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(f"{self.restrained_group}") 

114 self.stage_files() 

115 

116 self.cmd = [ 

117 str(self.binary_path), 

118 "genrestr", 

119 "-f", 

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

121 "-o", 

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

123 ] 

124 

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

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

127 

128 self.cmd.append("-fc") 

129 self.cmd.append(self.force_constants) 

130 

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

132 self.cmd.append("-n") 

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

134 

135 # Add stdin input file 

136 self.cmd.append("<") 

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

138 

139 if self.gmx_lib: 

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

141 

142 # Run Biobb block 

143 self.run_biobb() 

144 

145 # Copy files to host 

146 self.copy_to_host() 

147 

148 # Remove temporal files 

149 self.tmp_files.extend( 

150 [ 

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

152 ] 

153 ) 

154 self.remove_tmp_files() 

155 

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

157 return self.return_code 

158 

159 

160def genrestr( 

161 input_structure_path: Union[str, Path], 

162 output_itp_path: Union[str, Path], 

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

164 properties: Optional[dict] = None, 

165 **kwargs, 

166) -> int: 

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

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

169 

170 return Genrestr( 

171 input_structure_path=input_structure_path, 

172 output_itp_path=output_itp_path, 

173 input_ndx_path=input_ndx_path, 

174 properties=properties, 

175 **kwargs, 

176 ).launch() 

177 

178 

179genrestr.__doc__ = Genrestr.__doc__ 

180 

181 

182def main(): 

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

184 parser = argparse.ArgumentParser( 

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

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

187 ) 

188 parser.add_argument( 

189 "-c", 

190 "--config", 

191 required=False, 

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

193 ) 

194 

195 # Specific args of each building block 

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

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

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

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

200 

201 args = parser.parse_args() 

202 config = args.config if args.config else None 

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

204 

205 # Specific call of each building block 

206 genrestr( 

207 input_structure_path=args.input_structure_path, 

208 input_ndx_path=args.input_ndx_path, 

209 output_itp_path=args.output_itp_path, 

210 properties=properties, 

211 ) 

212 

213 

214if __name__ == "__main__": 

215 main()