aromaticAmbiguous
java.lang.String atomType
private int covalentHydrogenCount
boolean not
boolean selected
boolean hasSymbol
boolean isFirst
int jmolIndex
int elementNumber
int atomNumber
int residueNumber
int missingHydrogenCount
int implicitHydrogenCount
SmilesAtom parent
SmilesBond[] bonds
int bondCount
int iNested
private int atomicMass
private int charge
private int matchingIndex
SmilesStereo stereo
private boolean isAromatic
int component
int atomSite
int degree
int nonhydrogenDegree
int valence
int connectivity
int ringMembership
int ringSize
int ringConnectivity
private Node matchingNode
public boolean hasSubpattern
public int mapIndex
static boolean allowSmilesUnbracketed(java.lang.String xx)
public int getChiralClass()
public boolean isDefined()
void setBioAtom(char bioType)
void setAtomName(java.lang.String name)
public void setBonds(SmilesBond[] bonds)
public SmilesAtom appendAtomOr(SmilesAtom sAtom)
public SmilesAtom appendPrimitive(SmilesAtom sAtom)
public SmilesAtom setIndex(int index)
SmilesAtom
.index
- Atom number in the molecule.public SmilesAtom setAll(int iComponent, int ptAtom, int atomicNumber, int charge)
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()
public boolean isAromatic()
public boolean setSymbol(java.lang.String symbol)
symbol
- Atom symbol.public int getElementNumber()
getElementNumber
in interface Node
public int getAtomicMass()
public int getAtomNumber()
getAtomNumber
in interface BNode
getAtomNumber
in interface Node
public void setAtomicMass(int mass)
mass
- Atomic mass.public int getCharge()
public void setCharge(int charge)
charge
- Charge.public int getMatchingAtomIndex()
public Node getMatchingAtom()
public void setMatchingAtom(Node jmolAtom, int index)
jmolAtom
- index
- Temporary: number of a matching atom in a molecule.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 Node
public int getAtomSite()
getAtomSite
in interface Node
public int getImplicitHydrogenCount()
getImplicitHydrogenCount
in interface Node
public int getExplicitHydrogenCount()
public int getFormalCharge()
getFormalCharge
in interface Node
public int getIsotopeNumber()
getIsotopeNumber
in interface Node
public int getAtomicAndIsotopeNumber()
getAtomicAndIsotopeNumber
in interface Node
public java.lang.String getAtomName()
getAtomName
in interface Node
public java.lang.String getGroup3(boolean allowNull)
void addBond(SmilesBond bond)
bond
- Bond to add.public void setBondArray()
public SmilesBond getBond(int number)
number
.number
- Bond number.public int getCovalentBondCount()
getCovalentBondCount
in interface Node
public int getBondCount()
getBondCount
in interface Node
public int getMatchingBondedAtom(int i)
public int getBondedAtomIndex(int j)
getBondedAtomIndex
in interface Node
public int getCovalentHydrogenCount()
getCovalentHydrogenCount
in interface Node
public int getValence()
getValence
in interface Node
SmilesBond getBondTo(SmilesAtom atom)
atom
- SmilesBond getBondNotTo(SmilesAtom atom, boolean allowH)
public boolean isLeadAtom()
isLeadAtom
in interface BNode
public int getOffsetResidueAtom(java.lang.String name, int offset)
getOffsetResidueAtom
in interface BNode
public void getGroupBits(BS bs)
getGroupBits
in interface BNode
public boolean isCrossLinked(BNode node)
isCrossLinked
in interface BNode
public boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vLinks, boolean crosslinkCovalent, boolean crosslinkHBond)
getCrossLinkVector
in interface BNode
public java.lang.String getBioStructureTypeName()
getBioStructureTypeName
in interface BNode
public int getChainID()
getChainID
in interface BNode
public java.lang.String getChainIDStr()
getChainIDStr
in interface BNode
static java.lang.String getAtomLabel(int atomicNumber, int isotopeNumber, int valence, int charge, int nH, boolean isAromatic, java.lang.String stereo)
atomicNumber
- isotopeNumber
- valence
- set -1 to force bracketscharge
- nH
- isAromatic
- stereo
- public char getBioSmilesType()
getBioSmilesType
in interface BNode
public boolean isNucleic()
public boolean isPyrimidine()
isPyrimidine
in interface BNode
public void setAtomType(java.lang.String type)
public java.lang.String getAtomType()
getAtomType
in interface Node
public BS findAtomsLike(java.lang.String substring)
findAtomsLike
in interface Node
public java.lang.String toString()
javajs.util.T3
toString
in class javajs.util.T3