Coverage for biobb_amber/cphstats/cestats_run.py: 64%

1#!/usr/bin/env python3 

2 

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

4import argparse 

5from typing import Optional 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.configuration import settings 

8from biobb_common.tools.file_utils import launchlogger 

9from biobb_amber.cphstats.common import check_input_path, check_output_path 

10 

11 

12class CestatsRun(BiobbObject): 

13 """ 

14 | biobb_amber CestatsRun 

15 | Wrapper of the `AmberTools (AMBER MD Package) cestats tool <https://ambermd.org/AmberTools.php>`_ module. 

16 | Analyzing the results of constant Redox potential MD simulations using cestats tool from the AMBER MD package. 

17 

18 Args: 

19 input_cein_path (str): Input cein or cpein file (from pmemd or sander) with titrating residue information. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/cphstats/structure.cein>`_. Accepted formats: cein (edam:format_2330), cpein (edam:format_2330). 

20 input_ceout_path (str): Output ceout file (AMBER ceout). File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/cphstats/sander.ceout.gz>`_. Accepted formats: ceout (edam:format_2330), zip (edam:format_3987), gzip (edam:format_3987), gz (edam:format_3987). 

21 output_dat_path (str): Output file to which the standard calceo-type statistics are written. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). 

22 output_population_path (str) (Optional): Output file where protonation state populations are printed for every state of every residue. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). 

23 output_chunk_path (str) (Optional): Output file where the time series data calculated over chunks of the simulation are printed. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). 

24 output_cumulative_path (str) (Optional): Output file where the cumulative time series data is printed. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). 

25 output_conditional_path (str) (Optional): Output file with requested conditional probabilities. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). 

26 output_chunk_conditional_path (str) (Optional): Output file with a time series of the conditional probabilities over a trajectory split up into chunks. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). 

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

28 * **timestep** (*float*) - (0.002) Simulation time step -in ps-, used to print data as a function of time. 

29 * **verbose** (*bool*) - (False) Controls how much information is printed to the calceo-style output file. Options are: False - Just print fraction protonated. True - Print everything calceo prints. 

30 * **interval** (*int*) - (1000) Interval between which to print out time series data like chunks, cumulative data, and running averages. It is also used as the window of the conditional probability time series. 

31 * **reduced** (*bool*) - (True) Print out reduction fraction instead of oxidation fraction in time series data. 

32 * **eos** (*bool*) - (False) Print predicted Eos -via Nernst equation- in place of fraction reduced or oxidized. 

33 * **calceo** (*bool*) - (True) Triggers the calceo-style output. 

34 * **running_avg_window** (*int*) - (100) Defines a window size -in MD steps- for a moving, running average time series. 

35 * **chunk_window** (*int*) - (100) Computes the time series data over a chunk of the simulation of this specified size -window- time steps. 

36 * **cumulative** (*bool*) - (False) Computes the cumulative average time series data over the course of the trajectory. 

37 * **fix_remd** (*str*) - ("") This option will trigger cestats to reassemble the titration data into pH-specific ensembles. This is an exclusive mode of the program, no other analyses will be done. 

38 * **conditional** (*str*) - ("") Evaluates conditional probabilities. CONDITIONAL should be a string of the format: <resid>:<state>,<resid>:<state>,... or <resid>:PROT,<resid>:DEPROT,... or <resid>:<state1>;<state2>,<resid>:PROT,... where <resid> is the residue number in the prmtop and <state> is either the state number or -p-rotonated or -d-eprotonated, case-insensitive. 

39 * **binary_path** (*str*) - ("cestats") Path to the cestats executable binary. 

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

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

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

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

44 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition. 

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

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

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

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

49 

50 Examples: 

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

52 

53 from biobb_amber.cestats.cestats_run import cestats_run 

54 prop = { 

55 'timestep' : 0.002 

56 } 

57 cestats_run(input_cein_path='/path/to/cein.cein', 

58 input_ceout_path='/path/to/ceout.cpout', 

59 output_dat_path='/path/to/cestats.dat', 

60 properties=prop) 

61 

62 Info: 

63 * wrapped_software: 

64 * name: AMBER cestats 

65 * version: >=1.5 

66 * license: other 

67 * ontology: 

68 * name: EDAM 

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

70 

71 """ 

72 

73 def __init__(self, input_cein_path: str, input_ceout_path: str, output_dat_path: str, output_population_path: Optional[str] = None, 

74 output_chunk_path: Optional[str] = None, output_cumulative_path: Optional[str] = None, output_conditional_path: Optional[str] = None, output_chunk_conditional_path: Optional[str] = None, 

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

76 

77 properties = properties or {} 

78 

79 # Call parent class constructor 

80 super().__init__(properties) 

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

82 

83 # Input/Output files 

84 self.io_dict = { 

85 'in': {'input_cein_path': input_cein_path, 

86 'input_ceout_path': input_ceout_path}, 

87 'out': {'output_dat_path': output_dat_path, 

88 'output_population_path': output_population_path, 

89 'output_chunk_path': output_chunk_path, 

90 'output_cumulative_path': output_cumulative_path, 

91 'output_conditional_path': output_conditional_path, 

92 'output_chunk_conditional_path': output_chunk_conditional_path} 

93 } 

94 

95 # Properties specific for BB 

96 self.properties = properties 

97 self.timestep = properties.get('timestep', 0.002) 

98 self.verbose = properties.get('verbose', False) 

99 self.interval = properties.get('interval', 1000) 

100 self.reduced = properties.get('reduced', True) 

101 self.eos = properties.get('eos', False) 

102 self.calceo = properties.get('calceo', True) 

103 self.running_avg_window = properties.get('running_avg_window', 100) 

104 self.chunk_window = properties.get('chunk_window', 100) 

105 self.cumulative = properties.get('cumulative', False) 

106 self.fix_remd = properties.get('fix_remd', "") 

107 self.conditional = properties.get('conditional', "") 

108 self.binary_path = properties.get('binary_path', 'cestats') 

109 

110 # Check the properties 

111 self.check_properties(properties) 

112 self.check_arguments() 

113 

114 def check_data_params(self, out_log, err_log): 

115 """ Checks input/output paths correctness """ 

116 

117 # Check input(s) 

118 self.io_dict["in"]["input_cein_path"] = check_input_path(self.io_dict["in"]["input_cein_path"], "input_cein_path", False, out_log, self.__class__.__name__) 

119 self.io_dict["in"]["input_ceout_path"] = check_input_path(self.io_dict["in"]["input_ceout_path"], "input_ceout_path", False, out_log, self.__class__.__name__) 

120 

121 # Check output(s) 

122 self.io_dict["out"]["output_dat_path"] = check_output_path(self.io_dict["out"]["output_dat_path"], "output_dat_path", False, out_log, self.__class__.__name__) 

123 self.io_dict["out"]["output_population_path"] = check_output_path(self.io_dict["out"]["output_population_path"], "output_population_path", True, out_log, self.__class__.__name__) 

124 self.io_dict["out"]["output_chunk_path"] = check_output_path(self.io_dict["out"]["output_chunk_path"], "output_chunk_path", True, out_log, self.__class__.__name__) 

125 self.io_dict["out"]["output_cumulative_path"] = check_output_path(self.io_dict["out"]["output_cumulative_path"], "output_cumulative_path", True, out_log, self.__class__.__name__) 

126 self.io_dict["out"]["output_chunk_conditional_path"] = check_output_path(self.io_dict["out"]["output_chunk_conditional_path"], "output_chunk_conditional_path", True, out_log, self.__class__.__name__) 

127 self.io_dict["out"]["output_conditional_path"] = check_output_path(self.io_dict["out"]["output_conditional_path"], "output_conditional_path", True, out_log, self.__class__.__name__) 

128 

129 @launchlogger 

130 def launch(self): 

131 """Launches the execution of the CestatsRun module.""" 

132 

133 # check input/output paths and parameters 

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

135 

136 # Setup Biobb 

137 if self.check_restart(): 

138 return 0 

139 self.stage_files() 

140 

141 # Command line 

142 # cphstats -i 4LYT.equil.cpin 0/4LYT.md1.cpout -o pH0_calcpka.dat --population pH0_populations.dat 

143 self.cmd = [self.binary_path, 

144 '-O', 

145 '-i', self.stage_io_dict['in']['input_cein_path'], 

146 '-o', self.stage_io_dict['out']['output_dat_path'], 

147 self.stage_io_dict['in']['input_ceout_path'] 

148 ] 

149 

150 if self.io_dict['out']['output_population_path']: 

151 self.cmd.append('--population ') 

152 self.cmd.append(self.stage_io_dict['out']['output_population_path']) 

153 

154 if self.io_dict['out']['output_chunk_path']: 

155 self.cmd.append('--chunk-out ') 

156 self.cmd.append(self.stage_io_dict['out']['output_chunk_path']) 

157 if self.chunk_window: 

158 self.cmd.append('--chunk') 

159 self.cmd.append(str(self.chunk_window)) 

160 

161 if self.io_dict['out']['output_cumulative_path']: 

162 self.cmd.append('--cumulative-out ') 

163 self.cmd.append(self.stage_io_dict['out']['output_cumulative_path']) 

164 

165 if self.io_dict['out']['output_conditional_path']: 

166 self.cmd.append('--conditional-output ') 

167 self.cmd.append(self.stage_io_dict['out']['output_conditional_path']) 

168 

169 if self.io_dict['out']['output_chunk_conditional_path']: 

170 self.cmd.append('--chunk-conditional ') 

171 self.cmd.append(self.stage_io_dict['out']['output_chunk_conditional_path']) 

172 

173 if self.verbose: 

174 self.cmd.append('-v 1') 

175 

176 if self.interval: 

177 self.cmd.append('-n') 

178 self.cmd.append(str(self.interval)) 

179 

180 if self.reduced: 

181 self.cmd.append('-p') 

182 else: 

183 self.cmd.append('-d') 

184 

185 if self.eos: 

186 self.cmd.append('-a') 

187 

188 if self.calceo: 

189 self.cmd.append('--calceo') 

190 else: 

191 self.cmd.append('--no-calceo') 

192 

193 if self.running_avg_window: 

194 self.cmd.append('-r') 

195 self.cmd.append(str(self.running_avg_window)) 

196 

197 if self.cumulative: 

198 self.cmd.append('--cumulative') 

199 

200 if self.fix_remd: 

201 self.cmd.append('--fix-remd') 

202 self.cmd.append(str(self.fix_remd)) 

203 

204 if self.conditional: 

205 self.cmd.append('-c') 

206 self.cmd.append(str(self.conditional)) 

207 

208 # Run Biobb block 

209 self.run_biobb() 

210 

211 # Copy files to host 

212 self.copy_to_host() 

213 

214 # Remove temporary file(s) 

215 # self.tmp_files.extend([ 

216 # self.stage_io_dict.get("unique_dir", "") 

217 # ]) 

218 self.remove_tmp_files() 

219 

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

221 

222 return self.return_code 

223 

224 

225def cestats_run(input_cein_path: str, input_ceout_path: str, 

226 output_dat_path: str, 

227 output_population_path: Optional[str] = None, output_chunk_path: Optional[str] = None, 

228 output_conditional_path: Optional[str] = None, output_chunk_conditional_path: Optional[str] = None, 

229 output_cumulative_path: Optional[str] = None, 

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

231 """Create :class:`CestatsRun <cestats.chpstats_run.CestatsRun>`cestats.chpstats_run.CestatsRun class and 

232 execute :meth:`launch() <cestats.chpstats_run.CestatsRun.launch>` method""" 

233 

234 return CestatsRun(input_cein_path=input_cein_path, 

235 input_ceout_path=input_ceout_path, 

236 output_dat_path=output_dat_path, 

237 output_population_path=output_population_path, 

238 output_chunk_path=output_chunk_path, 

239 output_chunk_conditional_path=output_chunk_conditional_path, 

240 output_conditional_path=output_conditional_path, 

241 output_cumulative_path=output_cumulative_path, 

242 properties=properties).launch() 

243 

244 cestats_run.__doc__ = CestatsRun.__doc__ 

245 

246 

247def main(): 

248 parser = argparse.ArgumentParser(description='Analyzing the results of constant Redox potential MD simulations using cestats tool from the AMBER MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

249 parser.add_argument('--config', required=False, help='Configuration file') 

250 

251 # Specific args 

252 required_args = parser.add_argument_group('required arguments') 

253 required_args.add_argument('--input_cein_path', required=True, help='Input cein or cpein file (from pmemd or sander) with titrating residue information. Accepted formats: cein, cpein.') 

254 required_args.add_argument('--input_ceout_path', required=True, help='Output ceout file (AMBER ceout). Accepted formats: ceout.') 

255 required_args.add_argument('--output_dat_path', required=True, help='Output file to which the standard calceo-type statistics are written. Accepted formats: dat, out, txt, o.') 

256 required_args.add_argument('--output_population_path', required=False, help='Output file where protonation state populations are printed for every state of every residue. Accepted formats: dat, out, txt, o.') 

257 required_args.add_argument('--output_chunk_path', required=False, help='Output file where the time series data calculated over chunks of the simulation are printed. Accepted formats: dat, out, txt, o.') 

258 required_args.add_argument('--output_cumulative_path', required=False, help='Output file where the cumulative time series data is printed. Accepted formats: dat, out, txt, o.') 

259 required_args.add_argument('--output_conditional_path', required=False, help='Output file with requested conditional probabilities. Accepted formats: dat, out, txt, o.') 

260 required_args.add_argument('--output_chunk_conditional_path', required=False, help='Output file with a time series of the conditional probabilities over a trajectory split up into chunks. Accepted formats: dat, out, txt, o.') 

261 

262 args = parser.parse_args() 

263 config = args.config if args.config else None 

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

265 

266 # Specific call 

267 cestats_run(input_cein_path=args.input_cein_path, 

268 input_ceout_path=args.input_ceout_path, 

269 output_dat_path=args.output_dat_path, 

270 output_population_path=args.output_population_path, 

271 output_chunk_path=args.output_chunk_path, 

272 output_cumulative_path=args.output_cumulative_path, 

273 output_conditional_path=args.output_conditional_path, 

274 output_chunk_conditional_path=args.output_chunk_conditional_path, 

275 properties=properties) 

276 

277 

278if __name__ == '__main__': 

279 main()