Each molecule has the _Name I gave it.
Thank you for suggesting to interleave molecule indexes (or names)
with warning messages redirected to unbuffered stderr. It works.
I will use the trick together with Lukas (Thanks!) idea of redirecting
stderr
for in-script processing.
All the best,
On 1/21/19 1:42 PM, Jean-Marc Nuzillard wrote:
> sys.stderr.write("Bad: %s\n" % (mol.GetProp("_Name"),))
> I know which bond has a problem but I still do not know in which molecule.
Are you sure they all have _Name's? I'd just print the count outside of
the try/catch block and
Hi Jenke,
The reason why the resulting molecule contains no atoms is that the
3,5-dichlorophenyl substituent matches twice the 3-chlorophenyl
substructure. If you look at the deleteSubstructs() code in
ChemTransforms.cpp you may see that the atoms deleted from the main
structures are the
Adapting from https://github.com/rdkit/rdkit/issues/642 I wrote:
reader = Chem.SDMolSupplier(file_sdf, sanitize = False)
for mol in reader:
try:
Chem.SanitizeMol(mol)
except:
sys.stderr.write("Bad: %s\n" % (mol.GetProp("_Name"),))
Hi all,
I'm trying to remove the MCS between two molecules (attached, 02.pdb and
12.pdb) using rdFMCS.FindMCS and AllChem.DeleteSubstructs using the following
code:
#
from rdkit import Chem
from rdkit.Chem import AllChem, rdmolfiles, rdFMCS
On Mon, 21 Jan 2019 09:43:48 +0100
Markus Sitzmann wrote:
> There is no need for objects with SQLAlchemy, SQLAlchemy's Core and
> its expression language is pretty excellent without objects ...
I spent weeks last year rewriting code that I myself wrote back when I
believed that... When I wrote
Hi Jean-Marc,
Just a thought, but SDMolSupplier has a lazy eval, if I am not mistaken.
Technically you should get all the rdkit warnings and errors at the time of
processing that bit of the sdf file. You can always read the stderror output,
parse it and throw exception every time a 'funny'
Another option is dask (https://docs.dask.org/en/latest/). I've used
`map_partitions` from dask to bulk convert a column of smiles strings into
various computed properties. You could then output to a CSV or other
database file.
-- Peter
On Mon, Jan 21, 2019 at 1:45 AM Markus Sitzmann
wrote:
>
My problem is more to know which molecules cause problems
than avoiding the printing of warning messages in the console window.
I am looking for an option that would turn warnings into errors, if any.
Jean-Marc
Le 21/01/2019 à 13:44, Stephen O'hagan a écrit :
I've had similar problems; none
I've had similar problems; none of the claimed methods to switch off RDKit
logging of warnings has worked for me.
I ended up just re-directing stderr when running the script like this:
python myfile.py 2> myErrorLog.txt
Dr. Steve O'Hagan,
-Original Message-
Dear all,
The minimalist python code:
reader = Chem.SDMolSupplier('my_file.sdf')
for mol in reader:
pass
gives me warning messages when run on a particular SD file.
How can I simply run a specific action for the molecules that cause problem,
possibly using try/catch statements?
> SQLalchemy creates a fairly specific ecosystem that you have to buy
> into for it to make sense. When you don't have objects, only a table
> of properties, OR mapper is just bloat.
There is no need for objects with SQLAlchemy, SQLAlchemy's Core and its
expression language is pretty excellent
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