Package chemaxon.core.calculations.valencecheck

Interface MoleculeWithValence<AtomReference>

Type Parameters:
AtomReference -
All Known Implementing Classes:
Molecule, MoleculeGraph, RgMolecule, RxnMolecule, SelectionMolecule
@PublicApi public interface MoleculeWithValence<AtomReference>
Interface for molecule object for which valence calculations can be performed.

This interface is intended for internal use only (e.g. in Marvin JS).

Since:
Marvin 5.9

  • Method Details

    • atoms

      List<AtomReference> atoms()
      Returns list for the atom references in the molecule.
      Returns:
      the iterator

    • getLigandCount

      int getLigandCount(AtomReference atom)
      Gets the number of ligands of the given atom.
      Parameters:
      atom - the atom
      Returns:
      number of ligands

    • getLigand

      AtomReference getLigand(AtomReference atom, int n)
      Gets the n-th ligand of the given atom.
      Parameters:
      atom - the atom
      n - index
      Returns:
      the n-th ligand

    • getLigandBondType

      BondType getLigandBondType(AtomReference atom, int n)
      Gets the type of the n-th ligand bond of the given atom.
      Parameters:
      atom - the atom
      n - index
      Returns:
      the bond type

    • getLigandAtno

      int getLigandAtno(AtomReference atom, int n)
      Gets the atomic number of the n-th ligand of the given atom.
      Parameters:
      atom - the atom
      n - index
      Returns:
      the atomic number

    • getCharge

      int getCharge(AtomReference atom)
      Gets the charge of the given atom.
      Parameters:
      atom - the atom
      Returns:
      the charge

    • getAtomicNumber

      int getAtomicNumber(AtomReference atom)
      Gets the atomic number of the given atom.
      Parameters:
      atom - the atom
      Returns:
      the atomic number

    • getRadicalCount

      int getRadicalCount(AtomReference atom)
      Gets the number of free electrons of the given atom.
      Parameters:
      atom - the atom
      Returns:
      the number of free electrons

    • getValenceProperty

      int getValenceProperty(AtomReference atom)
      Gets the valence property of the given atom.
      Parameters:
      atom - the atom
      Returns:
      the valence or -1 if not set

    • getImplicitHCount

      int getImplicitHCount(AtomReference atom)
      Gets the number of implicit hydrogens attached to the given atom.
      Parameters:
      atom - the atom
      Returns:
      the number of implicit hydrogens

    • getFreeAttachmentPoints

      int getFreeAttachmentPoints(AtomReference atom)
      Returns the number of the free attachment points for the given atom.
      Parameters:
      atom - the atom
      Returns:
      the number of the free attachment points or 0 if the atom is not located in any SuperatomSgroup

    • isAtomInRing

      boolean isAtomInRing(AtomReference atom)
      Checks whether the atom is in ring.
      Parameters:
      atom - the atom reference
      Returns:
      true if the atom is in ring, false otherwise

    • isAcceptedSpecialLigand

      boolean isAcceptedSpecialLigand(AtomReference atom)
      Check if the ligand is a special atom which changes the ring atom column number with -1
      Parameters:
      atom - ligand
      Returns:
      true if the ligand modifies the reference atom column number with -1 else false.