mstk.forcefield.HarmonicAngleTerm

class mstk.forcefield.HarmonicAngleTerm(type1, type2, type3, theta, k, fixed=False)

Angle term in harmonic function form

The energy function is

>>> U = k * (theta-theta0)^2

The angle is in unit of radian, and the force constant is in unit of kJ/mol/rad^2.

During the initialization, the two side atom types will be sorted by their string.

Parameters:

• type1 (str) –

• type2 (str) –

• type3 (str) –

• theta (float) –

• k (float) –

• fixed (bool) –

type1

Type:

str

type2

Type:

str

type3

Type:

str

theta

Type:

float

k

Type:

float

fixed

Type:

bool

Methods

__init__(type1, type2, type3, theta, k[, fixed])
evaluate_energy(val)	Evaluate the energy for a force field term like HarmonicBondTerm, PeriodicDihedralTerm, etc...
get_alias()	Return a short alias for the name of this class
to_zff()	Pack the attributes of a term into a string so that can be saved into a line in ZFF file.
to_zff_header()	Header string to explain a line in ZFF format
to_zfp()	Pack the attributes of a term into a dict so that can be saved into ZFP xml file.

Attributes

is_linear	Whether or not this angle term is linear.
name	The name of this force field term.

evaluate_energy(val)

Evaluate the energy for a force field term like HarmonicBondTerm, PeriodicDihedralTerm, etc…

It is mainly for debugging. It is not (and can not be) implemented for all terms.

Parameters:

val (float) – The value of distance, angle, dihedral or improper.

Returns:

energy

Return type:

float

property is_linear

Whether or not this angle term is linear.

Returns:

is

Return type:

bool