Coverage for cvpack/base_radius_of_gyration.py: 100%

1""" 

2.. class:: BaseRadiusOfGyration 

3 :platform: Linux, MacOS, Windows 

4 :synopsis: Base class for the radius of gyration of an atom group 

5 

6.. classauthor:: Charlles Abreu <craabreu@gmail.com> 

7 

8""" 

9 

10import typing as t 

11import warnings 

12 

13import openmm 

14 

15from .collective_variable import CollectiveVariable 

16 

17 

18class BaseRadiusOfGyration(CollectiveVariable, openmm.CustomCVForce): 

19 """ 

20 Abstract class for the radius of gyration of a group of `n` atoms, computed by 

21 OpenMM's RGForce. 

22 

23 Parameters 

24 ---------- 

25 squared 

26 Whether the collective variable is the squared radius of gyration. 

27 group 

28 The indices of the atoms in the group. 

29 pbc 

30 Deprecated. It has no effect. 

31 weighByMass 

32 No longer supported. It must be False. 

33 """ 

34 

35 def __init__( 

36 self, 

37 squared: bool, 

38 group: t.Sequence[int], 

39 pbc: bool, 

40 weighByMass: bool, 

41 ) -> None: 

42 if not group: 

43 # OpenMM's RGForce would interpret an empty group as all atoms 

44 raise ValueError("The group of atoms must not be empty") 

45 if len(set(group)) != len(group): 

46 raise ValueError("The group of atoms must not have repeated indices") 

47 if weighByMass: 

48 raise ValueError( 

49 "weighByMass=True is no longer supported. It measured distances from " 

50 "the center of mass but averaged them without mass weights, which is " 

51 "not the usual mass-weighted radius of gyration." 

52 ) 

53 if pbc: 

54 warnings.warn( 

55 "The pbc argument of the radius of gyration is deprecated and has no " 

56 "effect. The group of atoms must not be split across periodic images.", 

57 DeprecationWarning, 

58 stacklevel=3, 

59 ) 

60 super().__init__("rg^2" if squared else "rg") 

61 self.addCollectiveVariable("rg", openmm.RGForce(group))