Coverage for biobb_flexserv/flexserv/bd_run.py: 92%

1#!/usr/bin/env python3 

2 

3"""Module containing the bd_run class and the command line interface.""" 

4from typing import Optional 

5from pathlib import PurePath 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools.file_utils import launchlogger 

8 

9 

10class BDRun(BiobbObject): 

11 """ 

12 | biobb_flexserv BDRun 

13 | Wrapper of the Browian Dynamics tool from the FlexServ module. 

14 | Generates protein conformational structures using the Brownian Dynamics (BD) method. 

15 

16 Args: 

17 input_pdb_path (str): Input PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/flexserv/structure.ca.pdb>`_. Accepted formats: pdb (edam:format_1476). 

18 output_log_path (str): Output log file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/bd_run_out.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). 

19 output_crd_path (str): Output ensemble. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/bd_run_out.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878). 

20 properties (dict - Python dictionary object containing the tool parameters, not input/output files): 

21 * **binary_path** (*str*) - ("bd") BD binary path to be used. 

22 * **time** (*int*) - (1000000) Total simulation time (ps) 

23 * **dt** (*float*) - (1e-15) Integration time (ps) 

24 * **wfreq** (*int*) - (1000) Writing frequency (ps) 

25 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. 

26 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. 

27 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. 

28 * **container_path** (*str*) - (None) Container path definition. 

29 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition. 

30 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. 

31 * **container_working_dir** (*str*) - (None) Container working directory definition. 

32 * **container_user_id** (*str*) - (None) Container user_id definition. 

33 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. 

34 

35 Examples: 

36 This is a use example of how to use the building block from Python:: 

37 

38 from biobb_flexserv.flexserv.bd_run import bd_run 

39 prop = { 

40 'binary_path': 'bd' 

41 } 

42 flexserv_run(input_pdb_path='/path/to/bd_input.pdb', 

43 output_log_path='/path/to/bd_log.log', 

44 output_crd_path='/path/to/bd_ensemble.crd', 

45 properties=prop) 

46 

47 Info: 

48 * wrapped_software: 

49 * name: FlexServ Brownian Dynamics 

50 * version: >=1.0 

51 * license: Apache-2.0 

52 * ontology: 

53 * name: EDAM 

54 * schema: http://edamontology.org/EDAM.owl 

55 

56 """ 

57 

58 def __init__(self, input_pdb_path: str, output_log_path: str, 

59 output_crd_path: str, properties: Optional[dict] = None, **kwargs) -> None: 

60 

61 properties = properties or {} 

62 

63 # Call parent class constructor 

64 super().__init__(properties) 

65 self.locals_var_dict = locals().copy() 

66 

67 # Input/Output files 

68 self.io_dict = { 

69 'in': {'input_pdb_path': input_pdb_path}, 

70 'out': {'output_log_path': output_log_path, 

71 'output_crd_path': output_crd_path} 

72 } 

73 

74 # Properties specific for BB 

75 self.properties = properties 

76 self.binary_path = properties.get('binary_path', 'bd') 

77 self.time = properties.get('time', 1000000) 

78 self.dt = properties.get('dt', 1e-15) 

79 self.wfreq = properties.get('wfreq', 1000) 

80 

81 # Check the properties 

82 self.check_properties(properties) 

83 self.check_arguments() 

84 

85 @launchlogger 

86 def launch(self): 

87 """Launches the execution of the FlexServ BDRun module.""" 

88 

89 # Setup Biobb 

90 if self.check_restart(): 

91 return 0 

92 self.stage_files() 

93 

94 if self.container_path: 

95 working_dir = self.container_volume_path if self.container_volume_path else "/data" 

96 else: 

97 working_dir = self.stage_io_dict.get("unique_dir", "") 

98 

99 # Command line 

100 # bd structure.ca.pdb 1000000 1e-15 1000 40 3.8 traj.crd > bd.log 

101 # itempsmax, dt, itsnap, const, r0 

102 self.cmd = ["cd", working_dir, ";", 

103 self.binary_path, 

104 PurePath(self.stage_io_dict["in"]["input_pdb_path"]).name, 

105 str(self.time), 

106 str(self.dt), 

107 str(self.wfreq), 

108 "40", # Hardcoded "Const", see https://mmb.irbbarcelona.org/gitlab/adam/FlexServ/blob/master/bd/bd2.f#L51 

109 "3.8", # Hardcoded "r0", see https://mmb.irbbarcelona.org/gitlab/adam/FlexServ/blob/master/bd/bd2.f#L52 

110 PurePath(self.stage_io_dict["out"]["output_crd_path"]).name, 

111 '>', PurePath(self.stage_io_dict["out"]["output_log_path"]).name 

112 ] 

113 

114 # Run Biobb block 

115 self.run_biobb() 

116 

117 # Copy files to host 

118 self.copy_to_host() 

119 

120 # Remove temporary folder(s) 

121 self.remove_tmp_files() 

122 self.check_arguments(output_files_created=True, raise_exception=False) 

123 

124 return self.return_code 

125 

126 

127def bd_run(input_pdb_path: str, 

128 output_log_path: str, output_crd_path: str, 

129 properties: Optional[dict] = None, **kwargs) -> int: 

130 """Create :class:`BDRun <flexserv.bd_run.BDRun>`flexserv.bd_run.BDRun class and 

131 execute :meth:`launch() <flexserv.bd_run.BDRun.launch>` method""" 

132 return BDRun(**dict(locals())).launch() 

133 

134 

135bd_run.__doc__ = BDRun.__doc__ 

136main = BDRun.get_main(bd_run, "Generates protein conformational structures using the Brownian Dynamics method.") 

137 

138if __name__ == '__main__': 

139 main()