Coverage for biobb_amber/test/unitests/test_sander/test_sander_mdrun.py: 100%

1# type: ignore 

2import re 

3from pathlib import Path 

4from biobb_common.tools import test_fixtures as fx 

5from biobb_amber.sander.sander_mdrun import SanderMDRun, sander_mdrun 

6 

7 

8class TestSanderMDRunParameterFiles(): 

9 # The mdin is written without executing sander (provenance of the executions skipped by restart) 

10 def setup_class(self): 

11 fx.test_setup(self, 'sander_mdrun') 

12 

13 def teardown_class(self): 

14 fx.test_teardown(self) 

15 

16 def test_write_parameter_files(self, tmp_path): 

17 paths = {k: v for k, v in self.paths.items() if not k.startswith('ref_')} 

18 mdin_path, = SanderMDRun(properties=self.properties, **paths).write_parameter_files(str(tmp_path)) 

19 assert Path(mdin_path) == tmp_path / 'sander.mdin' 

20 mdin = Path(mdin_path).read_text() 

21 assert re.search(r"imin = 1", mdin) and re.search(r"maxcyc = 500", mdin) 

22 

23 def test_write_parameter_files_input_mdin(self, tmp_path): 

24 # Nothing is staged when the execution is skipped: the input mdin is read from its path 

25 input_mdin_path = str(Path(self.paths['input_top_path']).parent / 'min.mdin') 

26 paths = {k: v for k, v in self.paths.items() if not k.startswith('ref_')} 

27 mdin_path, = SanderMDRun(properties=self.properties, input_mdin_path=input_mdin_path, **paths).write_parameter_files(str(tmp_path)) 

28 mdin = Path(mdin_path).read_text() 

29 assert f"Mdin read from input file: {input_mdin_path}" in mdin and re.search(r"maxcyc = 500", mdin) 

30 

31 

32class TestSanderMDRun(): 

33 def setup_class(self): 

34 fx.test_setup(self, 'sander_mdrun') 

35 

36 def teardown_class(self): 

37 fx.test_teardown(self) 

38 # pass 

39 

40 def test_sander_mdrun(self): 

41 sander_mdrun(properties=self.properties, **self.paths) 

42 assert fx.not_empty(self.paths['output_log_path']) 

43 assert fx.not_empty(self.paths['output_rst_path']) 

44 assert fx.not_empty(self.paths['output_traj_path']) 

45 # assert fx.equal(self.paths['output_traj_path'], self.paths['ref_output_traj_path']) 

46 # assert fx.equal(self.paths['output_rst_path'], self.paths['ref_output_rst_path']) 

47 

48 

49class TestSanderMDRunDirectMDin(): 

50 def setup_class(self): 

51 fx.test_setup(self, 'sander_mdrun_direct_mdin') 

52 

53 def teardown_class(self): 

54 fx.test_teardown(self) 

55 # pass 

56 

57 def test_sander_mdrun(self): 

58 sander_mdrun(properties=self.properties, **self.paths) 

59 assert fx.not_empty(self.paths['output_log_path']) 

60 assert fx.not_empty(self.paths['output_rst_path']) 

61 assert fx.not_empty(self.paths['output_traj_path']) 

62 # assert fx.equal(self.paths['output_traj_path'], self.paths['ref_output_traj_path']) 

63 # assert fx.equal(self.paths['output_rst_path'], self.paths['ref_output_rst_path'])