Class Atom
- java.lang.Object
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- com.actelion.research.chem.forcefield.mmff.type.Atom
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public class Atom extends java.lang.Object
The Atom type class provides static functions to perform atom typing on atoms in a Molecule. There are also several helper functions used in Atom typing provided here.
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Constructor Summary
Constructors Constructor Description Atom()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static int
degree(MMFFMolecule mol, int atom)
Returns the total number of atoms connected to an atom, including implicit and explicit hydrogens.static int
getType(MMFFMolecule mol, int atom)
Returns the MMFF type of an atom in a molecule.static boolean
inRingOfSize(MMFFMolecule mol, int atom, int size)
Returns true if the atom is in any ring of a given size.static int
inRings(MMFFMolecule mol, int atom)
Returns the number of rings that an atom is a member of in a molecule.static boolean
inSameRing(MMFFMolecule mol, int a1, int a2, int size)
Returns true if two atoms are in the same ring of a given size.static boolean
isInAromaticRingOfSize(MMFFMolecule mol, int atom, int size)
Returns true if the atom is in an aromatic ring of given size.static RingBoolean
ringIsMMFFAromatic(MMFFMolecule mol, int r)
Determine if a ring is aromatic according to MMFF criteria.
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Method Detail
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getType
public static int getType(MMFFMolecule mol, int atom)
Returns the MMFF type of an atom in a molecule.- Parameters:
mol
- The molecule that the atom is in.atom
- The atom to assign a type for.- Returns:
- The mmff atom type.
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inRings
public static int inRings(MMFFMolecule mol, int atom)
Returns the number of rings that an atom is a member of in a molecule.- Parameters:
mol
- The molecule that the atom is in.atom
- The atom to check.- Returns:
- The nuber of rings that the atom is a member of.
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isInAromaticRingOfSize
public static boolean isInAromaticRingOfSize(MMFFMolecule mol, int atom, int size)
Returns true if the atom is in an aromatic ring of given size.- Parameters:
mol
- The molecule that the atom is in.atom
- The atom to check.size
- The size of aromatic rings to check.- Returns:
- True if the atom is in an aromatic ring of given size, false otherwise.
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ringIsMMFFAromatic
public static RingBoolean ringIsMMFFAromatic(MMFFMolecule mol, int r)
Determine if a ring is aromatic according to MMFF criteria. Only designed to work with rings of size 5 and 6.- Parameters:
mol
- The molecule that the ring is in.r
- The ring.- Returns:
- True if the ring is aromatic, false otherwise.
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degree
public static int degree(MMFFMolecule mol, int atom)
Returns the total number of atoms connected to an atom, including implicit and explicit hydrogens.- Parameters:
mol
- The molecule that the atom is in.atom
- The atom to count the neighbours of.- Returns:
- The number of neighbours connected to this atom.
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inRingOfSize
public static boolean inRingOfSize(MMFFMolecule mol, int atom, int size)
Returns true if the atom is in any ring of a given size.- Parameters:
mol
- The molecule that the atom is in.atom
- The atom to check.size
- The size of rings to check.- Returns:
- True if the atom is in a ring of given size, false otherwise.
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inSameRing
public static boolean inSameRing(MMFFMolecule mol, int a1, int a2, int size)
Returns true if two atoms are in the same ring of a given size.- Parameters:
mol
- The molecule that both atoms are in.a1
- The first atom.a2
- The second atom.size
- The size of the ring both atoms must be a member of.- Returns:
- True if both atoms are in a ring of given size, false otherwise.
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