pycgtool.functionalforms

Utilities for describing the functional forms of bonded potentials being calculated.

See http://manual.gromacs.org/documentation/current/reference-manual/functions/bonded-interactions.html and http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#tab-topfile2

The links above list the bonded potentials available for use in GROMACS force fields. These can be implemented as functional forms in PyCGTOOL by subclassing FunctionalForm.

Module Contents

Classes

FunctionalForm

Parent class of any functional form used in Boltzmann Inversion to convert variance to a force constant.

Harmonic

Simple harmonic potential.

CosHarmonic

Cosine based angle potential.

MartiniDefaultLength

Dummy functional form which returns a fixed force constant.

MartiniDefaultAngle

Dummy functional form which returns a fixed force constant.

MartiniDefaultDihedral

Dummy functional form which returns a fixed force constant.

Functions

get_functional_forms() → enum.Enum

Get enum of known functional forms.
pycgtool.functionalforms.get_functional_forms() → enum.Enum[source]

Get enum of known functional forms.

class pycgtool.functionalforms.FunctionalForm(mean_func: Callable = np.nanmean, variance_func: Callable = np.nanvar)[source]

Parent class of any functional form used in Boltzmann Inversion to convert variance to a force constant.

eqm(self, values: Iterable[float], temp: float) → float[source]

Calculate equilibrium value.

May be overridden by functional forms.

Parameters

  • values – Measured internal coordinate values from which to calculate equilibrium value

  • temp – Temperature of simulation

Returns

Calculated equilibrium value

abstract fconst(self, values: Iterable[float], temp: float) → float[source]

Calculate force constant. Abstract static method to be defined by all functional forms.

Parameters

  • values – Measured internal coordinate values from which to calculate force constant

  • temp – Temperature of simulation

Returns

Calculated force constant

abstract gromacs_type_ids(self) → Tuple[int]

Return tuple of GROMACS potential type ids when used as length, angle, dihedral.

Return tuple[int]

Tuple of GROMACS potential type ids

classmethod gromacs_type_id_by_natoms(cls, natoms: int) → int[source]

Return the GROMACS potential type id for this functional form when used with natoms.

Parameters

natoms (int) – Number of atoms in bond

Return int

GROMACS potential type id

class pycgtool.functionalforms.Harmonic(mean_func: Callable = np.nanmean, variance_func: Callable = np.nanvar)[source]

Bases: FunctionalForm

Simple harmonic potential.

See http://manual.gromacs.org/documentation/current/reference-manual/functions/bonded-interactions.html#harmonic-potential # noqa

gromacs_type_ids = [1, 1, 1]
fconst(self, values: Iterable[float], temp: float) → float[source]

Calculate force constant. Abstract static method to be defined by all functional forms.

Parameters

  • values – Measured internal coordinate values from which to calculate force constant

  • temp – Temperature of simulation

Returns

Calculated force constant

class pycgtool.functionalforms.CosHarmonic(mean_func: Callable = np.nanmean, variance_func: Callable = np.nanvar)[source]

Bases: FunctionalForm

Cosine based angle potential.

See http://manual.gromacs.org/documentation/current/reference-manual/functions/bonded-interactions.html#cosine-based-angle-potential # noqa

Uses the transformation in eqn 20 of the above source.

gromacs_type_ids = [None, 2, None]
fconst(self, values: Iterable[float], temp: float) → float[source]

Calculate force constant. Abstract static method to be defined by all functional forms.

Parameters

  • values – Measured internal coordinate values from which to calculate force constant

  • temp – Temperature of simulation

Returns

Calculated force constant

class pycgtool.functionalforms.MartiniDefaultLength(mean_func: Callable = np.nanmean, variance_func: Callable = np.nanvar)[source]

Bases: FunctionalForm

Dummy functional form which returns a fixed force constant.

gromacs_type_ids = [1, None, None]
fconst(self, values: Iterable[float], temp: float) → float[source]

Calculate force constant. Abstract static method to be defined by all functional forms.

Parameters

  • values – Measured internal coordinate values from which to calculate force constant

  • temp – Temperature of simulation

Returns

Calculated force constant

class pycgtool.functionalforms.MartiniDefaultAngle(mean_func: Callable = np.nanmean, variance_func: Callable = np.nanvar)[source]

Bases: FunctionalForm

Dummy functional form which returns a fixed force constant.

gromacs_type_ids = [None, 2, None]
fconst(self, values: Iterable[float], temp: float) → float[source]

Calculate force constant. Abstract static method to be defined by all functional forms.

Parameters

  • values – Measured internal coordinate values from which to calculate force constant

  • temp – Temperature of simulation

Returns

Calculated force constant

class pycgtool.functionalforms.MartiniDefaultDihedral(mean_func: Callable = np.nanmean, variance_func: Callable = np.nanvar)[source]

Bases: FunctionalForm

Dummy functional form which returns a fixed force constant.

gromacs_type_ids = [None, None, 1]
fconst(self, values: Iterable[float], temp: float) → float[source]

Calculate force constant. Abstract static method to be defined by all functional forms.

Parameters

  • values – Measured internal coordinate values from which to calculate force constant

  • temp – Temperature of simulation

Returns

Calculated force constant