Merge pull request #13 from ECRL/dev

Error handling for PaDEL-Descriptor not returning any calculated values

padelpy/__init__.py

@@ -1,3 +1,3 @@
 from padelpy.wrapper import padeldescriptor
 from padelpy.functions import from_mdl, from_smiles
-__version__ = '0.1.6'
+__version__ = '0.1.7'

padelpy/functions.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # padelpy/functions.py
-# v.0.1.6
+# v.0.1.7
 # Developed in 2019 by Travis Kessler <[email protected]>
 #
 # Contains various functions commonly used with PaDEL-Descriptor
@@ -20,8 +20,8 @@
 from padelpy import padeldescriptor
 
 
-def from_smiles(smiles: str, output_csv: str=None, descriptors: bool=True,
-                fingerprints: bool=False, timeout: int=12) -> OrderedDict:
+def from_smiles(smiles: str, output_csv: str = None, descriptors: bool = True,
+                fingerprints: bool = False, timeout: int = 12) -> OrderedDict:
     ''' from_smiles: converts SMILES string to QSPR descriptors/fingerprints
 
     Args:
@@ -78,12 +78,16 @@ def from_smiles(smiles: str, output_csv: str=None, descriptors: bool=True,
     if not save_csv:
         remove(output_csv)
 
+    if len(rows) == 0:
+        raise RuntimeError('PaDEL-Descriptor returned no calculated values.' +
+                           ' Ensure the input structure is correct.')
+
     del rows[0]['Name']
     return rows[0]
 
 
-def from_mdl(mdl_file: str, output_csv: str=None, descriptors: bool=True,
-             fingerprints: bool=False, timeout: int=12) -> list:
+def from_mdl(mdl_file: str, output_csv: str = None, descriptors: bool = True,
+             fingerprints: bool = False, timeout: int = 12) -> list:
     ''' from_mdl: converts MDL file into QSPR descriptors/fingerprints;
     multiple molecules may be represented in the MDL file
 
@@ -141,6 +145,9 @@ def from_mdl(mdl_file: str, output_csv: str=None, descriptors: bool=True,
     desc_file.close()
     if not save_csv:
         remove(output_csv)
+    if len(rows) == 0:
+        raise RuntimeError('PaDEL-Descriptor returned no calculated values.' +
+                           ' Ensure the input structure is correct.')
     for row in rows:
         del row['Name']
     return rows

padelpy/wrapper.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # padelpy/wrapper.py
-# v.0.1.6
+# v.0.1.7
 # Developed in 2019 by Travis Kessler <[email protected]>
 #
 # Contains the `padeldescriptor` function, a wrapper for PaDEL-Descriptor
@@ -45,17 +45,19 @@ def _popen_timeout(command: str, timeout: int) -> tuple:
         return p.communicate()
 
 
-def padeldescriptor(maxruntime: int=-1, waitingjobs: int=-1, threads: int=-1,
-                    d_2d: bool=False, d_3d: bool=False, config: str=None,
-                    convert3d: bool=False, descriptortypes: str=None,
-                    detectaromaticity: bool=False, mol_dir: str=None,
-                    d_file: str=None, fingerprints: bool=False,
-                    log: bool=False, maxcpdperfile: int=0,
-                    removesalt: bool=False, retain3d: bool=False,
-                    retainorder: bool=False, standardizenitro: bool=False,
-                    standardizetautomers: bool=False, tautomerlist: str=None,
-                    usefilenameasmolname: bool=False,
-                    sp_timeout: int=None) -> None:
+def padeldescriptor(maxruntime: int = -1, waitingjobs: int = -1,
+                    threads: int = -1, d_2d: bool = False, d_3d: bool = False,
+                    config: str = None, convert3d: bool = False,
+                    descriptortypes: str = None,
+                    detectaromaticity: bool = False, mol_dir: str = None,
+                    d_file: str = None, fingerprints: bool = False,
+                    log: bool = False, maxcpdperfile: int = 0,
+                    removesalt: bool = False, retain3d: bool = False,
+                    retainorder: bool = False, standardizenitro: bool = False,
+                    standardizetautomers: bool = False,
+                    tautomerlist: str = None,
+                    usefilenameasmolname: bool = False,
+                    sp_timeout: int = None) -> None:
     ''' padeldescriptor: complete wrapper for PaDEL-Descriptor descriptor/
     fingerprint generation software
 

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='padelpy',
-    version='0.1.6',
+    version='0.1.7',
     description='A Python wrapper for PaDEL-Descriptor',
     url='https://github.com/ecrl/padelpy',
     author='Travis Kessler',