Coverage for biobb_flexserv/flexserv/dmd_run.py: 94%

1#!/usr/bin/env python3 

2 

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

4from typing import Optional 

5from pathlib import Path, PurePath 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools.file_utils import launchlogger 

8 

9 

10class DMDRun(BiobbObject): 

11 """ 

12 | biobb_flexserv DMDRun 

13 | Wrapper of the Discrete Molecular Dynamics tool from the FlexServ module. 

14 | Generates protein conformational structures using the Discrete Molecular Dynamics (DMD) 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/dmd_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/dmd_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*) - ("dmdgoopt") DMD binary path to be used. 

22 * **dt** (*float*) - (1e-12) Integration time (s) 

23 * **temperature** (*int*) - (300) Simulation temperature (K) 

24 * **frames** (*int*) - (1000) Number of frames in the final ensemble 

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.dmd_run import dmd_run 

39 prop = { 

40 'binary_path': 'dmdgoopt' 

41 } 

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

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

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

45 properties=prop) 

46 

47 Info: 

48 * wrapped_software: 

49 * name: FlexServ Discrete Molecular 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', 'dmdgoopt') 

77 # self.dt = properties.get('dt', 1.D-12) 

78 self.dt = properties.get('dt', 1e-12) 

79 self.temperature = properties.get('temperature', 300) 

80 self.frames = properties.get('frames', 1000) 

81 

82 # Check the properties 

83 self.check_properties(properties) 

84 self.check_arguments() 

85 

86 @launchlogger 

87 def launch(self): 

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

89 

90 # Setup Biobb 

91 if self.check_restart(): 

92 return 0 

93 self.stage_files() 

94 

95 if self.container_path: 

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

97 else: 

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

99 

100 # Config file 

101 instructions_file = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath("dmd.in")) 

102 with open(instructions_file, 'w') as dmdin: 

103 

104 dmdin.write("&INPUT\n") 

105 dmdin.write(" FILE9='{}',\n".format(PurePath(self.stage_io_dict["in"]["input_pdb_path"]).name)) 

106 dmdin.write(" FILE21='{}',\n".format(PurePath(self.stage_io_dict["out"]["output_crd_path"]).name)) 

107 dmdin.write(" TSNAP={},\n".format(self.dt)) 

108 dmdin.write(" NBLOC={},\n".format(self.frames)) 

109 dmdin.write(" TEMP={},\n".format(self.temperature)) 

110 dmdin.write(" RCUTGO=8,\n") 

111 dmdin.write(" RCA=0.5,\n") 

112 dmdin.write(" SIGMA=0.05,\n") 

113 dmdin.write(" SIGMAGO=0.1,\n") 

114 dmdin.write(" KKK=2839\n") 

115 dmdin.write("&END\n") 

116 

117 # Command line 

118 # dmdgoopt < dmd.in > dmd.log 

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

120 self.binary_path, 

121 '<', PurePath(instructions_file).name, 

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

123 ] 

124 

125 # Run Biobb block 

126 self.run_biobb() 

127 

128 # Copy files to host 

129 self.copy_to_host() 

130 

131 # Remove temporary folder(s) 

132 self.remove_tmp_files() 

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

134 

135 return self.return_code 

136 

137 

138def dmd_run(input_pdb_path: str, 

139 output_log_path: str, output_crd_path: str, 

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

141 """Create :class:`DMDRun <flexserv.dmd_run.DMDRun>`flexserv.dmd_run.DMDRun class and 

142 execute :meth:`launch() <flexserv.dmd_run.DMDRun.launch>` method""" 

143 return DMDRun(**dict(locals())).launch() 

144 

145 

146dmd_run.__doc__ = DMDRun.__doc__ 

147main = DMDRun.get_main(dmd_run, "Generates protein conformational structures using the Discrete Molecular Dynamics method.") 

148 

149if __name__ == '__main__': 

150 main()