public class SmilesAtom extends javajs.util.P3 implements Node
SmilesMolecule.| Modifier and Type | Field and Description |
|---|---|
(package private) boolean |
aromaticAmbiguous |
(package private) float |
atomClass |
private int |
atomicMass |
(package private) int |
atomNumber |
(package private) int |
atomSite |
(package private) java.lang.String |
atomType |
(package private) java.lang.String |
bioAtomName |
(package private) char |
bioType |
(package private) int |
bondCount |
(package private) SmilesBond[] |
bonds |
private int |
charge |
private int |
cipChirality |
(package private) int |
component |
(package private) int |
connectivity |
private int |
covalentHydrogenCount |
(package private) int |
degree |
(package private) boolean |
elementDefined |
(package private) int |
elementNumber |
(package private) int |
explicitHydrogenCount |
(package private) boolean |
hasSubpattern |
(package private) boolean |
hasSymbol |
(package private) int |
implicitHydrogenCount |
(package private) int |
index |
(package private) int |
iNested |
(package private) char |
insCode |
(package private) boolean |
isAND |
(package private) boolean |
isAromatic |
(package private) boolean |
isBioAtom |
(package private) boolean |
isBioAtomWild |
(package private) boolean |
isBioResidue |
(package private) boolean |
isFirst
true if this atom is the first SMILES atom or first after a .
|
(package private) boolean |
isLeadAtom |
private boolean |
isTopoAtom |
(package private) int |
jmolIndex |
(package private) int |
mapIndex |
(package private) int |
matchingComponent |
private int |
matchingIndex |
private Node |
matchingNode |
private int |
missingHydrogenCount |
(package private) int |
nonhydrogenDegree |
(package private) boolean |
not |
(package private) int |
notBondedIndex |
(package private) boolean |
notCrossLinked |
(package private) int |
nSubAtoms |
(package private) SmilesAtom |
parent |
(package private) java.lang.String |
pattern |
(package private) int |
patternIndex |
(package private) int |
primitiveType |
(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 |
SmilesStereo |
stereo |
(package private) SmilesAtom[] |
subAtoms |
(package private) java.lang.String |
symbol |
(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) SmilesAtom |
addSubAtom(SmilesAtom sAtom,
boolean isAND) |
(package private) static boolean |
allowSmilesUnbracketed(java.lang.String xx) |
javajs.util.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,
float osclass,
int nH,
boolean isAromatic,
java.lang.String stereo)
called from SmilesGenerator
|
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()
Get the total number of bonds, including hydrogen bonds.
|
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() |
java.lang.String |
getCIPChirality(boolean doCalculate) |
int |
getCIPChiralityCode() |
int |
getCovalentBondCount()
Returns the number of bonds of this atom.
|
int |
getCovalentBondCountPlusMissingH()
includes actual + missing
|
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()
Get the bond array, including hydrogen bonds.
|
int |
getElementNumber()
Returns the atomic number of the element or 0
|
int |
getExplicitHydrogenCount() |
float |
getFloatProperty(java.lang.String property) |
int |
getFormalCharge() |
java.lang.String |
getGroup1(char c0) |
java.lang.String |
getGroup3(boolean allowNull) |
void |
getGroupBits(javajs.util.BS bs) |
int |
getImplicitHydrogenCount()
can be > 0 for PDB model with no H atoms or for SMILES string CCC
|
int |
getIndex()
Returns the atom index of the atom.
|
char |
getInsertionCode() |
int |
getIsotopeNumber() |
float |
getMass() |
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 |
getMoleculeNumber(boolean inModel) |
int |
getOffsetResidueAtom(java.lang.String name,
int offset) |
int |
getPatternIndex() |
int |
getResno() |
SmilesStereo |
getStereo() |
int |
getTotalHydrogenCount() |
int |
getTotalValence() |
int |
getValence() |
javajs.util.P3 |
getXYZ() |
boolean |
isCrossLinked(Node node) |
boolean |
isDefined() |
boolean |
isDeleted() |
boolean |
isLeadAtom() |
boolean |
isNucleic() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
boolean |
modelIsRawPDB() |
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 |
setCIPChirality(int c) |
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()
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.
|
SmilesAtom |
setTopoAtom(int iComponent,
int ptAtom,
java.lang.String symbol,
int charge,
int patternIndex) |
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, floatToIntBits, hashCode, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSONstatic final java.lang.String UNBRACKETED_SET
int patternIndex
java.lang.String pattern
int primitiveType
boolean isAND
SmilesAtom[] subAtoms
int nSubAtoms
int index
java.lang.String referance
java.lang.String residueName
java.lang.String residueChar
char insCode
boolean isBioAtom
boolean isBioResidue
boolean isBioAtomWild
char bioType
boolean isLeadAtom
int notBondedIndex
boolean notCrossLinked
boolean aromaticAmbiguous
private int covalentHydrogenCount
boolean not
boolean selected
boolean hasSymbol
boolean elementDefined
java.lang.String atomType
java.lang.String bioAtomName
boolean isFirst
int jmolIndex
int elementNumber
int atomNumber
int residueNumber
int explicitHydrogenCount
int implicitHydrogenCount
SmilesAtom parent
SmilesBond[] bonds
int bondCount
int iNested
boolean isAromatic
private int atomicMass
private int charge
private int matchingIndex
public SmilesStereo stereo
int component
int matchingComponent
int atomSite
int degree
int nonhydrogenDegree
int valence
int connectivity
int ringMembership
int ringSize
int ringConnectivity
private Node matchingNode
boolean hasSubpattern
int mapIndex
float atomClass
java.lang.String symbol
private boolean isTopoAtom
private int missingHydrogenCount
private int cipChirality
static boolean allowSmilesUnbracketed(java.lang.String xx)
public java.lang.String getAtomType()
getAtomType in interface Nodepublic int getChiralClass()
public boolean isDefined()
void setBioAtom(char bioType)
void setAtomName(java.lang.String name)
public void setBonds(SmilesBond[] bonds)
SmilesAtom addSubAtom(SmilesAtom sAtom, boolean isAND)
public SmilesAtom setIndex(int index)
SmilesAtom.index - Atom number in the molecule.public SmilesAtom setTopoAtom(int iComponent, int ptAtom, java.lang.String symbol, int charge, int patternIndex)
public boolean setHydrogenCount()
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.static int getDefaultCount(int elementNumber,
boolean isAromatic)
public int getIndex()
getIndex in interface NodegetIndex in interface SimpleNodepublic boolean setSymbol(java.lang.String symbol)
symbol - Atom symbol.public int getElementNumber()
getElementNumber in interface NodegetElementNumber in interface SimpleNodepublic int getAtomicMass()
public int getAtomNumber()
getAtomNumber in interface Nodepublic 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 Nodepublic int getMoleculeNumber(boolean inModel)
getMoleculeNumber in interface Nodepublic int getAtomSite()
getAtomSite in interface Nodepublic int getFormalCharge()
getFormalCharge in interface NodegetFormalCharge in interface SimpleNodepublic int getIsotopeNumber()
getIsotopeNumber in interface NodegetIsotopeNumber in interface SimpleNodepublic int getAtomicAndIsotopeNumber()
getAtomicAndIsotopeNumber in interface Nodepublic java.lang.String getAtomName()
getAtomName in interface NodegetAtomName in interface SimpleNodepublic java.lang.String getGroup3(boolean allowNull)
void addBond(SmilesBond bond)
bond - Bond to add.public void setBondArray()
public Edge[] getEdges()
SimpleNodegetEdges in interface NodegetEdges in interface SimpleNodepublic SmilesBond getBond(int number)
number.number - Bond number.public int getCovalentBondCount()
getCovalentBondCount in interface NodegetCovalentBondCount in interface SimpleNodepublic int getBondCount()
SimpleNodegetBondCount in interface SimpleNodepublic int getCovalentBondCountPlusMissingH()
NodegetCovalentBondCountPlusMissingH in interface Nodepublic int getTotalHydrogenCount()
getTotalHydrogenCount in interface Nodepublic int getImplicitHydrogenCount()
NodegetImplicitHydrogenCount in interface Nodepublic int getExplicitHydrogenCount()
public int getMatchingBondedAtom(int i)
public int getBondedAtomIndex(int j)
getBondedAtomIndex in interface Nodepublic int getCovalentHydrogenCount()
getCovalentHydrogenCount in interface Nodepublic int getValence()
getValence in interface NodegetValence in interface SimpleNodepublic int getTotalValence()
getTotalValence in interface NodeSmilesBond getBondTo(SmilesAtom atom)
atom - SmilesBond getBondNotTo(SmilesAtom atom, boolean allowH)
public boolean isLeadAtom()
isLeadAtom in interface Nodepublic int getOffsetResidueAtom(java.lang.String name,
int offset)
getOffsetResidueAtom in interface Nodepublic void getGroupBits(javajs.util.BS bs)
getGroupBits in interface Nodepublic boolean isCrossLinked(Node node)
isCrossLinked in interface Nodepublic boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vLinks,
boolean crosslinkCovalent,
boolean crosslinkHBond)
getCrossLinkVector in interface Nodepublic java.lang.String getBioStructureTypeName()
getBioStructureTypeName in interface Nodepublic char getInsertionCode()
getInsertionCode in interface Nodepublic int getChainID()
getChainID in interface Nodepublic java.lang.String getChainIDStr()
getChainIDStr in interface Nodestatic java.lang.String getAtomLabel(int atomicNumber,
int isotopeNumber,
int valence,
int charge,
float osclass,
int nH,
boolean isAromatic,
java.lang.String stereo)
atomicNumber - isotopeNumber - valence - set -1 to force bracketscharge - osclass - OpenSMILES valuenH - isAromatic - stereo - public char getBioSmilesType()
getBioSmilesType in interface Nodepublic boolean isNucleic()
public boolean isPyrimidine()
isPyrimidine in interface Nodepublic javajs.util.BS findAtomsLike(java.lang.String substring)
findAtomsLike in interface Nodepublic java.lang.String toString()
javajs.util.T3toString in class javajs.util.T3public float getFloatProperty(java.lang.String property)
getFloatProperty in interface Nodeproperty - "property_xxxx"public float getMass()
getMass in interface NodegetMass in interface SimpleNodepublic java.lang.String getCIPChirality(boolean doCalculate)
getCIPChirality in interface Nodepublic void setCIPChirality(int c)
setCIPChirality in interface NodesetCIPChirality in interface SimpleNodepublic int getCIPChiralityCode()
getCIPChiralityCode in interface Nodepublic javajs.util.P3 getXYZ()
getXYZ in interface NodegetXYZ in interface SimpleNodepublic SmilesStereo getStereo()
public int getPatternIndex()
public boolean modelIsRawPDB()
modelIsRawPDB in interface Node