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annotate mordred_descriptors.py @ 0:ea68b86303e2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
author bgruening
date Thu, 23 May 2019 18:31:43 -0400
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children e2f40a02f31a
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ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
bgruening
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1 import argparse
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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2 import numpy as np
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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3 import pandas as pd
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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4 from mordred import Calculator, descriptors
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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5 from mordred.error import Missing, Error
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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6 from rdkit import Chem
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7 from rdkit.Chem.rdmolfiles import SDMolSupplier, SmilesMolSupplier
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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8
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ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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10 def convert_errors_to_nan(el):
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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11 """
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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12 Remove elements from the Mordred dataframe which are not
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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13 in float or int format
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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14 """
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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15 if type(el) == bool:
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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16 return int(el)
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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17 if type(el) not in [float, int, np.float64]:
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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18 return None
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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19 return el
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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22 def mol_supplier(filename, ext):
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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23 """
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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24 Based on the file extension, use the appropriate RDKit function to
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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25 load a chemical data file (SMILES or SDF) containing multiple molecules
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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26 and return a list of RDKit Mol objects
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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27 """
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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28 if ext == 'sdf':
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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29 return [n for n in SDMolSupplier(filename)]
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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30 with open(filename) as f:
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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31 mols = f.read().split('\n')
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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32 if ext == 'smi':
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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33 return [Chem.MolFromSmiles(mol, sanitize=True) for mol in mols]
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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34 if ext == 'inchi':
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35 return [Chem.inchi.MolFromInchi(mol, sanitize=True) for mol in mols]
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38 def mordred_descriptors(mols, output, header, use_3d):
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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39 """
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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40 Calculate Mordred descriptors and save as tabular
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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41 """
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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42 calc = Calculator(descriptors, ignore_3D=(not use_3d))
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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43 invalid_mols = np.where(np.array(mols) == None)[0] # indices of invalid SMILES/SDMols
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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44 mols = [Chem.MolFromSmiles('') if n is None else n for n in mols] # replace invalid mols with placeholder
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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45 df = calc.pandas(mols, quiet=True) # calculate descriptors
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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46 for mol in invalid_mols: # remove placeholders
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47 df.iloc[mol] = np.nan
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48 df = df.applymap(convert_errors_to_nan) # remove descriptors which errored
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49 df = df.round(6)
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50 df.to_csv(output, na_rep='', sep='\t', index=False, header=header) # write output
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51
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52
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53 if __name__ == "__main__":
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54 parser = argparse.ArgumentParser()
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55 parser.add_argument('-i', '--infile', required=True, help='Path to the input file.')
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56 parser.add_argument("--iformat", help="Specify the input file format.")
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57
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58 parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'),
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59 help="Path to the result file")
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60
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61 parser.add_argument("--3d", dest="use_3d", action="store_true",
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62 default=False,
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63 help="Use 3d descriptors - only with SDF input.")
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64
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65 parser.add_argument("--header", dest="header", action="store_true",
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66 default=False,
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67 help="Write header line.")
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68 args = parser.parse_args()
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69
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70 mols = mol_supplier(args.infile, args.iformat)
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71 mordred_descriptors(mols, args.outfile, args.header, args.use_3d)