Coverage for biobb_gromacs/gromacs/convert_tpr.py: 0%

1#!/usr/bin/env python3 

2 

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

4import argparse 

5from typing import Optional 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.configuration import settings 

8from biobb_common.tools.file_utils import launchlogger 

9from biobb_gromacs.gromacs.common import get_gromacs_version 

10 

11 

12class ConvertTpr(BiobbObject): 

13 """ 

14 | biobb_gromacs ConvertTpr 

15 | Wrapper of the `GROMACS convert-tpr <https://manual.gromacs.org/current/onlinehelp/gmx-convert-tpr.html>`_ module. 

16 | The GROMACS convert-tpr module can edit run input files (.tpr) 

17 

18 Args: 

19 input_tpr_path (str): Path to the input portable binary run file TPR. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr>`_. Accepted formats: tpr (edam:format_2333). 

20 output_tpr_path (str): Path to the output portable binary run file TPR. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr>`_. Accepted formats: tpr (edam:format_2333). 

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

22 * **extend** (*int*) - (0) Extend the runtime by this amount (ps). 

23 * **until** (*int*) - (0) Extend the runtime until this ending time (ps). 

24 * **nsteps** (*int*) - (0) Change the number of steps remaining to be made.  

25 * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable. 

26 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary. 

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

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

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

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

31 * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier. 

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

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

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

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

36 

37 Examples: 

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

39 

40 from biobb_gromacs.gromacs.convert_tpr import convert_tpr 

41 

42 prop = { 'extend': 100000} 

43 convert_tpr(input_tpr_path='/path/to/myStructure.tpr', 

44 output_tpr_path='/path/to/newCompiledBin.tpr', 

45 properties=prop) 

46 

47 Info: 

48 * wrapped_software: 

49 * name: GROMACS Convert-tpr 

50 * version: 2025.2 

51 * license: LGPL 2.1 

52 * ontology: 

53 * name: EDAM 

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

55 """ 

56 

57 def __init__(self, input_tpr_path: str, output_tpr_path: str, 

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

59 properties = properties or {} 

60 

61 # Call parent class constructor 

62 super().__init__(properties) 

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

64 

65 # Input/Output files 

66 self.io_dict = { 

67 "in": {"input_tpr_path": input_tpr_path}, 

68 "out": {"output_tpr_path": output_tpr_path} 

69 } 

70 

71 # Properties specific for BB 

72 self.extend = properties.get('extend') 

73 self.until = properties.get('until') 

74 self.nsteps = properties.get('nsteps') 

75 

76 # Properties common in all GROMACS BB 

77 self.gmx_lib = properties.get('gmx_lib', None) 

78 self.binary_path = properties.get('binary_path', 'gmx') 

79 self.gmx_nobackup = properties.get('gmx_nobackup', True) 

80 self.gmx_nocopyright = properties.get('gmx_nocopyright', True) 

81 if self.gmx_nobackup: 

82 self.binary_path += ' -nobackup' 

83 if self.gmx_nocopyright: 

84 self.binary_path += ' -nocopyright' 

85 if not self.container_path: 

86 self.gmx_version = get_gromacs_version(self.binary_path) 

87 

88 # Check the properties 

89 self.check_properties(properties) 

90 self.check_arguments() 

91 

92 @launchlogger 

93 def launch(self) -> int: 

94 """Execute the :class:`ConvertTpr <gromacs.convert_tpr.ConvertTpr>` object.""" 

95 

96 # Setup Biobb 

97 if self.check_restart(): 

98 return 0 

99 self.stage_files() 

100 

101 self.cmd = [self.binary_path, 'convert-tpr', 

102 '-s', self.stage_io_dict["in"]["input_tpr_path"], 

103 '-o', self.stage_io_dict["out"]["output_tpr_path"] 

104 ] 

105 

106 if self.extend: 

107 self.cmd.extend(['-extend', str(self.extend)]) 

108 if self.until: 

109 self.cmd.extend(['-until', str(self.until)]) 

110 if self.nsteps: 

111 self.cmd.extend(['-nsteps', str(self.nsteps)]) 

112 

113 if self.gmx_lib: 

114 self.env_vars_dict['GMXLIB'] = self.gmx_lib 

115 

116 # Run Biobb block 

117 self.run_biobb() 

118 

119 # Copy files to host 

120 self.copy_to_host() 

121 

122 self.remove_tmp_files() 

123 

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

125 return self.return_code 

126 

127 

128def convert_tpr(input_tpr_path: str, output_tpr_path: str, properties: Optional[dict] = None, **kwargs) -> int: 

129 """Create :class:`ConvertTpr <gromacs.convert_tpr.ConvertTpr>` class and 

130 execute the :meth:`launch() <gromacs.convert_tpr.ConvertTpr.launch>` method.""" 

131 

132 return ConvertTpr(input_tpr_path=input_tpr_path, output_tpr_path=output_tpr_path, 

133 properties=properties, **kwargs).launch() 

134 

135 

136convert_tpr.__doc__ = ConvertTpr.__doc__ 

137 

138 

139def main(): 

140 """Command line execution of this building block. Please check the command line documentation.""" 

141 parser = argparse.ArgumentParser(description="Wrapper for the GROMACS convert-tpr module.", 

142 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

143 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") 

144 

145 # Specific args of each building block 

146 required_args = parser.add_argument_group('required arguments') 

147 required_args.add_argument('--input_tpr_path', required=True) 

148 required_args.add_argument('--output_tpr_path', required=True) 

149 

150 args = parser.parse_args() 

151 config = args.config if args.config else None 

152 properties = settings.ConfReader(config=config).get_prop_dic() 

153 

154 # Specific call of each building block 

155 convert_tpr(input_tpr_path=args.input_tpr_path, output_tpr_path=args.output_tpr_path, 

156 properties=properties) 

157 

158if __name__ == '__main__': 

159 main()