Coverage for cvpack/angle.py: 100%

1""" 

2.. class:: Angle 

3 :platform: Linux, MacOS, Windows 

4 :synopsis: The angle formed by three atoms 

5 

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

7 

8""" 

9 

10import openmm 

11from openmm import unit as mmunit 

12 

13from .collective_variable import CollectiveVariable 

14 

15 

16class Angle(CollectiveVariable, openmm.CustomAngleForce): 

17 r""" 

18 The angle formed by three atoms: 

19 

20 .. math:: 

21 

22 \theta({\bf r}) = 

23 \mathrm{acos}\left( 

24 \frac{{\bf r}_{2,1} \cdot {\bf r}_{2,3} } 

25 {\| {\bf r}_{2,1} \| \| {\bf r}_{2,3} \|} 

26 \right), 

27 

28 where :math:`{\bf r}_{i,j} = {\bf r}_j - {\bf r}_i`. 

29 

30 Parameters 

31 ---------- 

32 atom1 

33 The index of the first atom. 

34 atom2 

35 The index of the second atom. 

36 atom3 

37 The index of the third atom. 

38 pbc 

39 Whether to use periodic boundary conditions. 

40 name 

41 The name of the collective variable. 

42 

43 Example 

44 ------- 

45 >>> import cvpack 

46 >>> import openmm 

47 >>> system = openmm.System() 

48 >>> [system.addParticle(1) for i in range(3)] 

49 [0, 1, 2] 

50 >>> angle = cvpack.Angle(0, 1, 2) 

51 >>> system.addForce(angle) 

52 0 

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

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

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

56 >>> positions = [[0, 0, 0], [1, 0, 0], [1, 1, 0]] 

57 >>> context.setPositions([openmm.Vec3(*pos) for pos in positions]) 

58 >>> angle.getValue(context) 

59 1.570796... rad 

60 

61 """ 

62 

63 def __init__( 

64 self, 

65 atom1: int, 

66 atom2: int, 

67 atom3: int, 

68 pbc: bool = False, 

69 name: str = "angle", 

70 ) -> None: 

71 super().__init__("theta") 

72 self.addAngle(atom1, atom2, atom3, []) 

73 self.setUsesPeriodicBoundaryConditions(pbc) 

74 self._registerCV( 

75 name, mmunit.radians, atom1=atom1, atom2=atom2, atom3=atom3, pbc=pbc 

76 ) 

77 

78 

79Angle.registerTag("!cvpack.Angle")