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 validConstructors 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.
-