Class SmilesAtom

Method Details

• allowSmilesUnbracketed

  static boolean allowSmilesUnbracketed(String xx)

• getAtomType

  public String getAtomType()

  Specified by:

  getAtomType in interface Node

• getChiralClass

  public int getChiralClass()

• isDefined

  public boolean isDefined()

• setBioAtom

  void setBioAtom(char bioType)

• setAtomName

  void setAtomName(String name)

• setBonds

  public void setBonds(SmilesBond[] bonds)

• addSubAtom

  SmilesAtom addSubAtom(SmilesAtom sAtom, boolean isAND)

• setIndex

  public SmilesAtom setIndex(int index)

  Constructs a SmilesAtom.

  Parameters:

  index - Atom number in the molecule.

  Returns:

  this

• setTopoAtom

  public SmilesAtom setTopoAtom(int iComponent, int ptAtom, String symbol, int charge, int patternIndex)

• setHydrogenCount

  public boolean setHydrogenCount()

  Finalizes the hydrogen count hydrogens in a 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.

  Returns:

  false if inappropriate

• getDefaultCount

  static int getDefaultCount(int elementNumber, boolean isAromatic)

• getIndex

  public int getIndex()

  Returns the atom index of the atom.

  Specified by:

  getIndex in interface Node

  Specified by:

  getIndex in interface SimpleNode

  Returns:

  Atom index.

• setSymbol

  public boolean setSymbol(String symbol)

  Sets the symbol of the atm.

  Parameters:

  symbol - Atom symbol.

  Returns:

  false if invalid symbol

• getElementNumber

  public int getElementNumber()

  Returns the atomic number of the element or 0

  Specified by:

  getElementNumber in interface Node

  Specified by:

  getElementNumber in interface SimpleNode

  Returns:

  atomicNumber

• getAtomicMass

  public int getAtomicMass()

  Returns the atomic mass of the atom.

  Returns:

  Atomic mass.

• getAtomNumber

  public int getAtomNumber()

  Returns the Jmol atom number

  Specified by:

  getAtomNumber in interface Node

• setAtomicMass

  public void setAtomicMass(int mass)

  Sets the atomic mass of the atom.

  Parameters:

  mass - Atomic mass.

• getCharge

  public int getCharge()

  Returns the charge of the atom.

  Returns:

  Charge.

• setCharge

  public void setCharge(int charge)

  Sets the charge of the atom.

  Parameters:

  charge - Charge.

• getMatchingAtomIndex

  public int getMatchingAtomIndex()

  Returns the number of a matching atom in a molecule. This value is temporary, it is used during the pattern matching algorithm.

  Returns:

  matching atom index

• getMatchingAtom

  public Node getMatchingAtom()

  Returns the matching atom or null.

  Returns:

  matching atom

• setMatchingAtom

  public void setMatchingAtom(Node jmolAtom, int index)

  Sets the number of a matching atom in a molecule. This value is temporary, it is used during the pattern matching algorithm.

  Parameters:

  jmolAtom -

  index - Temporary: number of a matching atom in a molecule.

• setExplicitHydrogenCount

  public void setExplicitHydrogenCount(int count)

  Sets the number of explicit hydrogen atoms bonded with this atom.

  Parameters:

  count - Number of hydrogen atoms.

• setImplicitHydrogenCount

  public void setImplicitHydrogenCount(int count)

  Sets the number of implicit hydrogen atoms bonded with this atom.

  Parameters:

  count - Number of hydrogen atoms.

• setDegree

  public void setDegree(int degree)

• setNonhydrogenDegree

  public void setNonhydrogenDegree(int degree)

• setValence

  public void setValence(int valence)

• setConnectivity

  public void setConnectivity(int connectivity)

• setRingMembership

  public void setRingMembership(int rm)

• setRingSize

  public void setRingSize(int rs)

• setRingConnectivity

  public void setRingConnectivity(int rc)

• getModelIndex

  public int getModelIndex()

  Specified by:

  getModelIndex in interface Node

• getMoleculeNumber

  public int getMoleculeNumber(boolean inModel)

  Specified by:

  getMoleculeNumber in interface Node

• getAtomSite

  public int getAtomSite()

  Specified by:

  getAtomSite in interface Node

• getFormalCharge

  public int getFormalCharge()

  Specified by:

  getFormalCharge in interface Node

  Specified by:

  getFormalCharge in interface SimpleNode

  Returns:

  the formal charge for this atom

• getIsotopeNumber

  public int getIsotopeNumber()

  Specified by:

  getIsotopeNumber in interface Node

  Specified by:

  getIsotopeNumber in interface SimpleNode

• getAtomicAndIsotopeNumber

  public int getAtomicAndIsotopeNumber()

  Specified by:

  getAtomicAndIsotopeNumber in interface Node

• getAtomName

  public String getAtomName()

  Specified by:

  getAtomName in interface Node

  Specified by:

  getAtomName in interface SimpleNode

• getGroup3

  public String getGroup3(boolean allowNull)

  Specified by:

  getGroup3 in interface Node

• getGroup1

  public String getGroup1(char c0)

  Specified by:

  getGroup1 in interface Node

• addBond

  void addBond(SmilesBond bond)

  Add a bond to the atom.

  Parameters:

  bond - Bond to add.

• setBondArray

  public void setBondArray()

• getEdges

  public Edge[] getEdges()

  Description copied from interface: SimpleNode

  Get the bond array, including hydrogen bonds.

  Specified by:

  getEdges in interface Node

  Specified by:

  getEdges in interface SimpleNode

  Returns:

  number of bonds

• getBond

  public SmilesBond getBond(int number)

  Returns the bond at index number.

  Parameters:

  number - Bond number.

  Returns:

  Bond.

• getCovalentBondCount

  public int getCovalentBondCount()

  Returns the number of bonds of this atom.

  Specified by:

  getCovalentBondCount in interface Node

  Specified by:

  getCovalentBondCount in interface SimpleNode

  Returns:

  Number of bonds.

• getBondCount

  public int getBondCount()

  Description copied from interface: SimpleNode

  Get the total number of bonds, including hydrogen bonds.

  Specified by:

  getBondCount in interface SimpleNode

  Returns:

  number of bonds

• getCovalentBondCountPlusMissingH

  public int getCovalentBondCountPlusMissingH()

  Description copied from interface: Node

  includes actual + missing

  Specified by:

  getCovalentBondCountPlusMissingH in interface Node

  Returns:

  actual + missing

• getTotalHydrogenCount

  public int getTotalHydrogenCount()

  Specified by:

  getTotalHydrogenCount in interface Node

• getImplicitHydrogenCount

  public int getImplicitHydrogenCount()

  Description copied from interface: Node

  can be > 0 for PDB model with no H atoms or for SMILES string CCC

  Specified by:

  getImplicitHydrogenCount in interface Node

  Returns:

  number of missing H atoms

• getExplicitHydrogenCount

  public int getExplicitHydrogenCount()

  Description copied from interface: Node

  [CH2] for example

  Specified by:

  getExplicitHydrogenCount in interface Node

  Returns:

  number of H atoms in brackets

• getMatchingBondedAtom

  public int getMatchingBondedAtom(int i)

• getBondedAtomIndex

  public int getBondedAtomIndex(int j)

  Specified by:

  getBondedAtomIndex in interface Node

• getCovalentHydrogenCount

  public int getCovalentHydrogenCount()

  Specified by:

  getCovalentHydrogenCount in interface Node

• getValence

  public int getValence()

  Specified by:

  getValence in interface Node

  Specified by:

  getValence in interface SimpleNode

  Returns:

  the sum of the bond orders for this atom

• getTotalValence

  public int getTotalValence()

  Specified by:

  getTotalValence in interface Node

• getBondTo

  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

  Parameters:

  atom -

  Returns:

  bond

• getBondNotTo

  SmilesBond getBondNotTo(SmilesAtom atom, boolean allowH)

• isLeadAtom

  public boolean isLeadAtom()

  Specified by:

  isLeadAtom in interface Node

• getOffsetResidueAtom

  public int getOffsetResidueAtom(String name, int offset)

  Specified by:

  getOffsetResidueAtom in interface Node

• getGroupBits

  public void getGroupBits(javajs.util.BS bs)

  Specified by:

  getGroupBits in interface Node

• isCrossLinked

  public boolean isCrossLinked(Node node)

  Specified by:

  isCrossLinked in interface Node

• getCrossLinkVector

  public boolean getCrossLinkVector(javajs.util.Lst<Integer> vLinks, boolean crosslinkCovalent, boolean crosslinkHBond)

  Specified by:

  getCrossLinkVector in interface Node

• getBioStructureTypeName

  public String getBioStructureTypeName()

  Specified by:

  getBioStructureTypeName in interface Node

• getInsertionCode

  public char getInsertionCode()

  Specified by:

  getInsertionCode in interface Node

• getResno

  public int getResno()

  Specified by:

  getResno in interface Node

• getChainID

  public int getChainID()

  Specified by:

  getChainID in interface Node

• getChainIDStr

  public String getChainIDStr()

  Specified by:

  getChainIDStr in interface Node

• getAtomLabel

  static String getAtomLabel(int atomicNumber, int isotopeNumber, int valence, int charge, float osclass, int nH, boolean isAromatic, String stereo, boolean is2D)

  called from SmilesGenerator

  Parameters:

  atomicNumber -

  isotopeNumber -

  valence - set -1 to force brackets

  charge -

  osclass - OpenSMILES value

  nH -

  isAromatic -

  stereo -

  is2D -

  Returns:

  label

• getBioSmilesType

  public char getBioSmilesType()

  Specified by:

  getBioSmilesType in interface Node

• isNucleic

  public boolean isNucleic()

• isPurine

  public boolean isPurine()

  Specified by:

  isPurine in interface Node

• isPyrimidine

  public boolean isPyrimidine()

  Specified by:

  isPyrimidine in interface Node

• isDeleted

  public boolean isDeleted()

  Specified by:

  isDeleted in interface Node

• findAtomsLike

  public javajs.util.BS findAtomsLike(String substring)

  Specified by:

  findAtomsLike in interface Node

• toString

  public String toString()

  Description copied from class: javajs.util.T3

  Returns a string that contains the values of this Tuple3f. The form is (x,y,z).

  Overrides:

  toString in class javajs.util.T3

  Returns:

  the String representation

• getFloatProperty

  public float getFloatProperty(String property)

  Specified by:

  getFloatProperty in interface Node

  Parameters:

  property - "property_xxxx"

  Returns:

  value or Float.NaN

• getMass

  public float getMass()

  Specified by:

  getMass in interface Node

  Specified by:

  getMass in interface SimpleNode

  Returns:

  the mass or, if specified, the mass number

• getCIPChirality

  public String getCIPChirality(boolean doCalculate)

  Specified by:

  getCIPChirality in interface Node

• setCIPChirality

  public void setCIPChirality(int c)

  Specified by:

  setCIPChirality in interface Node

  Specified by:

  setCIPChirality in interface SimpleNode

• getCIPChiralityCode

  public int getCIPChiralityCode()

  Specified by:

  getCIPChiralityCode in interface Node

• getXYZ

  public javajs.util.P3 getXYZ()

  Specified by:

  getXYZ in interface Node

  Specified by:

  getXYZ in interface SimpleNode

  Returns:

  the position of this atom

• getStereo

  public SmilesStereo getStereo()

• getPatternIndex

  public int getPatternIndex()

• modelIsRawPDB

  public boolean modelIsRawPDB()

  Specified by:

  modelIsRawPDB in interface Node

• definesStereo

  public boolean definesStereo()

  for InChI or any other system that self-defines stereochemistry.

  Returns:

  false

• getStereoAtAt

  public String getStereoAtAt(SimpleNode[] nodes)

• isStereoOpposite

  public Boolean isStereoOpposite(int i2, int iA, int iB)

  Parameters:

  i2 -

  iA -

  iB -

  Returns:

  TRUE if opposite