Coverage for biobb_amber / leap / leap_gen_top.py: 64%

1#!/usr/bin/env python3 

2 

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

4 

5import os 

6from pathlib import PurePath 

7from typing import List, Optional 

8 

9from biobb_common.generic.biobb_object import BiobbObject 

10from biobb_common.tools import file_utils as fu 

11from biobb_common.tools.file_utils import launchlogger 

12 

13from biobb_amber.leap.common import _from_string_to_list 

14 

15 

16class LeapGenTop(BiobbObject): 

17 """ 

18 | biobb_amber.leap.leap_gen_top LeapGenTop 

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

20 | Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package. 

21 

22 Args: 

23 input_pdb_path (str): Input 3D structure PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/structure.leapin.pdb>`_. Accepted formats: pdb (edam:format_1476). 

24 input_lib_path (str) (Optional): Input ligand library parameters file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.lib>`_. Accepted formats: lib (edam:format_3889), zip (edam:format_3987). 

25 input_frcmod_path (str) (Optional): Input ligand frcmod parameters file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.frcmod>`_. Accepted formats: frcmod (edam:format_3888), zip (edam:format_3987). 

26 input_params_path (str) (Optional): Additional leap parameter files to load with loadAmberParams Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/frcmod.ionsdang_spce.txt>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987). 

27 input_prep_path (str) (Optional): Additional leap parameter files to load with loadAmberPrep Leap command. File type: input. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987). 

28 input_source_path (str) (Optional): Additional leap command files to load with source Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/leaprc.water.spce.txt>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987). 

29 output_pdb_path (str): Output 3D structure PDB file matching the topology file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.leap.pdb>`_. Accepted formats: pdb (edam:format_1476). 

30 output_top_path (str): Output topology file (AMBER ParmTop). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.leap.top>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881). 

31 output_crd_path (str): Output coordinates file (AMBER crd). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.leap.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878). 

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

33 * **forcefield** (*list*) - (["protein.ff14SB","DNA.bsc1","gaff"]) Forcefields to be used for the structure generation. Each item should be either a path to a leaprc file or a string with the leaprc file name if the force field is included with Amber (e.g. "/path/to/leaprc.protein.ff14SB" or "protein.ff14SB"). Default values: ["protein.ff14SB","DNA.bsc1","gaff"]. 

34 * **binary_path** (*str*) - ("tleap") Path to the tleap executable binary. 

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

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

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

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

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

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

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

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

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

44 

45 Examples: 

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

47 

48 from biobb_amber.leap.leap_gen_top import leap_gen_top 

49 prop = { 

50 'forcefield': ['protein.ff14SB'] 

51 } 

52 leap_gen_top(input_pdb_path='/path/to/structure.pdb', 

53 output_pdb_path='/path/to/newStructure.pdb', 

54 output_top_path='/path/to/newTopology.top', 

55 output_crd_path='/path/to/newCoordinates.crd', 

56 properties=prop) 

57 

58 Info: 

59 * wrapped_software: 

60 * name: AmberTools tLeap 

61 * version: >20.9 

62 * license: LGPL 2.1 

63 * ontology: 

64 * name: EDAM 

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

66 

67 """ 

68 

69 def __init__( 

70 self, 

71 input_pdb_path: str, 

72 output_pdb_path: str, 

73 output_top_path: str, 

74 output_crd_path: str, 

75 input_lib_path: Optional[str] = None, 

76 input_frcmod_path: Optional[str] = None, 

77 input_params_path: Optional[str] = None, 

78 input_prep_path: Optional[str] = None, 

79 input_source_path: Optional[str] = None, 

80 properties: Optional[dict] = None, 

81 **kwargs, 

82 ): 

83 properties = properties or {} 

84 

85 # Call parent class constructor 

86 super().__init__(properties) 

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

88 

89 # Input/Output files 

90 self.io_dict = { 

91 "in": { 

92 "input_pdb_path": input_pdb_path, 

93 "input_lib_path": input_lib_path, 

94 "input_frcmod_path": input_frcmod_path, 

95 "input_params_path": input_params_path, 

96 "input_prep_path": input_prep_path, 

97 "input_source_path": input_source_path, 

98 }, 

99 "out": { 

100 "output_pdb_path": output_pdb_path, 

101 "output_top_path": output_top_path, 

102 "output_crd_path": output_crd_path, 

103 }, 

104 } 

105 

106 # # Ligand Parameter lists 

107 # self.ligands_lib_list = [] 

108 # if input_lib_path: 

109 # self.ligands_lib_list.append(input_lib_path) 

110 # 

111 # self.ligands_frcmod_list = [] 

112 # if input_frcmod_path: 

113 # self.ligands_frcmod_list.append(input_frcmod_path) 

114 

115 # Properties specific for BB 

116 self.properties = properties 

117 

118 # Set default forcefields 

119 if self.container_path: 

120 #self.forcefield = "leaprc.protein.ff14SB" 

121 self.forcefield = _from_string_to_list( 

122 properties.get("forcefield", ['leaprc.protein.ff14SB', 'leaprc.DNA.bsc1', 'leaprc.gaff']) 

123 ) 

124 else: 

125 amber_home_path = os.getenv("AMBERHOME") 

126 protein_ff14SB_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.protein.ff14SB') 

127 dna_bsc1_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.DNA.bsc1') 

128 gaff_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.gaff') 

129 

130 self.forcefield = _from_string_to_list( 

131 properties.get("forcefield", [protein_ff14SB_path, dna_bsc1_path, gaff_path]) 

132 ) 

133 # Find the paths of the leaprc files if only the force field names are provided 

134 self.forcefield = self.find_leaprc_paths(self.forcefield) 

135 

136 self.binary_path = properties.get("binary_path", "tleap") 

137 

138 # Check the properties 

139 self.check_properties(properties) 

140 self.check_arguments() 

141 

142 def find_leaprc_paths(self, forcefields: List[str]) -> List[str]: 

143 """ 

144 Find the leaprc paths for the force fields provided. 

145 

146 For each item in the forcefields list, the function checks if the str is a path to an existing file. 

147 If not, it tries to find the file in the $AMBERHOME/dat/leap/cmd/ directory or the $AMBERHOME/dat/leap/cmd/oldff/ 

148 directory with and without the leaprc prefix. 

149 

150 Args: 

151 forcefields (List[str]): List of force fields to find the leaprc files for. 

152 

153 Returns: 

154 List[str]: List of leaprc file paths. 

155 """ 

156 

157 leaprc_paths = [] 

158 

159 for forcefield in forcefields: 

160 

161 num_paths = len(leaprc_paths) 

162 

163 # Check if the forcefield is a path to an existing file 

164 if os.path.exists(forcefield): 

165 leaprc_paths.append(forcefield) 

166 continue 

167 

168 # Check if the forcefield is in the leaprc directory 

169 leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', f"leaprc.{forcefield}") 

170 if os.path.exists(leaprc_path): 

171 leaprc_paths.append(leaprc_path) 

172 continue 

173 

174 # Check if the forcefield is in the oldff directory 

175 leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', 'oldff', f"leaprc.{forcefield}") 

176 if os.path.exists(leaprc_path): 

177 leaprc_paths.append(leaprc_path) 

178 continue 

179 

180 # Check if the forcefield is in the leaprc directory without the leaprc prefix 

181 leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', f"{forcefield}") 

182 if os.path.exists(leaprc_path): 

183 leaprc_paths.append(leaprc_path) 

184 continue 

185 

186 # Check if the forcefield is in the oldff directory without the leaprc prefix 

187 leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', 'oldff', f"{forcefield}") 

188 if os.path.exists(leaprc_path): 

189 leaprc_paths.append(leaprc_path) 

190 continue 

191 

192 new_num_paths = len(leaprc_paths) 

193 

194 if new_num_paths == num_paths: 

195 raise ValueError(f"Force field {forcefield} not found. Check the $AMBERHOME/dat/leap/cmd/ directory for available force fields or provide the path to an existing leaprc file.") 

196 

197 return leaprc_paths 

198 

199 # def check_data_params(self, out_log, err_log): 

200 # """ Checks input/output paths correctness """ 

201 

202 # # Check input(s) 

203 # self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", False, out_log, self.__class__.__name__) 

204 # self.io_dict["in"]["input_lib_path"] = check_input_path(self.io_dict["in"]["input_lib_path"], "input_lib_path", True, out_log, self.__class__.__name__) 

205 # self.io_dict["in"]["input_frcmod_path"] = check_input_path(self.io_dict["in"]["input_frcmod_path"], "input_frcmod_path", True, out_log, self.__class__.__name__) 

206 # # self.io_dict["in"]["input_params_path"] = check_input_path(self.io_dict["in"]["input_params_path"], "input_params_path", True, out_log, self.__class__.__name__) 

207 # # self.io_dict["in"]["input_prep_path"] = check_input_path(self.io_dict["in"]["input_params_path"], "input_params_path", True, out_log, self.__class__.__name__) 

208 # # self.io_dict["in"]["input_source_path"] = check_input_path(self.io_dict["in"]["input_source_path"], "input_source_path", True, out_log, self.__class__.__name__) 

209 

210 # # Check output(s) 

211 # self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, out_log, self.__class__.__name__) 

212 # self.io_dict["out"]["output_top_path"] = check_output_path(self.io_dict["out"]["output_top_path"], "output_top_path", False, out_log, self.__class__.__name__) 

213 # self.io_dict["out"]["output_crd_path"] = check_output_path(self.io_dict["out"]["output_crd_path"], "output_crd_path", False, out_log, self.__class__.__name__) 

214 

215 @launchlogger 

216 def launch(self): 

217 """Launches the execution of the LeapGenTop module.""" 

218 

219 # check input/output paths and parameters 

220 # self.check_data_params(self.out_log, self.err_log) 

221 

222 # Setup Biobb 

223 if self.check_restart(): 

224 return 0 

225 self.stage_files() 

226 

227 # Creating temporary folder & Leap configuration (instructions) file 

228 if self.container_path: 

229 instructions_file = str( 

230 PurePath(self.stage_io_dict["unique_dir"]).joinpath("leap.in") 

231 ) 

232 instructions_file_path = str( 

233 PurePath(self.container_volume_path).joinpath("leap.in") 

234 ) 

235 tmp_folder = None 

236 else: 

237 tmp_folder = fu.create_unique_dir() 

238 instructions_file = str(PurePath(tmp_folder).joinpath("leap.in")) 

239 fu.log("Creating %s temporary folder" % tmp_folder, self.out_log) 

240 instructions_file_path = instructions_file 

241 

242 ligands_lib_list = [] 

243 if self.io_dict["in"]["input_lib_path"] is not None: 

244 if self.io_dict["in"]["input_lib_path"].endswith(".zip"): 

245 ligands_lib_list = fu.unzip_list( 

246 self.stage_io_dict["in"]["input_lib_path"], 

247 dest_dir=tmp_folder, 

248 out_log=self.out_log, 

249 ) 

250 else: 

251 ligands_lib_list.append(self.stage_io_dict["in"]["input_lib_path"]) 

252 

253 ligands_frcmod_list = [] 

254 if self.io_dict["in"]["input_frcmod_path"] is not None: 

255 if self.io_dict["in"]["input_frcmod_path"].endswith(".zip"): 

256 ligands_frcmod_list = fu.unzip_list( 

257 self.stage_io_dict["in"]["input_frcmod_path"], 

258 dest_dir=tmp_folder, 

259 out_log=self.out_log, 

260 ) 

261 else: 

262 ligands_frcmod_list.append( 

263 self.stage_io_dict["in"]["input_frcmod_path"] 

264 ) 

265 

266 amber_params_list = [] 

267 if self.io_dict["in"]["input_params_path"] is not None: 

268 if self.io_dict["in"]["input_params_path"].endswith(".zip"): 

269 amber_params_list = fu.unzip_list( 

270 self.stage_io_dict["in"]["input_params_path"], 

271 dest_dir=tmp_folder, 

272 out_log=self.out_log, 

273 ) 

274 else: 

275 amber_params_list.append(self.stage_io_dict["in"]["input_params_path"]) 

276 

277 amber_prep_list = [] 

278 if self.io_dict["in"]["input_prep_path"] is not None: 

279 if self.io_dict["in"]["input_prep_path"].endswith(".zip"): 

280 amber_prep_list = fu.unzip_list( 

281 self.stage_io_dict["in"]["input_prep_path"], 

282 dest_dir=tmp_folder, 

283 out_log=self.out_log, 

284 ) 

285 else: 

286 amber_prep_list.append(self.stage_io_dict["in"]["input_prep_path"]) 

287 

288 leap_source_list = [] 

289 if self.io_dict["in"]["input_source_path"] is not None: 

290 if self.io_dict["in"]["input_source_path"].endswith(".zip"): 

291 leap_source_list = fu.unzip_list( 

292 self.stage_io_dict["in"]["input_source_path"], 

293 dest_dir=tmp_folder, 

294 out_log=self.out_log, 

295 ) 

296 else: 

297 leap_source_list.append(self.stage_io_dict["in"]["input_source_path"]) 

298 

299 with open(instructions_file, "w") as leapin: 

300 # Forcefields loaded by default: 

301 # Protein: ff14SB (PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA) 

302 # leapin.write("source leaprc.protein.ff14SB \n") 

303 # DNA: parmBSC1 (ParmBSC1 (ff99 + bsc0 + bsc1) for DNA. Ivani et al. Nature Methods 13: 55, 2016) 

304 # leapin.write("source leaprc.DNA.bsc1 \n") 

305 # Ligands: GAFF (General Amber Force field, J. Comput. Chem. 2004 Jul 15;25(9):1157-74) 

306 # leapin.write("source leaprc.gaff \n") 

307 

308 # Forcefields loaded from input forcefield property 

309 for t in self.forcefield: 

310 if self.container_path: 

311 leapin.write("source leaprc.{}\n".format(t)) 

312 else: 

313 leapin.write("source {}\n".format(t)) 

314 

315 # Additional Leap commands 

316 for leap_commands in leap_source_list: 

317 leapin.write("source " + leap_commands + "\n") 

318 

319 # Additional Amber parameters 

320 for amber_params in amber_params_list: 

321 leapin.write("loadamberparams " + amber_params + "\n") 

322 

323 # Additional Amber prep files 

324 for amber_prep in amber_prep_list: 

325 leapin.write("loadamberprep " + amber_prep + "\n") 

326 

327 # Ions libraries 

328 leapin.write("loadOff atomic_ions.lib \n") 

329 

330 # Ligand(s) libraries (if any) 

331 for amber_lib in ligands_lib_list: 

332 leapin.write("loadOff " + amber_lib + "\n") 

333 for amber_frcmod in ligands_frcmod_list: 

334 leapin.write("loadamberparams " + amber_frcmod + "\n") 

335 

336 # Loading PDB file 

337 leapin.write( 

338 "mol = loadpdb " + self.stage_io_dict["in"]["input_pdb_path"] + " \n" 

339 ) 

340 

341 # Saving output PDB file, coordinates and topology 

342 leapin.write( 

343 "savepdb mol " + self.stage_io_dict["out"]["output_pdb_path"] + " \n" 

344 ) 

345 leapin.write( 

346 "saveAmberParm mol " + self.stage_io_dict["out"]["output_top_path"] + " " + self.stage_io_dict["out"]["output_crd_path"] + "\n" 

347 ) 

348 leapin.write("quit \n") 

349 

350 # Command line 

351 self.cmd = [self.binary_path, "-f", instructions_file_path] 

352 

353 # Run Biobb block 

354 self.run_biobb() 

355 

356 # Copy files to host 

357 self.copy_to_host() 

358 

359 # remove temporary folder(s) 

360 self.tmp_files.extend([str(tmp_folder), "leap.log"]) 

361 self.remove_tmp_files() 

362 

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

364 

365 return self.return_code 

366 

367 

368def leap_gen_top( 

369 input_pdb_path: str, 

370 output_pdb_path: str, 

371 output_top_path: str, 

372 output_crd_path: str, 

373 input_lib_path: Optional[str] = None, 

374 input_frcmod_path: Optional[str] = None, 

375 input_params_path: Optional[str] = None, 

376 input_prep_path: Optional[str] = None, 

377 input_source_path: Optional[str] = None, 

378 properties: Optional[dict] = None, 

379 **kwargs, 

380) -> int: 

381 """Create the :class:`LeapGenTop <leap.leap_gen_top.LeapGenTop>` class and 

382 execute the :meth:`launch() <leap.leap_gen_top.LeapGenTop.launch>` method.""" 

383 return LeapGenTop(**dict(locals())).launch() 

384 

385 

386leap_gen_top.__doc__ = LeapGenTop.__doc__ 

387main = LeapGenTop.get_main(leap_gen_top, "Generating a MD topology from a molecule structure using tLeap program from AmberTools MD package.") 

388 

389if __name__ == "__main__": 

390 main()