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annotate rdkit_descriptors.py @ 0:55a2082540a9 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
author bgruening
date Sat, 04 Dec 2021 16:36:56 +0000
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55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import inspect
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5 import sys
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6
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7 from rdkit import Chem
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8 from rdkit.Chem import Descriptors
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9
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10
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11 def get_supplier(infile, format="smiles"):
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12 """
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13 Returns a generator over a SMILES or InChI file. Every element is of RDKit
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14 molecule and has its original string as _Name property.
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15 """
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16 with open(infile) as handle:
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17 for line in handle:
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18 line = line.strip()
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19 if format == "smiles":
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20 mol = Chem.MolFromSmiles(line, sanitize=True)
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21 elif format == "inchi":
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22 mol = Chem.inchi.MolFromInchi(
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23 line,
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24 sanitize=True,
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25 removeHs=True,
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26 logLevel=None,
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27 treatWarningAsError=False,
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28 )
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29 if mol is None:
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30 yield False
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31 else:
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32 mol.SetProp("_Name", line.split("\t")[0])
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33 yield mol
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34
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35
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36 def get_rdkit_descriptor_functions():
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37 """
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38 Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function)
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39 """
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40 ret = [
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41 (name, f)
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42 for name, f in inspect.getmembers(Descriptors)
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43 if inspect.isfunction(f) and not name.startswith("_")
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44 ]
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45 # some which are not in the official Descriptors module we need to add manually
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46 ret.extend([("FormalCharge", Chem.GetFormalCharge), ("SSSR", Chem.GetSSSR)])
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47 ret.sort()
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48 return ret
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49
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50
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51 def descriptors(mol, functions):
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52 """
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53 Calculates the descriptors of a given molecule.
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54 """
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55 for name, function in functions:
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56 yield (name, function(mol))
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57
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58
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59 if __name__ == "__main__":
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60 parser = argparse.ArgumentParser()
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61 parser.add_argument("-i", "--infile", required=True, help="Path to the input file.")
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62 parser.add_argument("--iformat", help="Specify the input file format.")
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63
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64 parser.add_argument(
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65 "-o",
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66 "--outfile",
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67 type=argparse.FileType("w+"),
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68 default=sys.stdout,
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69 help="path to the result file, default is stdout",
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70 )
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71
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72 parser.add_argument(
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73 "-s",
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74 "--select",
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75 default=None,
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76 help="select a subset of comma-separated descriptors to use",
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77 )
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78
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79 parser.add_argument(
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80 "--header",
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81 dest="header",
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82 action="store_true",
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83 default=False,
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84 help="Write header line.",
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85 )
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86
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87 args = parser.parse_args()
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88
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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89 if args.iformat == "sdf":
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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90 supplier = Chem.SDMolSupplier(args.infile)
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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91 elif args.iformat == "smi":
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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92 supplier = get_supplier(args.infile, format="smiles")
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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93 elif args.iformat == "inchi":
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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94 supplier = get_supplier(args.infile, format="inchi")
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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95 elif args.iformat == "pdb":
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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96 supplier = [Chem.MolFromPDBFile(args.infile)]
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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97 elif args.iformat == "mol2":
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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98 supplier = [Chem.MolFromMol2File(args.infile)]
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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99
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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100 functions = get_rdkit_descriptor_functions()
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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101 if args.select and args.select != "None":
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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102 selected = args.select.split(",")
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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103 functions = [(name, f) for name, f in functions if name in selected]
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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104
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
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105 if args.header:
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
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106 args.outfile.write(
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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107 "%s\n" % "\t".join(["MoleculeID"] + [name for name, f in functions])
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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108 )
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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109
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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110 for mol in supplier:
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
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111 if not mol:
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
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112 continue
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
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113 descs = descriptors(mol, functions)
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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114 try:
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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115 molecule_id = mol.GetProp("_Name")
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
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116 except KeyError:
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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117 molecule_id = Chem.MolToSmiles(mol)
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
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118 args.outfile.write(
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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119 "%s\n"
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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120 % "\t".join([molecule_id] + [str(round(res, 6)) for name, res in descs])
55a2082540a9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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121 )