Coverage for ufedmm/testmodels.py: 100%

1""" 

2.. module:: testmodels 

3 :platform: Unix, Windows 

4 :synopsis: Unified Free Energy Dynamics Test Model Systems 

5 

6.. moduleauthor:: Charlles Abreu <abreu@eq.ufrj.br> 

7 

8.. _System: 

9 http://docs.openmm.org/latest/api-python/generated/openmm.openmm.System.html 

10.. _Topology: 

11 http://docs.openmm.org/latest/api-python/generated/openmm.app.topology.Topology.html 

12 

13""" 

14 

15import os 

16 

17import openmm 

18from openmm import app, unit 

19 

20import ufedmm 

21 

22 

23class AlanineDipeptideModel(object): 

24 """A system consisting of a single alanine-dipeptide molecule in a vacuum or 

25 solvated in explicit water. 

26 

27 Keyword Args 

28 ------------ 

29 force_field : str, default="amber03" 

30 The force field to be used for the alanine dipeptide molecule. 

31 water : str, default=None 

32 The water model to be used if the alanine dipeptide is supposed to be 

33 solvated. Available options are "spce", "tip3p", "tip4pew", and "tip5p". 

34 box_length : unit.Quantity, default=25*unit.angstroms 

35 The size of the simulation box. This is only effective if water is not 

36 `None`. 

37 constraints : object, default=`openmm.app.HBonds` 

38 Specifies which bonds and angles should be implemented with constraints. 

39 Allowed values are `None`, `openmm.app.HBonds`, `openmm.app.AllBonds`, or 

40 `openmm.app.HAngles`. 

41 rigidWater : bool, boolean=True 

42 Whether water molecules will be fully rigid regardless of the value passed 

43 for the constraints argument. 

44 

45 Attributes 

46 ---------- 

47 system : openmm.System 

48 The system. 

49 topology : openmm.app.Topology 

50 The topology. 

51 positions : list of openmm.Vec3 

52 The positions. 

53 phi : openm.CustomTorsionForce 

54 The Ramachandran dihedral angle :math:`\\phi` of the alanine dipeptide 

55 molecule. 

56 psi : openm.CustomTorsionForce 

57 The Ramachandran dihedral angle :math:`\\psi` of the alanine dipeptide 

58 molecule. 

59 """ 

60 

61 def __init__( 

62 self, 

63 force_field="amber03", 

64 water=None, 

65 box_length=25 * unit.angstroms, 

66 constraints=openmm.app.HBonds, 

67 rigidWater=True, 

68 ): 

69 pdb = app.PDBFile( 

70 os.path.join(ufedmm.__path__[0], "data", "alanine-dipeptide.pdb") 

71 ) 

72 if water is None: 

73 force_field = app.ForceField(f"{force_field}.xml") 

74 self.topology = pdb.topology 

75 self.positions = pdb.positions 

76 L = box_length.value_in_unit(unit.nanometers) 

77 vectors = [openmm.Vec3(L, 0, 0), openmm.Vec3(0, L, 0), openmm.Vec3(0, 0, L)] 

78 self.topology.setPeriodicBoxVectors(vectors) 

79 else: 

80 force_field = app.ForceField(f"{force_field}.xml", f"{water}.xml") 

81 modeller = app.Modeller(pdb.topology, pdb.positions) 

82 modeller.addSolvent( 

83 force_field, model=water, boxSize=box_length * openmm.Vec3(1, 1, 1) 

84 ) 

85 self.topology = modeller.topology 

86 self.positions = modeller.positions 

87 self.system = force_field.createSystem( 

88 self.topology, 

89 nonbondedMethod=app.NoCutoff if water is None else app.PME, 

90 constraints=constraints, 

91 rigidWater=rigidWater, 

92 removeCMMotion=False, 

93 ) 

94 atoms = [(a.name, a.residue.name) for a in self.topology.atoms()] 

95 phi_atoms = [("C", "ACE"), ("N", "ALA"), ("CA", "ALA"), ("C", "ALA")] 

96 self.phi = ufedmm.CollectiveVariable("phi", openmm.CustomTorsionForce("theta")) 

97 self.phi.force.addTorsion(*[atoms.index(i) for i in phi_atoms], []) 

98 psi_atoms = [("N", "ALA"), ("CA", "ALA"), ("C", "ALA"), ("N", "NME")] 

99 self.psi = ufedmm.CollectiveVariable("psi", openmm.CustomTorsionForce("theta")) 

100 self.psi.force.addTorsion(*[atoms.index(i) for i in psi_atoms], [])