diff mordred_descriptors.py @ 0:ea68b86303e2 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mordred_descriptors.py	Thu May 23 18:31:43 2019 -0400
@@ -0,0 +1,71 @@
+import argparse
+import numpy as np
+import pandas as pd
+from mordred import Calculator, descriptors
+from mordred.error import Missing, Error
+from rdkit import Chem
+from rdkit.Chem.rdmolfiles import SDMolSupplier, SmilesMolSupplier
+
+
+def convert_errors_to_nan(el):
+    """
+    Remove elements from the Mordred dataframe which are not
+    in float or int format 
+    """
+    if type(el) == bool:
+        return int(el)
+    if type(el) not in [float, int, np.float64]:
+        return None
+    return el
+
+
+def mol_supplier(filename, ext):
+    """
+    Based on the file extension, use the appropriate RDKit function to
+    load a chemical data file (SMILES or SDF) containing multiple molecules
+    and return a list of RDKit Mol objects
+    """
+    if ext == 'sdf':
+        return [n for n in SDMolSupplier(filename)]
+    with open(filename) as f: 
+        mols = f.read().split('\n') 
+    if ext == 'smi':
+        return [Chem.MolFromSmiles(mol, sanitize=True) for mol in mols]
+    if ext == 'inchi':
+        return [Chem.inchi.MolFromInchi(mol, sanitize=True) for mol in mols]
+
+
+def mordred_descriptors(mols, output, header, use_3d):
+    """
+    Calculate Mordred descriptors and save as tabular
+    """
+    calc = Calculator(descriptors, ignore_3D=(not use_3d))
+    invalid_mols = np.where(np.array(mols) == None)[0]  # indices of invalid SMILES/SDMols
+    mols = [Chem.MolFromSmiles('') if n is None else n for n in mols]  # replace invalid mols with placeholder
+    df = calc.pandas(mols, quiet=True)  # calculate descriptors
+    for mol in invalid_mols:  # remove placeholders
+        df.iloc[mol] = np.nan
+    df = df.applymap(convert_errors_to_nan)  # remove descriptors which errored
+    df = df.round(6)
+    df.to_csv(output, na_rep='', sep='\t', index=False, header=header)  # write output
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--infile', required=True, help='Path to the input file.')
+    parser.add_argument("--iformat", help="Specify the input file format.")
+
+    parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), 
+                    help="Path to the result file")
+
+    parser.add_argument("--3d", dest="use_3d", action="store_true",
+                    default=False,
+                    help="Use 3d descriptors - only with SDF input.")
+
+    parser.add_argument("--header", dest="header", action="store_true",
+                    default=False,
+                    help="Write header line.")
+    args = parser.parse_args()
+
+    mols = mol_supplier(args.infile, args.iformat)
+    mordred_descriptors(mols, args.outfile, args.header, args.use_3d)
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