Coverage for biobb_analysis/gromacs/gmx_energy.py: 81%

1#!/usr/bin/env python3 

2 

3"""Module containing the GMX Energy class and the command line interface.""" 

4 

5import argparse 

6from pathlib import PurePath 

7from typing import Optional 

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_analysis.gromacs.common import ( 

15 _from_string_to_list, 

16 check_energy_path, 

17 check_out_xvg_path, 

18 copy_instructions_file_to_container, 

19 get_binary_path, 

20 get_default_value, 

21 get_terms, 

22 get_xvg, 

23) 

24 

25 

26class GMXEnergy(BiobbObject): 

27 """ 

28 | biobb_analysis GMXEnergy 

29 | Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file. 

30 | `GROMACS energy <http://manual.gromacs.org/current/onlinehelp/gmx-energy.html>`_ extracts energy components from an energy file. The user is prompted to interactively select the desired energy terms. 

31 

32 Args: 

33 input_energy_path (str): Path to the input EDR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/energy.edr>`_. Accepted formats: edr (edam:format_2330). 

34 output_xvg_path (str): Path to the XVG output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_energy.xvg>`_. Accepted formats: xvg (edam:format_2030). 

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

36 * **xvg** (*str*) - ("none") XVG plot formatting. Values: xmgrace, xmgr, none. 

37 * **terms** (*list*) - (["Potential"]) Energy terms. Values: Angle, Proper-Dih., Improper-Dih., LJ-14, Coulomb-14, LJ-\(SR\), Coulomb-\(SR\), Coul.-recip., Position-Rest., Potential, Kinetic-En., Total-Energy, Temperature, Pressure, Constr.-rmsd, Box-X, Box-Y, Box-Z, Volume, Density, pV, Enthalpy, Vir-XX, Vir-XY, Vir-XZ, Vir-YX, Vir-YY, Vir-YZ, Vir-ZX, Vir-ZY, Vir-ZZ, Pres-XX, Pres-XY, Pres-XZ, Pres-YX, Pres-YY, Pres-YZ, Pres-ZX, Pres-ZY, Pres-ZZ, #Surf*SurfTen, Box-Vel-XX, Box-Vel-YY, Box-Vel-ZZ, Mu-X, Mu-Y, Mu-Z, T-Protein, T-non-Protein, Lamb-Protein, Lamb-non-Protein. 

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

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

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

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

42 * **container_path** (*str*) - (None) Container path definition. 

43 * **container_image** (*str*) - ('gromacs/gromacs:2022.2') Container image definition. 

44 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. 

45 * **container_working_dir** (*str*) - (None) Container working directory definition. 

46 * **container_user_id** (*str*) - (None) Container user_id definition. 

47 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. 

48 

49 Examples: 

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

51 

52 from biobb_analysis.gromacs.gmx_energy import gmx_energy 

53 prop = { 

54 'xvg': 'xmgr', 

55 'terms': ['Potential', 'Pressure'] 

56 } 

57 gmx_energy(input_energy_path='/path/to/myEnergyFile.edr', 

58 output_xvg_path='/path/to/newXVG.xvg', 

59 properties=prop) 

60 

61 Info: 

62 * wrapped_software: 

63 * name: GROMACS energy 

64 * version: >=2019.1 

65 * license: LGPL 2.1 

66 * ontology: 

67 * name: EDAM 

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

69 

70 """ 

71 

72 def __init__( 

73 self, input_energy_path, output_xvg_path, properties=None, **kwargs 

74 ) -> None: 

75 properties = properties or {} 

76 

77 # Call parent class constructor 

78 super().__init__(properties) 

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

80 

81 # Input/Output files 

82 self.io_dict = { 

83 "in": {"input_energy_path": input_energy_path}, 

84 "out": {"output_xvg_path": output_xvg_path}, 

85 } 

86 

87 # Properties specific for BB 

88 self.xvg = properties.get("xvg", "none") 

89 self.terms = _from_string_to_list(properties.get("terms", ["Potential"])) 

90 self.instructions_file = get_default_value("instructions_file") 

91 self.properties = properties 

92 

93 # Properties common in all GROMACS BB 

94 self.binary_path = get_binary_path(properties, "binary_path") 

95 

96 # Check the properties 

97 self.check_properties(properties) 

98 self.check_arguments() 

99 

100 def check_data_params(self, out_log, err_log): 

101 """Checks all the input/output paths and parameters""" 

102 self.io_dict["in"]["input_energy_path"] = check_energy_path( 

103 self.io_dict["in"]["input_energy_path"], out_log, self.__class__.__name__ 

104 ) 

105 self.io_dict["out"]["output_xvg_path"] = check_out_xvg_path( 

106 self.io_dict["out"]["output_xvg_path"], out_log, self.__class__.__name__ 

107 ) 

108 self.xvg = get_xvg(self.properties, out_log, self.__class__.__name__) 

109 self.terms = get_terms(self.properties, out_log, self.__class__.__name__) 

110 

111 def create_instructions_file(self): 

112 """Creates an input file using the properties file settings""" 

113 instructions_list = [] 

114 # different path if container execution or not 

115 if self.container_path: 

116 self.instructions_file = str( 

117 PurePath(self.container_volume_path).joinpath(self.instructions_file) 

118 ) 

119 else: 

120 self.instructions_file = str( 

121 PurePath(fu.create_unique_dir()).joinpath(self.instructions_file) 

122 ) 

123 # self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file)) 

124 fu.create_name(prefix=self.prefix, step=self.step, name=self.instructions_file) 

125 

126 for t in self.terms: 

127 instructions_list.append(t) 

128 

129 # create instructions file 

130 with open(self.instructions_file, "w") as mdp: 

131 for line in instructions_list: 

132 mdp.write(line.strip() + "\n") 

133 

134 return self.instructions_file 

135 

136 @launchlogger 

137 def launch(self) -> int: 

138 """Execute the :class:`GMXEnergy <gromacs.gmx_energy.GMXEnergy>` gromacs.gmx_energy.GMXEnergy object.""" 

139 

140 # check input/output paths and parameters 

141 self.check_data_params(self.out_log, self.err_log) 

142 

143 # Setup Biobb 

144 if self.check_restart(): 

145 return 0 

146 self.stage_files() 

147 

148 # create instructions file 

149 self.create_instructions_file() 

150 

151 # if container execution, copy intructions file to container 

152 if self.container_path: 

153 copy_instructions_file_to_container( 

154 self.instructions_file, self.stage_io_dict.get("unique_dir") 

155 ) 

156 

157 self.cmd = [ 

158 self.binary_path, 

159 "energy", 

160 "-f", 

161 self.stage_io_dict["in"]["input_energy_path"], 

162 "-o", 

163 self.stage_io_dict["out"]["output_xvg_path"], 

164 "-xvg", 

165 self.xvg, 

166 "<", 

167 self.instructions_file, 

168 ] 

169 

170 # Run Biobb block 

171 self.run_biobb() 

172 

173 # Copy files to host 

174 self.copy_to_host() 

175 

176 self.tmp_files.extend( 

177 [ 

178 self.stage_io_dict.get("unique_dir", ""), 

179 str(str(PurePath(self.instructions_file).parent)), 

180 ] 

181 ) 

182 self.remove_tmp_files() 

183 

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

185 

186 return self.return_code 

187 

188 

189def gmx_energy( 

190 input_energy_path: str, 

191 output_xvg_path: str, 

192 properties: Optional[dict] = None, 

193 **kwargs, 

194) -> int: 

195 """Execute the :class:`GMXEnergy <gromacs.gmx_energy.GMXEnergy>` class and 

196 execute the :meth:`launch() <gromacs.gmx_energy.GMXEnergy.launch>` method.""" 

197 

198 return GMXEnergy( 

199 input_energy_path=input_energy_path, 

200 output_xvg_path=output_xvg_path, 

201 properties=properties, 

202 **kwargs, 

203 ).launch() 

204 

205 

206def main(): 

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

208 parser = argparse.ArgumentParser( 

209 description="Extracts energy components from a given GROMACS energy file.", 

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

211 ) 

212 parser.add_argument("--config", required=False, help="Configuration file") 

213 

214 # Specific args of each building block 

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

216 required_args.add_argument( 

217 "--input_energy_path", 

218 required=True, 

219 help="Path to the input EDR file. Accepted formats: edr.", 

220 ) 

221 required_args.add_argument( 

222 "--output_xvg_path", 

223 required=True, 

224 help="Path to the XVG output file. Accepted formats: xvg.", 

225 ) 

226 

227 args = parser.parse_args() 

228 args.config = args.config or "{}" 

229 properties = settings.ConfReader(config=args.config).get_prop_dic() 

230 

231 # Specific call of each building block 

232 gmx_energy( 

233 input_energy_path=args.input_energy_path, 

234 output_xvg_path=args.output_xvg_path, 

235 properties=properties, 

236 ) 

237 

238 

239if __name__ == "__main__": 

240 main()