Uses of Class
com.actelion.research.chem.forcefield.mmff.MMFFMolecule

Packages that use MMFFMolecule

Package	Description
com.actelion.research.chem.forcefield.mmff
com.actelion.research.chem.forcefield.mmff.table
com.actelion.research.chem.forcefield.mmff.type

Uses of MMFFMolecule in com.actelion.research.chem.forcefield.mmff

Fields in com.actelion.research.chem.forcefield.mmff declared as MMFFMolecule

Modifier and Type	Field	Description
MMFFMolecule	Electrostatic.mol
MMFFMolecule	StretchBend.mol

Methods in com.actelion.research.chem.forcefield.mmff that return MMFFMolecule

Modifier and Type	Method	Description
MMFFMolecule	ForceFieldMMFF94.getMMFFMolecule()

Methods in com.actelion.research.chem.forcefield.mmff with parameters of type MMFFMolecule

Modifier and Type	Method	Description
static java.util.List<AngleBend>	AngleBend.findIn(Tables t, MMFFMolecule mol)	Helper function that builds a list of AngleBends for a molecule.
static java.util.List<BondStretch>	BondStretch.findIn(Tables t, MMFFMolecule mol)	Finds all bond stretch energy terms in the current molecule.
static java.util.List<Electrostatic>	Electrostatic.findIn(Tables table, MMFFMolecule mol, Separation sep)	Overloaded wrapper function for 'findIn' which sets default values for the nonbonded cutoff, dielectric model and dielectric constant.
static java.util.List<Electrostatic>	Electrostatic.findIn(Tables table, MMFFMolecule mol, Separation sep, double nonbondedCutoff, boolean dielModel, double dielConst)	Finds all Electrostatic energy terms in the current molecule.
static java.util.List<OutOfPlane>	OutOfPlane.findIn(MMFFMolecule mol)
static java.util.List<OutOfPlane>	OutOfPlane.findIn(Tables t, MMFFMolecule mol)	Finds all out of plane angles in the current molecule.
static java.util.List<StretchBend>	StretchBend.findIn(Tables t, MMFFMolecule mol)	Helper function that builds a list of StretchBends for a molecule.
static java.util.List<TorsionAngle>	TorsionAngle.findIn(Tables t, MMFFMolecule mol)	Helper function that builds a list of TorsionAngles for a molecule.
static java.util.List<VanDerWaals>	VanDerWaals.findIn(Tables table, MMFFMolecule mol, Separation sep, double nonbondedCutoff)	Finds all van der Waals energy terms in the current molecule.
static boolean	StretchBend.valid(Tables table, MMFFMolecule mol, int a1, int a2, int a3)	Checks if a Stretch Bend is valid

Constructors in com.actelion.research.chem.forcefield.mmff with parameters of type MMFFMolecule

Constructor	Description
AngleBend(Tables table, MMFFMolecule mol, int a1, int a2, int a3)	Construct a new angle bend energy term.
BondStretch(Tables table, MMFFMolecule mol, int bond)	Creates a new bond stretch given a force field and a bond.
BondStretch(Tables table, MMFFMolecule mol, int a1, int a2)	Creates a new bond stretch given a force field and two bonded atoms.
Electrostatic(MMFFMolecule mol, int a1, int a2, Separation.Relation rel, double chge1, double chge2)	Constructor with default values for distModel and dielConst.
Electrostatic(MMFFMolecule mol, int a1, int a2, Separation.Relation rel, double chge1, double chge2, boolean distModel, double dielConst)	Construct a new electrostatic energy term.
OutOfPlane(Tables table, MMFFMolecule mol, int ac, int a1, int a2, int a3)	Construct a new out of plane energy term.
Separation(MMFFMolecule mol)	Constructs a new separation table for a molecule.
StretchBend(Tables table, MMFFMolecule mol, int a1, int a2, int a3)	Constructs a new stretch bend object.
TorsionAngle(Tables table, MMFFMolecule mol, int a1, int a2, int a3, int a4)	Construct a new torsion angle energy term.
VanDerWaals(Tables table, MMFFMolecule mol, int a1, int a2)	Construct a new van der Waals energy term.
Vector3(MMFFMolecule mol, int atom)	Constructs a new vector from the x, y, z coordinates of an atom in a molecule.
Vector3(MMFFMolecule mol, int atom1, int atom2)	Constructs a vector that represents the line travelling from the position of atom1 to the position of atom2.

Uses of MMFFMolecule in com.actelion.research.chem.forcefield.mmff.table

Methods in com.actelion.research.chem.forcefield.mmff.table with parameters of type MMFFMolecule

Modifier and Type	Method	Description
Torsion.Kb	Torsion.getForceConstants(MMFFMolecule mol, int a1, int a2, int a3, int a4)	Gets the force constants associated with a torsion angle.
double	OutOfPlane.getKoop(MMFFMolecule mol, int ac, int a1, int a2, int a3)	Returns the Koop parameters from the OutOfPlane table.
int	Angle.index(MMFFMolecule mol, int a1, int a2, int a3)	Returns the index of a row for a given molecule and three connected atoms which form an angle.
int	Dfsb.index(MMFFMolecule mol, int a1, int a2, int a3)	Returns the index that a given set of three atoms have in the Dfsb table.
int	Stbn.index(MMFFMolecule mol, int a1, int a2, int a3)	Returns the index of a row for a given molecule and three connected atoms which form an angle.
double	Angle.ka(MMFFMolecule mol, int a1, int a2, int a3)	Returns 'ka' given a molecule and three connected atoms which form an angle.
double	Bond.kb(MMFFMolecule mol, int atom1, int atom2)	Returns 'kb' given a molecule and two atoms in that molecule that form a bond.
double	Dfsb.kb(MMFFMolecule mol, int a1, int a2, int a3)	Returns the equivalent 'kb' value for a given set of three atoms.
double	Stbn.kba(MMFFMolecule mol, int a1, int a2, int a3)	Returns 'kba' for a given index in the table.
double	Bond.r0(MMFFMolecule mol, int atom1, int atom2)	Returns 'r0' given a molecule and two atoms in that molecule that form a bond.
double	Angle.theta(MMFFMolecule mol, int a1, int a2, int a3)	Returns 'theta0' the ideal angle given a molecule and three connected atoms which form an angle.

Uses of MMFFMolecule in com.actelion.research.chem.forcefield.mmff.type

Methods in com.actelion.research.chem.forcefield.mmff.type with parameters of type MMFFMolecule

Modifier and Type	Method	Description
static int	Atom.degree(MMFFMolecule mol, int atom)	Returns the total number of atoms connected to an atom, including implicit and explicit hydrogens.
static int	Charge.degree(MMFFMolecule mol, int atom)
static double[]	Charge.getCharges(Tables table, MMFFMolecule mol)	Computes the partial MMFF charges.
static double[]	Charge.getFormalCharges(MMFFMolecule mol)	Computes the MMFF formal charges for a molecules atoms.
static int	Angle.getStbnType(Tables table, MMFFMolecule mol, int a1, int a2, int a3)	Given three atoms which form an angle, returns the MMFF stretch-bend type of the angle.
static int	Angle.getType(Tables table, MMFFMolecule mol, int a1, int a2, int a3)	Gets the angle type of an angle bend.
static int	Atom.getType(MMFFMolecule mol, int atom)	Returns the MMFF type of an atom in a molecule.
static int	Bond.getType(Tables table, MMFFMolecule mol, int bond)	Returns the MMFF bond type of a bond on a molecule.
static int	Bond.getType(Tables table, MMFFMolecule mol, int atom1, int atom2)	Returns the MMFF bond type of a bond on a molecule.
static int	Torsion.getType(Tables table, MMFFMolecule mol, int a1, int a2, int a3, int a4)	Returns the torsion type of a torsion angle.
static boolean	Angle.inRingOfSize(MMFFMolecule mol, int a1, int a2, int a3, int size)	Checks if an angle is in a ring of given size.
static boolean	Atom.inRingOfSize(MMFFMolecule mol, int atom, int size)	Returns true if the atom is in any ring of a given size.
static int	Torsion.inRingOfSize(MMFFMolecule mol, int a1, int a2, int a3, int a4)	Checks and returns the minimum ring size that a torsion is contained in.
static int	Atom.inRings(MMFFMolecule mol, int atom)	Returns the number of rings that an atom is a member of in a molecule.
static boolean	Atom.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	Atom.isInAromaticRingOfSize(MMFFMolecule mol, int atom, int size)	Returns true if the atom is in an aromatic ring of given size.
static RingBoolean	Atom.ringIsMMFFAromatic(MMFFMolecule mol, int r)	Determine if a ring is aromatic according to MMFF criteria.