Mercurial > repos > bgruening > mordred
comparison mordred_descriptors.py @ 1:e2f40a02f31a draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7c47e7409a8cb19e20b4424329f5d0d9470f3b00
| author | bgruening |
|---|---|
| date | Tue, 04 Jun 2019 10:29:10 -0400 |
| parents | ea68b86303e2 |
| children | d074b0c2b54f |
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| 0:ea68b86303e2 | 1:e2f40a02f31a |
|---|---|
| 28 if ext == 'sdf': | 28 if ext == 'sdf': |
| 29 return [n for n in SDMolSupplier(filename)] | 29 return [n for n in SDMolSupplier(filename)] |
| 30 with open(filename) as f: | 30 with open(filename) as f: |
| 31 mols = f.read().split('\n') | 31 mols = f.read().split('\n') |
| 32 if ext == 'smi': | 32 if ext == 'smi': |
| 33 return [Chem.MolFromSmiles(mol, sanitize=True) for mol in mols] | 33 return [Chem.MolFromSmiles(mol, sanitize=True) for mol in mols if mol != ''] |
| 34 if ext == 'inchi': | 34 if ext == 'inchi': |
| 35 return [Chem.inchi.MolFromInchi(mol, sanitize=True) for mol in mols] | 35 return [Chem.inchi.MolFromInchi(mol, sanitize=True) for mol in mols if mol != ''] |
| 36 | 36 |
| 37 | 37 |
| 38 def mordred_descriptors(mols, output, header, use_3d): | 38 def mordred_descriptors(mols, output, header, use_3d): |
| 39 """ | 39 """ |
| 40 Calculate Mordred descriptors and save as tabular | 40 Calculate Mordred descriptors and save as tabular |