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¶
Parent class of any functional form used in Boltzmann Inversion to convert variance to a force constant. |
|
Simple harmonic potential. |
|
Cosine based angle potential. |
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Dummy functional form which returns a fixed force constant. |
|
Dummy functional form which returns a fixed force constant. |
|
Dummy functional form which returns a fixed force constant. |
Functions¶
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Get enum of known functional forms. |
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pycgtool.functionalforms.
get_functional_forms
() → enum.Enum[source]¶ Get enum of known functional forms.
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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.
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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
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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
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class
pycgtool.functionalforms.
Harmonic
(mean_func: Callable = np.nanmean, variance_func: Callable = np.nanvar)[source]¶ Bases:
FunctionalForm
Simple harmonic potential.
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gromacs_type_ids
= [1, 1, 1]¶
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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.
Uses the transformation in eqn 20 of the above source.
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gromacs_type_ids
= [None, 2, None]¶
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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
-
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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
-
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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]¶
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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
-
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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
-