Force field

Typing engine

Typer()	Base class for typing engines.
SmartsTyper([file])	SmartsTyper assign atom types with local environment defined by SMARTS and a hierarchical rule.
GaffTyper([file])	GaffTyper is specifically designed for GAFF atom type assignment.

Force field definition

ForceField()	ForceField is a set of FFTerm objects describing the energy function of a Topology with regard to the positions of atoms.
FFTermFactory()	Factory class for force field terms.
FFTerm()	Base class for all force field terms like AtomType, BondTerm, etc...
AtomType(name[, mass, charge, eqt_bci, ...])	AtomType is the most fundamental element in a force field.

vdW terms

VdwTerm(type1, type2)	Base class for all vdW terms.
LJ126Term(type1, type2, epsilon, sigma)	vdW term in LJ-12-6 function form.
MieTerm(type1, type2, epsilon, sigma, ...)	vdW term with generalized LJ function form.

Charge increment terms

ChargeIncrementTerm(type1, type2, value)

ChargeIncrementTerm describes the offset of charge between two atom types when they are bonded.

Polarization terms

PolarTerm(type)	Base class for all polarization terms.
DrudePolarTerm(type, alpha, thole[, k, ...])	Polarization term described by Drude induced dipole.

Virtual site terms

VirtualSiteTerm(type)	Base class for all virtual site terms.
TIP4PSiteTerm(type, type_O, type_H, d)	TIP4P style virtual site term.

Bond terms

BondTerm(type1, type2, length[, fixed])	Base class for all bond terms.
HarmonicBondTerm(type1, type2, length, k[, ...])	Bond term in harmonic function form
MorseBondTerm(type1, type2, length, k, depth)	Bond term in Morse function form

Angle terms

AngleTerm(type1, type2, type3, theta[, fixed])	Base class for all angle terms.
HarmonicAngleTerm(type1, type2, type3, theta, k)	Angle term in harmonic function form
SDKAngleTerm(type1, type2, type3, theta, k)	Angle term in SDK function form
LinearAngleTerm(type1, type2, type3, k)	Linear angle described by the distance between the center atom and its equilibrated position

Dihedral terms

DihedralTerm(type1, type2, type3, type4)	Base class for all dihedral terms.
OplsDihedralTerm(type1, type2, type3, type4, ...)	Dihedral term in OPLS form
PeriodicDihedralTerm(type1, type2, type3, type4)	Dihedral term in periodic cosine function form

Improper terms

ImproperTerm(type1, type2, type3, type4)	Base class for all improper terms.
OplsImproperTerm(type1, type2, type3, type4, k)	Improper term in OPLS cosine function form
HarmonicImproperTerm(type1, type2, type3, ...)	Improper term in harmonic function form.

Force field parser

Zff(file)	Parse ForceField from ZFF file.
Ppf(file)	Parse ForceField from PPF file.
Padua(file)	Generate ForceField from the force field file of fftool.
PaduaLJScaler(file)	PaduaLJScaler implements the empirical LJ scaling scheme of Goloviznina Kateryna.