Coverage for biobb_flexdyn/flexdyn/imod_imove.py: 92%

1#!/usr/bin/env python3 

2 

3"""Module containing the imode 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 ImodImove(BiobbObject): 

11 """ 

12 | biobb_flexdyn imod_imove 

13 | Wrapper of the imove tool 

14 | Compute the normal modes of a macromolecule using the imove tool from the iMODS package. 

15 

16 Args: 

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

18 input_dat_path (str): Input dat with normal modes. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/imod_imode_evecs.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330). 

19 output_pdb_path (str): Output multi-model PDB file with the generated animation by Principal Component. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/imod_imove_output.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

21 * **binary_path** (*str*) - ("imove") iMODS imove binary path to be used. 

22 * **pc** (*int*) - (1) Principal Component. 

23 * **num_frames** (*int*) - (11) Number of frames to be generated 

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

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

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

27 * **container_path** (*str*) - (None) Path to the binary executable of your container. 

28 * **container_image** (*str*) - ("cmip/cmip:latest") Container Image identifier. 

29 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container. 

30 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container. 

31 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container. 

32 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell. 

33 

34 Examples: 

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

36 

37 from biobb_flexdyn.flexdyn.imod_imove import imod_imove 

38 prop = { 

39 'pc' : 1 

40 } 

41 imod_imove( input_pdb_path='/path/to/structure.pdb', 

42 input_dat_path='/path/to/input_evecs.dat', 

43 output_pdb_path='/path/to/output_anim.pdb', 

44 properties=prop) 

45 

46 Info: 

47 * wrapped_software: 

48 * name: iMODS 

49 * version: >=1.0.4 

50 * license: other 

51 * ontology: 

52 * name: EDAM 

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

54 

55 """ 

56 

57 def __init__(self, input_pdb_path: str, input_dat_path: str, output_pdb_path: str, 

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

59 

60 properties = properties or {} 

61 

62 # Call parent class constructor 

63 super().__init__(properties) 

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

65 

66 # Input/Output files 

67 self.io_dict = { 

68 'in': {'input_pdb_path': input_pdb_path, 'input_dat_path': input_dat_path}, 

69 'out': {'output_pdb_path': output_pdb_path} 

70 } 

71 

72 # Properties specific for BB 

73 self.properties = properties 

74 self.binary_path = properties.get('binary_path', 'imove') 

75 

76 self.pc = properties.get('pc', 1) 

77 self.num_frames = properties.get('num_frames', 11) 

78 

79 # Check the properties 

80 self.check_properties(properties) 

81 self.check_arguments() 

82 

83 @launchlogger 

84 def launch(self): 

85 """Launches the execution of the FlexDyn iMOD imove module.""" 

86 

87 # Setup Biobb 

88 if self.check_restart(): 

89 return 0 

90 self.stage_files() 

91 

92 # Determine working directory (host unique_dir or container volume path) 

93 if self.container_path: 

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

95 else: 

96 working_dir = self.stage_io_dict.get('unique_dir', '') 

97 

98 # Command line 

99 # imove 1ake_backbone.pdb 1ake_backbone_evecs.dat -o 1ake_backbone.ensemble.pdb 1 -c 500 

100 # self.cmd = [self.binary_path, 

101 # str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())), 

102 # str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path.cwd())), 

103 # str(Path(self.stage_io_dict["out"]["output_pdb_path"]).relative_to(Path.cwd())), 

104 # str(self.pc) 

105 # ] 

106 

107 self.cmd = ['cd', working_dir, ';', 

108 self.binary_path, 

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

110 PurePath(self.stage_io_dict["in"]["input_dat_path"]).name, 

111 PurePath(self.stage_io_dict["out"]["output_pdb_path"]).name, 

112 str(self.pc) 

113 ] 

114 

115 # Properties 

116 if self.num_frames: 

117 self.cmd.append('-c') 

118 self.cmd.append(str(self.num_frames)) 

119 

120 # Run Biobb block 

121 self.run_biobb() 

122 

123 # Copy files to host 

124 self.copy_to_host() 

125 

126 # remove temporary folder(s) 

127 self.remove_tmp_files() 

128 

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

130 

131 return self.return_code 

132 

133 

134def imod_imove(input_pdb_path: str, input_dat_path: str, output_pdb_path: str, 

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

136 """Create :class:`ImodImove <flexdyn.imod_imove.ImodImove>`flexdyn.imod_imove.ImodImove class and 

137 execute :meth:`launch() <flexdyn.imod_imove.ImodImove.launch>` method""" 

138 return ImodImove(**dict(locals())).launch() 

139 

140 

141imod_imove.__doc__ = ImodImove.__doc__ 

142main = ImodImove.get_main(imod_imove, "Animate the normal modes of a macromolecule using the imove tool from the iMODS package.") 

143 

144if __name__ == '__main__': 

145 main()