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Pandastools improvements (#9251)

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* Added automatic parsing functionality

* Added documentation

* Slightly changed check for gzip extension

* Apply suggestions from code review

Added small changes for readability

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
This commit is contained in:
Marco Ballarotto
2026-05-05 17:02:49 +01:00
committed by GitHub
parent 6d75052459
commit b54cbac151
1 changed files with 26 additions and 8 deletions
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34
rdkit/Chem/PandasTools.py
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@@ -240,17 +240,35 @@ else:
def LoadSDF(filename, idName='ID', molColName='ROMol', includeFingerprints=False,
isomericSmiles=True, smilesName=None, embedProps=False, removeHs=True,
strictParsing=True, sanitize=True):
strictParsing=True, sanitize=True, autoConvertStrings=False):
'''Read file in SDF format and return as Pandas data frame.
If embedProps=True all properties also get embedded in Mol objects in the molecule column.
If molColName=None molecules would not be present in resulting DataFrame (only properties
would be read).
Arguments:
- filename: path to the SDF file or a file-like object.
- idName: name of the column to be used for the molecule title. Defaults to "ID".
- molColName: name of the column to be used for the RDKit molecule objects. If None, molecules will not be included in resulting DataFrame. Defaults to "ROMol".
- includeFingerprints: if True, precompute fingerprints and store them within the molecule objects to accelerate substructure matching. Defaults to False.
- isomericSmiles: if True, generated SMILES will include isomeric information. Defaults to True.
- smilesName: if set, add a column with the specified name to the DataFrame that contains the SMILES representation of the molecule. If None, SMILES will not be included in final DataFrame. Defaults to None.
- embedProps: if True, properties will also be embedded in the molecule objects instead of only being added as separate columns to the Dataframe. Defaults to False.
- removeHs: if True, explicit hydrogens will be removed from the molecules. Defaults to True.
- strictParsing: if True, an exception will be raised if a molecule cannot be parsed; if False, unparseable molecules will be skipped. Defaults to True.
- sanitize: if True, molecules will be sanitized during parsing. It is passed on to Chem.ForwardSDMolSupplier sanitize. Defaults to True.
- autoConvertStrings: if True, allows to automatically convert properties to numeric or boolean types where possible. Properties that cannot be converted are left as strings. Defaults to False.
Sanitize boolean is passed on to Chem.ForwardSDMolSupplier sanitize.
Returns:
A pandas DataFrame containing the data from the SDF file.
Note:
If neither molColName nor smilesName are set, sanitize=false.
'''
if isinstance(filename, str):
if filename.lower()[-3:] == ".gz":
if filename.lower().endswith("gz"):
import gzip
f = gzip.open(filename, "rb")
else:
@@ -268,7 +286,7 @@ else:
strictParsing=strictParsing)):
if mol is None:
continue
row = dict((k, mol.GetProp(k)) for k in mol.GetPropNames())
row = mol.GetPropsAsDict(autoConvertStrings=autoConvertStrings)
if molColName is not None and not embedProps:
for prop in mol.GetPropNames():
mol.ClearProp(prop)
@@ -416,7 +434,7 @@ def WriteSDF(df, out, molColName='ROMol', idName=None, properties=None, allNumer
'''
close = None
if isinstance(out, str):
if out.lower()[-3:] == ".gz":
if out.lower().endswith("gz"):
import gzip
out = gzip.open(out, "wt")
close = out.close