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

1#!/usr/bin/env python3 

2 

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

4from typing import Optional 

5from pathlib import Path 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools import file_utils as fu 

8from biobb_common.tools.file_utils import launchlogger 

9from biobb_gromacs.gromacs.common import get_gromacs_version 

10 

11 

12class Gmxselect(BiobbObject): 

13 """ 

14 | biobb_gromacs Gmxselect 

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

16 | The GROMACS select module writes out basic data about dynamic selections. It can be used for some simple analyses, or the output can be combined with output from other programs and/or external analysis programs to calculate more complex things. 

17 

18 Args: 

19 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: pdb (edam:format_1476), gro (edam:format_2033), tpr (edam:format_2333). 

20 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_select.ndx>`_. Accepted formats: ndx (edam:format_2033). 

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

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

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

24 * **append** (*bool*) - (False) Append the content of the input_ndx_path to the output_ndx_path. 

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

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

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.gmxselect import gmxselect 

41 prop = { 'selection': '"Mynewgroup" group "Protein-H" and not same residue as within 0.4 of resname ARG' } 

42 gmxselect(input_structure_path='/path/to/myStructure.gro', 

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

44 properties=prop) 

45 

46 Info: 

47 * wrapped_software: 

48 * name: GROMACS Gmxselect 

49 * version: 2025.2 

50 * license: LGPL 2.1 

51 * ontology: 

52 * name: EDAM 

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

54 """ 

55 

56 def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: Optional[str] = None, 

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

58 properties = properties or {} 

59 

60 # Call parent class constructor 

61 super().__init__(properties) 

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

63 

64 # Input/Output files 

65 self.io_dict = { 

66 "in": {"input_structure_path": input_structure_path, "input_ndx_path": input_ndx_path}, 

67 "out": {"output_ndx_path": output_ndx_path} 

68 } 

69 

70 # Properties specific for BB 

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

72 self.append = properties.get('append', False) 

73 

74 # Properties common in all GROMACS BB 

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

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

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:`Gmxselect <gromacs.gmxselect.Gmxselect>` object.""" 

93 

94 # Setup Biobb 

95 if self.check_restart(): 

96 return 0 

97 self.stage_files() 

98 

99 self.cmd = [self.binary_path, 'select', 

100 '-s', self.stage_io_dict["in"]["input_structure_path"], 

101 '-on', self.stage_io_dict["out"]["output_ndx_path"] 

102 ] 

103 

104 if self.stage_io_dict["in"].get("input_ndx_path") and Path( 

105 self.stage_io_dict["in"].get("input_ndx_path")).exists(): 

106 self.cmd.append('-n') 

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

108 

109 self.cmd.append('-select') 

110 self.cmd.append("\'"+self.selection+"\'") 

111 

112 if self.gmx_lib: 

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

114 

115 # Run Biobb block 

116 self.run_biobb() 

117 

118 # Copy files to host 

119 self.copy_to_host() 

120 

121 if self.io_dict["in"].get("input_ndx_path"): 

122 if self.append: 

123 fu.log(f"Appending {self.io_dict['in'].get('input_ndx_path')} to {self.io_dict['out']['output_ndx_path']}", self.out_log, self.global_log) 

124 with open(self.io_dict["out"]["output_ndx_path"], 'a') as out_ndx_file: 

125 out_ndx_file.write('\n') 

126 with open(self.io_dict["in"].get("input_ndx_path", '')) as in_ndx_file: 

127 for line in in_ndx_file: 

128 out_ndx_file.write(line) 

129 

130 # Remove temporal files 

131 self.remove_tmp_files() 

132 

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

134 return self.return_code 

135 

136 

137def gmxselect(input_structure_path: str, output_ndx_path: str, 

138 input_ndx_path: Optional[str] = None, properties: Optional[dict] = None, 

139 **kwargs) -> int: 

140 """Create :class:`Gmxselect <gromacs.gmxselect.Gmxselect>` class and 

141 execute the :meth:`launch() <gromacs.gmxselect.Gmxselect.launch>` method.""" 

142 return Gmxselect(**dict(locals())).launch() 

143 

144 

145gmxselect.__doc__ = Gmxselect.__doc__ 

146main = Gmxselect.get_main(gmxselect, "Wrapper for the GROMACS select module.") 

147 

148 

149if __name__ == '__main__': 

150 main()