Package org.openscience.cdk.interfaces

Interface IAtom

All Superinterfaces:
Cloneable, IAtomType, ICDKObject, IChemObject, IElement, IIsotope
All Known Subinterfaces:
IFragmentAtom, IPDBAtom, IPseudoAtom, IQueryAtom
All Known Implementing Classes:
AliphaticAtom, AliphaticSymbolAtom, AnyAtom, AromaticAtom, AromaticSymbolAtom, Atom, Atom, AtomicNumberAtom, AtomRef, ChiralityAtom, DebugAtom, DebugFragmentAtom, DebugPDBAtom, DebugPseudoAtom, EnzymeResidueLocator, ExplicitConnectionAtom, FormalChargeAtom, FragmentAtom, FragmentAtom, HybridizationNumberAtom, HydrogenAtom, ImplicitHCountAtom, InverseSymbolSetQueryAtom, LogicalOperatorAtom, MassAtom, NonCHHeavyAtom, PDBAtom, PDBAtom, PeriodicGroupNumberAtom, PharmacophoreAtom, PharmacophoreQueryAtom, PseudoAtom, PseudoAtom, QueryAtom, ReactionRoleQueryAtom, RecursiveSmartsAtom, RingIdentifierAtom, RingMembershipAtom, SmallestRingAtom, SMARTSAtom, SymbolAndChargeQueryAtom, SymbolChargeIDQueryAtom, SymbolQueryAtom, SymbolSetQueryAtom, TotalConnectionAtom, TotalHCountAtom, TotalRingConnectionAtom, TotalValencyAtom
public interface IAtom extends IAtomType
Represents the idea of an chemical atom.
Author:
egonw
Keywords:
atom
Created on:
2005-08-24

  • Method Details

    • setCharge

      void setCharge(Double charge)
      Sets the partial charge of this atom.
      Parameters:
      charge - The partial charge
      See Also:

    • getCharge

      Double getCharge()
      Returns the partial charge of this atom.
      Returns:
      the charge of this atom
      See Also:

    • setImplicitHydrogenCount

      void setImplicitHydrogenCount(Integer hydrogenCount)
      Sets the implicit hydrogen count of this atom.
      Parameters:
      hydrogenCount - The number of hydrogen atoms bonded to this atom.
      See Also:

    • getImplicitHydrogenCount

      Integer getImplicitHydrogenCount()
      Returns the implicit hydrogen count of this atom.
      Returns:
      The hydrogen count of this atom.
      See Also:

    • getTotalHydrogenCount

      default Integer getTotalHydrogenCount()
      Calculates the total number of hydrogens connected to this atom. The value is determined on demand from the implicit hydrogen count and the number of connected hydrogen atoms.
      Note: some hydrogens may be bridged (e.g. B2H6) so although the total number of hydrogens in the molecule is 6, each atom has a total hydrogen count of 4.
      Returns:
      the total hydrogen count or null if the implicit count is not set

    • setPoint2d

      void setPoint2d(javax.vecmath.Point2d point2d)
      Sets a point specifying the location of this atom in a 2D space.
      Parameters:
      point2d - A point in a 2D plane
      See Also:

    • setPoint3d

      void setPoint3d(javax.vecmath.Point3d point3d)
      Sets a point specifying the location of this atom in 3D space.
      Parameters:
      point3d - A point in a 3-dimensional space
      See Also:

    • setFractionalPoint3d

      void setFractionalPoint3d(javax.vecmath.Point3d point3d)
      Sets a point specifying the location of this atom in a Crystal unit cell.
      Parameters:
      point3d - A point in a 3d fractional unit cell space
      See Also:

    • setStereoParity

      @Deprecated void setStereoParity(Integer stereoParity)
      Deprecated.
      use IStereoElements for storing stereochemistry
      Sets the stereo parity for this atom.
      Parameters:
      stereoParity - The stereo parity for this atom
      See Also:

    • getPoint2d

      javax.vecmath.Point2d getPoint2d()
      Returns a point specifying the location of this atom in a 2D space.
      Returns:
      A point in a 2D plane. Null if unset.
      See Also:

    • getPoint3d

      javax.vecmath.Point3d getPoint3d()
      Returns a point specifying the location of this atom in a 3D space.
      Returns:
      A point in 3-dimensional space. Null if unset.
      See Also:

    • getFractionalPoint3d

      javax.vecmath.Point3d getFractionalPoint3d()
      Returns a point specifying the location of this atom in a Crystal unit cell.
      Returns:
      A point in 3d fractional unit cell space. Null if unset.
      See Also:

    • getStereoParity

      @Deprecated Integer getStereoParity()
      Deprecated.
      use IStereoElements for storing stereochemistry
      Returns the stereo parity of this atom. It uses the predefined values found in CDKConstants.
      Returns:
      The stereo parity for this atom
      See Also:

    • getContainer

      IAtomContainer getContainer()
      Access the IAtomContainer of which this atom is a member of. Because atoms can be in multiple molecules this method will only work if the atom has been accessed in the context of an IAtomContainer, for example: 
      
 IAtomContainer mol  = new AtomContainer();
 IAtom          atom = new Atom(6);

 atom.getContainer(); // null
 mol.add(atom);
 atom.getContainer(); // still null
 mol.getAtom(0).getContainer(); // not-null, returns 'mol'
      Returns:
      the atom container or null if not accessed in the context of a container

    • getIndex

      int getIndex()
      Acces the index of an atom in the context of an IAtomContainer. If the index is not known, < 0 is returned.
      Returns:
      atom index or < 0 if the index is not known

    • bonds

      Iterable<IBond> bonds()
      Returns the bonds connected to this atom. If the bonds are not known an exception is thrown. This method will only throw an exception if getIndex() returns < 0 or getContainer() returns null. 
      

 IAtom atom = ...;

 if (atom.getIndex() >= 0) {
   for (IBond bond : atom.bonds()) {

   }
 }

 if (atom.getContainer() != null) {
   for (IBond bond : atom.bonds()) {

   }
 }

 IAtomContainer mol = ...;
 // guaranteed not throw an exception
 for (IBond bond : mol.getAtom(i).bonds()) {

 }
      Returns:
      iterable of bonds
      Throws:
      UnsupportedOperationException - thrown if the bonds are not known

    • neighbors

      default Iterable<IAtom> neighbors()
      Iterable over the atoms connected to this atom (the neighbors). This is a convenience function which calls IBond.getOther(IAtom). If you need both the bond and the atom the idiom is: 
      
 for (IBond bond : atom.bonds()) {
     IAtom nbor = bond.getOther(atom);
 }
      This will work but is less efficient: 
      
 for (IAtom nbor : atom.neighbors()) {
     IAtom bond = atom.getBond(nbor); // slow!
 }
      Returns:
      the neighbors

    • getBondCount

      int getBondCount()
      Get the number of explicit bonds connected to this atom.
      Returns:
      the total bond count

    • getBond

      IBond getBond(IAtom atom)
      Returns the bond connecting 'this' atom to the provided atom. If the atoms are not bonded, null is returned.
      Parameters:
      atom - the other atom
      Returns:
      the bond connecting the atoms
      Throws:
      UnsupportedOperationException - thrown if the bonds are not known

    • isAromatic

      default boolean isAromatic()
      Access whether this atom has been marked as aromatic. The default value is false and you must explicitly perceive aromaticity with one of the available models.
      Returns:
      aromatic status
      See Also:

    • setIsAromatic

      default void setIsAromatic(boolean arom)
      Mark this atom as being aromatic.
      Parameters:
      arom - aromatic status
      See Also:

    • isInRing

      default boolean isInRing()
      Access whether this atom has been flagged as in a ring. The default value is false and you must explicitly find rings first.
      Returns:
      ring status
      See Also:

    • setIsInRing

      default void setIsInRing(boolean ring)
      Mark this atom as being in a ring.
      Parameters:
      ring - ring status
      See Also:

    • getMapIdx

      int getMapIdx()
      Access the map index for this atom.
      Returns:
      the map index (0 if not set)

    • setMapIdx

      void setMapIdx(int mapidx)
      Set the map index for this atom.
      Parameters:
      mapidx - the new map index

    • clone

      IAtom clone() throws CloneNotSupportedException
      Returns a deep clone of this IChemObject.
      Specified by:
      clone in interface IChemObject
      Returns:
      Object the clone of this IChemObject.
      Throws:
      CloneNotSupportedException - if the IChemObject cannot be cloned