Coverage for cvpack/radius_of_gyration_sq.py: 100%

1""" 

2.. class:: RadiusOfGyrationSq 

3 :platform: Linux, MacOS, Windows 

4 

5 :synopsis: The square of the radius of gyration of a group of atoms 

6 

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

8 

9""" 

10 

11import typing as t 

12 

13from openmm import unit as mmunit 

14 

15from .base_radius_of_gyration import BaseRadiusOfGyration 

16 

17 

18class RadiusOfGyrationSq(BaseRadiusOfGyration): 

19 r""" 

20 The square of the radius of gyration of a group of :math:`n` atoms: 

21 

22 .. math:: 

23 

24 r_g^2({\bf r}) = \frac{1}{n} \sum_{i=1}^n \left\| 

25 {\bf r}_i - {\bf r}_c({\bf r}) 

26 \right\|^2. 

27 

28 where :math:`{\bf r}_c({\bf r})` is the geometric center of the group: 

29 

30 .. math:: 

31 

32 {\bf r}_c({\bf r}) = \frac{1}{n} \sum_{i=j}^n {\bf r}_j 

33 

34 Optionally, the radius of gyration can be computed with respect to the center of 

35 mass of the group. In this case, the geometric center is replaced by: 

36 

37 .. math:: 

38 

39 {\bf r}_m({\bf r}) = \frac{1}{M} \sum_{i=1}^n m_i {\bf r}_i 

40 

41 where :math:`M = \sum_{i=1}^n m_i` is the total mass of the group. 

42 

43 .. note:: 

44 

45 This collective variable is better parallelized than :class:`RadiusOfGyration` 

46 and might be preferred over :class:`RadiusOfGyration` when the group of atoms is 

47 large. 

48 

49 Parameters 

50 ---------- 

51 group 

52 The indices of the atoms in the group. 

53 pbc 

54 Whether to use periodic boundary conditions. 

55 weighByMass 

56 Whether to use the center of mass of the group instead of its geometric center. 

57 name 

58 The name of the collective variable. 

59 

60 Example 

61 ------- 

62 >>> import cvpack 

63 >>> import openmm 

64 >>> from openmmtools import testsystems 

65 >>> model = testsystems.AlanineDipeptideVacuum() 

66 >>> num_atoms = model.system.getNumParticles() 

67 >>> rgsq = cvpack.RadiusOfGyrationSq(list(range(num_atoms))) 

68 >>> rgsq.addToSystem(model.system) 

69 >>> platform = openmm.Platform.getPlatformByName('Reference') 

70 >>> integrator = openmm.VerletIntegrator(0) 

71 >>> context = openmm.Context(model.system, integrator, platform) 

72 >>> context.setPositions(model.positions) 

73 >>> print(rgsq.getValue(context)) # doctest: +ELLIPSIS 

74 0.0871... nm**2 

75 

76 """ 

77 

78 def __init__( 

79 self, 

80 group: t.Iterable[int], 

81 pbc: bool = False, 

82 weighByMass: bool = False, 

83 name: str = "radius_of_gyration_sq", 

84 ) -> None: 

85 group = list(group) 

86 num_atoms = len(group) 

87 super().__init__(2, f"distance(g1, g2)^2/{num_atoms}", group, pbc, weighByMass) 

88 for atom in group: 

89 self.addBond([atom, num_atoms]) 

90 self._registerCV( 

91 name, mmunit.nanometers**2, group=group, pbc=pbc, weighByMass=weighByMass 

92 ) 

93 

94 

95RadiusOfGyrationSq.registerTag("!cvpack.RadiusOfGyrationSq")