mstk.forcefield.FFTerm

class mstk.forcefield.FFTerm

Base class for all force field terms like AtomType, BondTerm, etc…

version

Version is used mainly in PPF format by DFF.

Type:

str

comments

Comments is useful for debugging when generating input files for simulation engines.

Type:

list of str

Methods

__init__()
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

Attributes

name	The name of this force field term.

classmethod get_alias()

Return a short alias for the name of this class

It is used to keep the line more compact in ZFF file

property name

The name of this force field term.

Returns:

name

Return type:

str

to_zff()

Pack the attributes of a term into a string so that can be saved into a line in ZFF file.

Every class to be packed should have a class property _term_attrs. This dict records which attributes should be saved into ZFF file, and it is also used as the arguments for initializing a FFTerm. It also tells the data type of these attributes.

Returns:

line

Return type:

string

to_zff_header()

Header string to explain a line in ZFF format

Returns:

header

Return type:

str

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