Coverage for biobb_gromacs/gromacs/make_ndx.py: 77%

1#!/usr/bin/env python3 

2 

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

4import argparse 

5from typing import Optional 

6from pathlib import Path 

7from biobb_common.generic.biobb_object import BiobbObject 

8from biobb_common.configuration import settings 

9from biobb_common.tools import file_utils as fu 

10from biobb_common.tools.file_utils import launchlogger 

11from biobb_gromacs.gromacs.common import get_gromacs_version 

12 

13 

14class MakeNdx(BiobbObject): 

15 """ 

16 | biobb_gromacs MakeNdx 

17 | Wrapper of the `GROMACS make_ndx <http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_ module. 

18 | The GROMACS make_ndx module, generates an index file using the atoms of the selection. 

19 

20 Args: 

21 input_structure_path (str): Path to the input GRO/PDB/TPR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/make_ndx.tpr>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476), tpr (edam:format_2333). 

22 output_ndx_path (str): Path to the output index NDX file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_make_ndx.ndx>`_. Accepted formats: ndx (edam:format_2033). 

23 input_ndx_path (str) (Optional): Path to the input index NDX file. File type: input. Accepted formats: ndx (edam:format_2033). 

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

25 * **selection** (*str*) - ("a CA C N O") Heavy atoms. Atom selection string. 

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

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

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

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

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

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

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

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

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

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

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

37 

38 Examples: 

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

40 

41 from biobb_gromacs.gromacs.make_ndx import make_ndx 

42 prop = { 'selection': 'a CA C N O' } 

43 make_ndx(input_structure_path='/path/to/myStructure.gro', 

44 output_ndx_path='/path/to/newIndex.ndx', 

45 properties=prop) 

46 

47 Info: 

48 * wrapped_software: 

49 * name: GROMACS MakeNdx 

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_structure_path: str, output_ndx_path: str, input_ndx_path: Optional[str] = None, 

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_structure_path": input_structure_path, "input_ndx_path": input_ndx_path}, 

68 "out": {"output_ndx_path": output_ndx_path} 

69 } 

70 

71 # Properties specific for BB 

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

73 self.selection = properties.get('selection', "a CA C N O") 

74 

75 # Properties common in all GROMACS BB 

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

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

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

79 if self.gmx_nobackup: 

80 self.binary_path += ' -nobackup' 

81 if self.gmx_nocopyright: 

82 self.binary_path += ' -nocopyright' 

83 if not self.container_path: 

84 self.gmx_version = get_gromacs_version(self.binary_path) 

85 

86 # Check the properties 

87 self.check_properties(properties) 

88 self.check_arguments() 

89 

90 @launchlogger 

91 def launch(self) -> int: 

92 """Execute the :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` object.""" 

93 

94 # Setup Biobb 

95 if self.check_restart(): 

96 return 0 

97 

98 self.selection = self.selection.replace("\\n", "\n") 

99 self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.selection}\nq\n') 

100 self.stage_files() 

101 

102 # Create command line 

103 self.cmd = [self.binary_path, 'make_ndx', 

104 '-f', self.stage_io_dict["in"]["input_structure_path"], 

105 '-o', self.stage_io_dict["out"]["output_ndx_path"]] 

106 

107 if self.stage_io_dict["in"].get("input_ndx_path")\ 

108 and Path(self.stage_io_dict["in"].get("input_ndx_path")).exists(): 

109 self.cmd.append('-n') 

110 self.cmd.append(self.stage_io_dict["in"].get("input_ndx_path")) 

111 

112 # Add stdin input file 

113 self.cmd.append('<') 

114 self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"]) 

115 

116 if self.gmx_lib: 

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

118 

119 # create_cmd_line and execute_command 

120 self.run_biobb() 

121 

122 # Retrieve results 

123 self.copy_to_host() 

124 

125 # Remove temporal files 

126 self.tmp_files.extend([ 

127 # self.stage_io_dict.get("unique_dir", ""), 

128 self.io_dict['in'].get("stdin_file_path", '') 

129 ]) 

130 self.remove_tmp_files() 

131 

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

133 return self.return_code 

134 

135 

136def make_ndx(input_structure_path: str, output_ndx_path: str, 

137 input_ndx_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int: 

138 """Create :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` class and 

139 execute the :meth:`launch() <gromacs.make_ndx.MakeNdx.launch>` method.""" 

140 return MakeNdx(input_structure_path=input_structure_path, 

141 output_ndx_path=output_ndx_path, 

142 input_ndx_path=input_ndx_path, 

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

144 

145 

146make_ndx.__doc__ = MakeNdx.__doc__ 

147 

148 

149def main(): 

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

151 parser = argparse.ArgumentParser(description="Wrapper for the GROMACS make_ndx module.", 

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

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

154 

155 # Specific args of each building block 

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

157 required_args.add_argument('--input_structure_path', required=True) 

158 required_args.add_argument('--output_ndx_path', required=True) 

159 parser.add_argument('--input_ndx_path', required=False) 

160 

161 args = parser.parse_args() 

162 config = args.config if args.config else None 

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

164 

165 # Specific call of each building block 

166 make_ndx(input_structure_path=args.input_structure_path, 

167 output_ndx_path=args.output_ndx_path, 

168 input_ndx_path=args.input_ndx_path, 

169 properties=properties) 

170 

171 

172if __name__ == '__main__': 

173 main()