Coverage for biobb_gromacs/gromacs/genrestr.py: 79%

1#!/usr/bin/env python3 

2 

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

4 

5import argparse 

6from pathlib import Path 

7from typing import Optional, Union 

8 

9from biobb_common.configuration import settings 

10from biobb_common.generic.biobb_object import BiobbObject 

11from biobb_common.tools import file_utils as fu 

12from biobb_common.tools.file_utils import launchlogger 

13 

14from biobb_gromacs.gromacs.common import get_gromacs_version 

15 

16 

17class Genrestr(BiobbObject): 

18 """ 

19 | biobb_gromacs Genrestr 

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

21 | The GROMACS genrestr module, produces an #include file for a topology containing a list of atom numbers and three force constants for the x-, y-, and z-direction based on the contents of the -f file. A single isotropic force constant may be given on the command line instead of three components. 

22 

23 Args: 

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

25 output_itp_path (str): Path the output ITP topology file with restrains. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genrestr.itp>`_. Accepted formats: itp (edam:format_3883). 

26 input_ndx_path (str) (Optional): Path to the input GROMACS index file, NDX format. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genrestr.ndx>`_. Accepted formats: ndx (edam:format_2033). 

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

28 * **restrained_group** (*str*) - ("system") Index group that will be restrained. 

29 * **force_constants** (*str*) - ("500 500 500") Array of three floats defining the force constants 

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

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

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

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

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

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

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

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

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

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

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

41 

42 Examples: 

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

44 

45 from biobb_gromacs.gromacs.genrestr import genrestr 

46 prop = { 'restrained_group': 'system', 

47 'force_constants': '500 500 500' } 

48 genrestr(input_structure_path='/path/to/myStructure.gro', 

49 output_itp_path='/path/to/newTopologyAddOn.itp', 

50 properties=prop) 

51 

52 Info: 

53 * wrapped_software: 

54 * name: GROMACS Genrestr 

55 * version: 2025.2 

56 * license: LGPL 2.1 

57 * ontology: 

58 * name: EDAM 

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

60 """ 

61 

62 def __init__( 

63 self, 

64 input_structure_path: Union[str, Path], 

65 output_itp_path: Union[str, Path], 

66 input_ndx_path: Optional[Union[str, Path]] = None, 

67 properties: Optional[dict] = None, 

68 **kwargs, 

69 ) -> None: 

70 properties = properties or {} 

71 

72 # Call parent class constructor 

73 super().__init__(properties) 

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

75 

76 # Input/Output files 

77 self.io_dict = { 

78 "in": { 

79 "input_structure_path": input_structure_path, 

80 "input_ndx_path": input_ndx_path, 

81 }, 

82 "out": {"output_itp_path": output_itp_path}, 

83 } 

84 

85 # Properties specific for BB 

86 self.force_constants = str(properties.get("force_constants", "500 500 500")) 

87 self.restrained_group = properties.get("restrained_group", "system") 

88 

89 # Properties common in all GROMACS BB 

90 self.gmx_lib = properties.get("gmx_lib", None) 

91 self.binary_path = properties.get("binary_path", "gmx") 

92 self.gmx_nobackup = properties.get("gmx_nobackup", True) 

93 self.gmx_nocopyright = properties.get("gmx_nocopyright", True) 

94 if self.gmx_nobackup: 

95 self.binary_path = f"{self.binary_path} -nobackup" 

96 if self.gmx_nocopyright: 

97 self.binary_path = f"{self.binary_path} -nocopyright" 

98 if not self.container_path: 

99 self.gmx_version = get_gromacs_version(str(self.binary_path)) 

100 

101 # Check the properties 

102 self.check_properties(properties) 

103 self.check_arguments() 

104 

105 @launchlogger 

106 def launch(self) -> int: 

107 """Execute the :class:`Grompp <gromacs.grompp.Grompp>` object.""" 

108 

109 # Setup Biobb 

110 if self.check_restart(): 

111 return 0 

112 

113 self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file( 

114 f"{self.restrained_group}" 

115 ) 

116 self.stage_files() 

117 

118 self.cmd = [ 

119 str(self.binary_path), 

120 "genrestr", 

121 "-f", 

122 self.stage_io_dict["in"]["input_structure_path"], 

123 "-o", 

124 self.stage_io_dict["out"]["output_itp_path"], 

125 ] 

126 

127 if not isinstance(self.force_constants, str): 

128 self.force_constants = " ".join(map(str, self.force_constants)) 

129 

130 self.cmd.append("-fc") 

131 self.cmd.append(self.force_constants) 

132 

133 if self.stage_io_dict["in"].get("input_ndx_path"): 

134 self.cmd.append("-n") 

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

136 

137 # Add stdin input file 

138 self.cmd.append("<") 

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

140 

141 if self.gmx_lib: 

142 self.env_vars_dict["GMXLIB"] = self.gmx_lib 

143 

144 # Run Biobb block 

145 self.run_biobb() 

146 

147 # Copy files to host 

148 self.copy_to_host() 

149 

150 # Remove temporal files 

151 self.tmp_files.extend( 

152 [ 

153 # str(self.stage_io_dict.get("unique_dir", "")), 

154 str(self.io_dict["in"].get("stdin_file_path")), 

155 ] 

156 ) 

157 self.remove_tmp_files() 

158 

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

160 return self.return_code 

161 

162 

163def genrestr( 

164 input_structure_path: Union[str, Path], 

165 output_itp_path: Union[str, Path], 

166 input_ndx_path: Optional[Union[str, Path]] = None, 

167 properties: Optional[dict] = None, 

168 **kwargs, 

169) -> int: 

170 """Create :class:`Genrestr <gromacs.genrestr.Genrestr>` class and 

171 execute the :meth:`launch() <gromacs.genrestr.Genrestr.launch>` method.""" 

172 

173 return Genrestr( 

174 input_structure_path=input_structure_path, 

175 output_itp_path=output_itp_path, 

176 input_ndx_path=input_ndx_path, 

177 properties=properties, 

178 **kwargs, 

179 ).launch() 

180 

181 

182genrestr.__doc__ = Genrestr.__doc__ 

183 

184 

185def main(): 

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

187 parser = argparse.ArgumentParser( 

188 description="Wrapper for the GROMACS genion module.", 

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

190 ) 

191 parser.add_argument( 

192 "-c", 

193 "--config", 

194 required=False, 

195 help="This file can be a YAML file, JSON file or JSON string", 

196 ) 

197 

198 # Specific args of each building block 

199 required_args = parser.add_argument_group("required arguments") 

200 required_args.add_argument("--input_structure_path", required=True) 

201 required_args.add_argument("--output_itp_path", required=True) 

202 parser.add_argument("--input_ndx_path", required=False) 

203 

204 args = parser.parse_args() 

205 config = args.config if args.config else None 

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

207 

208 # Specific call of each building block 

209 genrestr( 

210 input_structure_path=args.input_structure_path, 

211 input_ndx_path=args.input_ndx_path, 

212 output_itp_path=args.output_itp_path, 

213 properties=properties, 

214 ) 

215 

216 

217if __name__ == "__main__": 

218 main()