Coverage for local_installation/dynasor/trajectory/abstract_trajectory_reader.py: 77%

1from abc import ABC, abstractmethod 

2 

3 

4class AbstractTrajectoryReader(ABC): 

5 """Provides a way to iterate through a molecular dynamics (MD) trajectory 

6 file. 

7 

8 Each frame/time-step is returned as a trajectory_frame. 

9 """ 

10 

11 # unit conversion tables 

12 lengthunits_to_nm_table = { 

13 'Angstrom': 1.0, 

14 'nm': 10.0, 

15 'pm': 1e3, 

16 'fm': 1e6, 

17 } 

18 

19 timeunits_to_fs_table = { 

20 'fs': 1.0, 

21 'ps': 1000, 

22 'ns': 1000000, 

23 } 

24 

25 @abstractmethod 

26 def __iter__(self): 

27 """ Iterates through the trajectory file, frame by frame. """ 

28 pass 

29 

30 @abstractmethod 

31 def __next__(self): 

32 """ Gets next trajectory frame. """ 

33 pass 

34 

35 @abstractmethod 

36 def close(self): 

37 """ Closes down, release resources etc. """ 

38 pass