ample.modelling.energy_functions module

class DynamicDistances[source]

Bases: object

Dynamic distance calculator

The data stored in this class corresponds to Supplementary Table 3 in [1].

Examples

>>> DynamicDistances.cutoff('A', 'Y')
9.121
>>> DynamicDistances.percentile('A', 'Y')
0.443

References

[1]Kamisetty et al. (2013). Assessing the utility of coevolution based residue-residue contact predictions in a sequence and structure rich era. PNAS 110(39), 15674-9.
classmethod cutoff(x, y)[source]

Return the amino acid pair-specific cB-cB cutoff

Parameters:
  • x (str) – Single-letter amino acid
  • y (str) – Single-letter amino acid
classmethod percentile(x, y)[source]

Return 95-97 percentile data

Parameters:
  • x (str) – Single-letter amino acid
  • y (str) – Single-letter amino acid
class RosettaFunctionConstructs[source]

Bases: object

Storage for string formats of different Rosetta energy function constructs

For more information on the different energy functions, please refer to the corresponding references or the official RosettaCommons documentation

BOUNDED_default

Simple bounded energy function

BOUNDED_gremlin

Energy function according to [2]_

References

[2]Ovchinnekov et al. (2015). Large-scale determination of previously unsolved protein structures using evolutionary information. Elife 3(4), e09248.
FADE

Energy function according to [3] and [4]_

References

[3]Simkovic et al. (2016). Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. IUCrJ 3(Pt 4), 259-270.
[4]Michel et al. (2014). PconsFold: improved contact predictions improve protein models. Bioinformatics 30(17), i482-i488
FADE_default

Energy function according to [4]_

References

[4]Michel et al. (2014). PconsFold: improved contact predictions improve protein models. Bioinformatics 30(17), i482-i488
FLAT_HARMONIC

ROSETTA FLAT_HARMONIC energy function

GAUSSIAN

Simple Gaussian energy function

SIGMOID_default

Simple sigmoidal energy function

SIGMOID_gremlin

Energy function according to [2]_

References

[2]Ovchinnekov et al. (2015). Large-scale determination of previously unsolved protein structures using evolutionary information. Elife 4, e09248.
class Saint2FunctionConstructs[source]

Bases: object

Storage for string formats of different SAINT2 energy function constructs

DEFAULT

Default format