Uses of Class
com.actelion.research.chem.forcefield.mmff.Tables
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Packages that use Tables Package Description com.actelion.research.chem.forcefield.mmff com.actelion.research.chem.forcefield.mmff.table com.actelion.research.chem.forcefield.mmff.type -
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Uses of Tables in com.actelion.research.chem.forcefield.mmff
Fields in com.actelion.research.chem.forcefield.mmff with type parameters of type Tables Modifier and Type Field Description static java.util.Map<java.lang.String,Tables>
ForceFieldMMFF94. mTables
Methods in com.actelion.research.chem.forcefield.mmff that return Tables Modifier and Type Method Description static Tables
Tables. newMMFF94(java.lang.String tableSet)
Returns a new MMFF94 table.static Tables
ForceFieldMMFF94. table(java.lang.String name)
Returns a table given a table name.Methods in com.actelion.research.chem.forcefield.mmff with parameters of type Tables 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(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 void
ForceFieldMMFF94. loadTable(java.lang.String name, Tables table)
Loads and registers a tables object with the ForceField class so it can be used by new ForceField instances.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 Tables 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.OutOfPlane(Tables table, MMFFMolecule mol, int ac, int a1, int a2, int a3)
Construct a new out of plane energy term.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. -
Uses of Tables in com.actelion.research.chem.forcefield.mmff.table
Constructors in com.actelion.research.chem.forcefield.mmff.table with parameters of type Tables Constructor Description Angle(Tables t, java.lang.String csvpath)
Atom(Tables t, java.lang.String csvpath)
Bndk(Tables t, java.lang.String csvpath)
Bond(Tables t, java.lang.String csvpath)
Charge(Tables t, java.lang.String csv_pbci, java.lang.String csv_bci)
CovRad(Tables t, java.lang.String csvpath)
Def(Tables t, java.lang.String csvpath)
Dfsb(Tables t, java.lang.String csvpath)
HerschbachLaurie(Tables t, java.lang.String csvpath)
OutOfPlane(Tables t, java.lang.String csvpath)
Stbn(Tables t, java.lang.String csvpath)
Torsion(Tables t, java.lang.String csvpath)
VanDerWaals(Tables t, java.lang.String csvpath)
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Uses of Tables in com.actelion.research.chem.forcefield.mmff.type
Methods in com.actelion.research.chem.forcefield.mmff.type with parameters of type Tables Modifier and Type Method Description static double[]
Charge. getCharges(Tables table, MMFFMolecule mol)
Computes the partial MMFF charges.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
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.
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