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comparison qed.py @ 1:ab73abead7fa draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:41:23 -0400
parents 5ccd3a432785
children 52a8d34dd08f
comparison
equal deleted inserted replaced
0:5ccd3a432785 1:ab73abead7fa
328 args = parser.parse_args() 328 args = parser.parse_args()
329 329
330 # Elucidate filetype and open supplier 330 # Elucidate filetype and open supplier
331 ifile = os.path.abspath(args.input) 331 ifile = os.path.abspath(args.input)
332 if not os.path.isfile(ifile): 332 if not os.path.isfile(ifile):
333 print "Error: ", ifile, " is not a file or cannot be found." 333 print("Error: ", ifile, " is not a file or cannot be found.")
334 sys.exit(1) 334 sys.exit(1)
335 if not os.path.exists(ifile): 335 if not os.path.exists(ifile):
336 print "Error: ", ifile, " does not exist or cannot be found." 336 print("Error: ", ifile, " does not exist or cannot be found.")
337 sys.exit(1) 337 sys.exit(1)
338 if not os.access(ifile, os.R_OK): 338 if not os.access(ifile, os.R_OK):
339 print "Error: ", ifile, " is not readable." 339 print("Error: ", ifile, " is not readable.")
340 sys.exit(1) 340 sys.exit(1)
341 341
342 if not args.iformat: 342 if not args.iformat:
343 # try to guess the filetype 343 # try to guess the filetype
344 filetype = check_filetype( ifile ) 344 filetype = check_filetype(ifile)
345 else: 345 else:
346 filetype = args.iformat # sdf or smi 346 filetype = args.iformat # sdf or smi
347 347
348 348
349 """ 349 """
350 We want to store the original SMILES in the output. So in case of a SMILES file iterate over the file and convert each line separate. 350 We want to store the original SMILES in the output. So in case of a SMILES file iterate over the file and convert each line separate.
351 """ 351 """
352 if filetype == 'sdf': 352 if filetype == 'sdf':
353 supplier = Chem.SDMolSupplier( ifile ) 353 supplier = Chem.SDMolSupplier(ifile)
354 # Process file 354 # Process file
355 if args.header: 355 if args.header:
356 args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n") 356 args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n")
357 count = 0 357 count = 0
358 for mol in supplier: 358 for mol in supplier:
359 count += 1 359 count += 1
360 if mol is None: 360 if mol is None:
361 print "Warning: skipping molecule ", count, " and continuing with next." 361 print("Warning: skipping molecule ", count, " and continuing with next.")
362 continue 362 continue
363 props = properties(mol) 363 props = properties(mol)
364 364
365 if args.method == 'max': 365 if args.method == 'max':
366 calc_qed = weights_max(mol, True, props) 366 calc_qed = weights_max(mol, True, props)
397 smiles = tokens[0] 397 smiles = tokens[0]
398 title = '' 398 title = ''
399 mol = Chem.MolFromSmiles(smiles) 399 mol = Chem.MolFromSmiles(smiles)
400 count += 1 400 count += 1
401 if mol is None: 401 if mol is None:
402 print "Warning: skipping molecule ", count, " and continuing with next." 402 print("Warning: skipping molecule ", count, " and continuing with next.")
403 continue 403 continue
404 props = properties(mol) 404 props = properties(mol)
405 405
406 if args.method == 'max': 406 if args.method == 'max':
407 calc_qed = weights_max(mol, True, props) 407 calc_qed = weights_max(mol, True, props)