Coverage for biobb_gromacs / gromacs / genrestr.py: 93%

1#!/usr/bin/env python3 

2 

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

4 

5from pathlib import Path 

6from typing import Optional, Union 

7 

8from biobb_common.generic.biobb_object import BiobbObject 

9from biobb_common.tools import file_utils as fu 

10from biobb_common.tools.file_utils import launchlogger 

11 

12from biobb_gromacs.gromacs.common import get_gromacs_version 

13 

14 

15class Genrestr(BiobbObject): 

16 """ 

17 | biobb_gromacs Genrestr 

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

19 | 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. 

20 

21 Args: 

22 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). 

23 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). 

24 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). 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

39 

40 Examples: 

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

42 

43 from biobb_gromacs.gromacs.genrestr import genrestr 

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

45 'force_constants': '500 500 500' } 

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

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

48 properties=prop) 

49 

50 Info: 

51 * wrapped_software: 

52 * name: GROMACS Genrestr 

53 * version: 2025.2 

54 * license: LGPL 2.1 

55 * ontology: 

56 * name: EDAM 

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

58 """ 

59 

60 def __init__( 

61 self, 

62 input_structure_path: Union[str, Path], 

63 output_itp_path: Union[str, Path], 

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

65 properties: Optional[dict] = None, 

66 **kwargs, 

67 ) -> None: 

68 properties = properties or {} 

69 

70 # Call parent class constructor 

71 super().__init__(properties) 

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

73 

74 # Input/Output files 

75 self.io_dict = { 

76 "in": { 

77 "input_structure_path": input_structure_path, 

78 "input_ndx_path": input_ndx_path, 

79 }, 

80 "out": {"output_itp_path": output_itp_path}, 

81 } 

82 

83 # Properties specific for BB 

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

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

86 

87 # Properties common in all GROMACS BB 

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

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

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

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

92 if self.gmx_nobackup: 

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

94 if self.gmx_nocopyright: 

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

96 if not self.container_path: 

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

98 

99 # Check the properties 

100 self.check_properties(properties) 

101 self.check_arguments() 

102 

103 @launchlogger 

104 def launch(self) -> int: 

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

106 

107 # Setup Biobb 

108 if self.check_restart(): 

109 return 0 

110 

111 self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(f"{self.restrained_group}") 

112 self.stage_files() 

113 

114 self.cmd = [ 

115 str(self.binary_path), 

116 "genrestr", 

117 "-f", 

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

119 "-o", 

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

121 ] 

122 

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

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

125 

126 self.cmd.append("-fc") 

127 self.cmd.append(self.force_constants) 

128 

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

130 self.cmd.append("-n") 

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

132 

133 # Add stdin input file 

134 self.cmd.append("<") 

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

136 

137 if self.gmx_lib: 

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

139 

140 # Run Biobb block 

141 self.run_biobb() 

142 

143 # Copy files to host 

144 self.copy_to_host() 

145 

146 # Remove temporal files 

147 self.tmp_files.append(str(self.io_dict["in"].get("stdin_file_path"))) 

148 self.remove_tmp_files() 

149 

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

151 return self.return_code 

152 

153 

154def genrestr( 

155 input_structure_path: Union[str, Path], 

156 output_itp_path: Union[str, Path], 

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

158 properties: Optional[dict] = None, 

159 **kwargs, 

160) -> int: 

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

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

163 return Genrestr(**dict(locals())).launch() 

164 

165 

166genrestr.__doc__ = Genrestr.__doc__ 

167main = Genrestr.get_main(genrestr, "Wrapper for the GROMACS genrestr module.") 

168 

169 

170if __name__ == "__main__": 

171 main()