Re: [Rdkit-discuss] Warning as error
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,
Jean-Marc
Le 21/01/2019 à 21:04, Dimitri Maziuk via Rdkit-discuss a écrit :
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 ignore ones not followed by the warning message.
(And run with #!/usr/bin/python -u and/or flush sys.stdout/stderr on
every iteration for good measure.)
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Re: [Rdkit-discuss] Warning as error
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 ignore ones not followed by the warning message.
(And run with #!/usr/bin/python -u and/or flush sys.stdout/stderr on
every iteration for good measure.)
--
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Re: [Rdkit-discuss] DeleteSubstructs using an MCS object
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 union of all possible matches (two in this case).
Therefore, both the 3- and the 5-chloro substituents are deleted, and as
all other atoms are part of the MCS, you are left with an empty molecule.
If you wish to delete matches one at a time, rather than deleting the
union of all matches, you may use the DeleteSubstructs() Python
implementation that I drafted in this gist:
https://gist.github.com/ptosco/1b6bc727ddee32b4d411cf5c2aea7291
(disclaimer: I wrote it very quickly and tested it only with your
example, so I don't guarantee it is bug-free)
This DeleteSubstructs() implementation returns a list of all structures
obtained by deleting the matched substructures one at a time. As I see
you are using 3D structures, the code deletes all orphaned hydrogens and
caps the fragments remaining after deleting substructures with
hydrogens. If you don't care about 3D coordinates you may want to
uniquify results based on canonical SMILES and, for example in the case
of lig12, keep the remaining HCl fragment only once.
Another observation is that the PDB reader implemented in the RDKit
autoconnects atoms based on proximity, but does not guess bond orders,
so your structures are not chemically correct as they are all
single-bonded even if you have carbonyls, aromatic rings, etc.
In my gist I used Flare to perceive bond orders as I was running the
code in the Flare Jupyter Notebook; you may also use other
cheminformatics toolkit for that purpose.
I hope the above helps; please feel free to get back to me off-list if
something is not clear.
Cheers,
p.
On 01/21/19 15:51, SCHEEN Jenke wrote:
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
#
# load molecules:
lig02_pdb = open("02.pdb", 'r').read()
lig12_pdb = open("12.pdb", 'r').read()
lig02_mol = rdmolfiles.MolFromPDBBlock(lig02_pdb)
lig12_mol = rdmolfiles.MolFromPDBBlock(lig12_pdb)
# make list of molecules to map the MCS to:
perturbation_pair = []
perturbation_pair.append(lig02_mol)
perturbation_pair.append(lig12_mol)
MCS_object = rdFMCS.FindMCS(perturbation_pair, completeRingsOnly=True)
MCS_SMARTS = Chem.MolFromSmarts(MCS_object.smartsString)
# remove MCS from each molecule:
lig02_stripped = AllChem.DeleteSubstructs(lig02_mol, MCS_SMARTS)
lig12_stripped = AllChem.DeleteSubstructs(lig12_mol, MCS_SMARTS)
# print SMILES of each stripped molecule:
print("lig02: " + str(Chem.MolToSmiles(lig02_stripped)))
print("lig12: " + str(Chem.MolToSmiles(lig12_stripped)))
#print(Chem.MolToMolBlock(MCS_SMARTS),file=open('./MCS.mol','w+'))
#
I attached the MCS.mol file as well. The lig12.pdb contains an extra
Cl atom, and lig12_stripped should thus contain a single Cl atom after
deletion of the MCS substructure (the MCS substructure is equal to
lig02.pdb). When running the script it actually contains 0 atoms.
I haven't been able to locate the source of the issue in the
AllChem.DeleteSubstructs documentation, does anyone have a suggestion?
I'm using a conda install of rdkit (2018.09.1.0).
Best,
Jenke
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Re: [Rdkit-discuss] Warning as error
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"),))
continue
A good point is that this code does not produce any warning, and that it
does
when I remove the "sanitize = False" option.
However Chem.SanitizeMol(mol) never raises an error,
unless something is missing in my try/except statements.
The warning message I want to track is:
[19:58:01] Conflicting single bond directions around double bond at
index 27.
[19:58:01] BondStereo set to STEREONONE and single bond directions set
to NONE.
I know which bond has a problem but I still do not know in which molecule.
Jean-Marc
PS. Markus, sorry for the duplicated message.
Le 21/01/2019 à 14:55, Markus Sitzmann a écrit :
Maybe this helps (at least, it is from Greg):
https://github.com/rdkit/rdkit/issues/642
Markus
On Mon, Jan 21, 2019 at 2:25 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> 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 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-
> From: Jean-Marc Nuzillard [mailto:jm.nuzill...@univ-reims.fr
]
> Sent: 21 January 2019 12:33
> To: RDKit Discuss mailto:rdkit-discuss@lists.sourceforge.net>>
> Subject: [Rdkit-discuss] Warning as error
>
> 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?
> Best,
>
> Jean-Marc
>
>
> --
> Jean-Marc Nuzillard
> Directeur de Recherches au CNRS
>
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, Bâtiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
>
> Tel : 03 26 91 82 10
> Fax : 03 26 91 31 66
> http://www.univ-reims.fr/ICMR
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>
> http://www.univ-reims.fr/LSD/
> http://www.univ-reims.fr/LSD/JmnSoft/
>
>
> ---
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> https://www.avast.com/antivirus
>
>
>
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CNRS UMR 7312
Moulin de la Housse
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BP 1039
51687 REIMS Cedex 2
France
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CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
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[Rdkit-discuss] DeleteSubstructs using an MCS object
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
#
# load molecules:
lig02_pdb = open("02.pdb", 'r').read()
lig12_pdb = open("12.pdb", 'r').read()
lig02_mol = rdmolfiles.MolFromPDBBlock(lig02_pdb)
lig12_mol = rdmolfiles.MolFromPDBBlock(lig12_pdb)
# make list of molecules to map the MCS to:
perturbation_pair = []
perturbation_pair.append(lig02_mol)
perturbation_pair.append(lig12_mol)
MCS_object = rdFMCS.FindMCS(perturbation_pair, completeRingsOnly=True)
MCS_SMARTS = Chem.MolFromSmarts(MCS_object.smartsString)
# remove MCS from each molecule:
lig02_stripped = AllChem.DeleteSubstructs(lig02_mol, MCS_SMARTS)
lig12_stripped = AllChem.DeleteSubstructs(lig12_mol, MCS_SMARTS)
# print SMILES of each stripped molecule:
print("lig02: " + str(Chem.MolToSmiles(lig02_stripped)))
print("lig12: " + str(Chem.MolToSmiles(lig12_stripped)))
#print(Chem.MolToMolBlock(MCS_SMARTS),file=open('./MCS.mol','w+'))
#
I attached the MCS.mol file as well. The lig12.pdb contains an extra Cl atom,
and lig12_stripped should thus contain a single Cl atom after deletion of the
MCS substructure (the MCS substructure is equal to lig02.pdb). When running the
script it actually contains 0 atoms.
I haven't been able to locate the source of the issue in the
AllChem.DeleteSubstructs documentation, does anyone have a suggestion?
I'm using a conda install of rdkit (2018.09.1.0).
Best,
Jenke
--
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Edinburgh, EH9 3FJ
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12.pdb
Description: 12.pdb
02.pdb
Description: 02.pdb
MCS.pdb
Description: MCS.pdb
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Re: [Rdkit-discuss] Dividing inputstream over threads
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 it originally, as I was getting deeper in, SQLAlchemy changed my mind. -- Dmitri Maziuk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Warning as error
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' molecule comes in.
I use a routine similar to this:
from io import StringIO
import sys
import rdkit
saved_std_err = sys.stderr
log = sys.stderr = StringIO()
rdkit.Chem.WrapLogs()
reader = Chem.SDMolSupplier('my_file.sdf')
for mol in reader:
error_msgs = log.getvalue()
# check error_msgs content if it there are any particular errors and
act accordingly, erhaps even flush the stream
sys.stderr = saved_std_err
Lukas
On 21/01/2019, 13:24, "Jean-Marc Nuzillard" wrote:
Chem.SDMolSupplier
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Re: [Rdkit-discuss] Dividing inputstream over threads
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: > > 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 without objects ... > > >With parallel processing your bottleneck is going to be database > >inserts. One option is write out CSV file(s) from each thread/job, > >concatenate them in the final node, and then bulk-import into the > >database: typically CSV (or other such format) bulk import is orders > >of magnitude faster than inserting one SQL statement at a time. > > ... and bulk-inserts of Python data types into the database. > > Markus > > On Sun, Jan 20, 2019 at 9:17 PM Dmitri Maziuk via Rdkit-discuss < > rdkit-discuss@lists.sourceforge.net> wrote: > >> On Sun, 20 Jan 2019 12:03:50 +0100 >> Shojiro Shibayama wrote: >> >> > ... I guess SQLalchemy >> > in python might be good, but I'm not sure. Hope that you'll find out >> > a good library of SQL OR mapper for python. >> >> 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. >> >> With parallel processing your bottleneck is going to be database >> inserts. One option is write out CSV file(s) from each thread/job, >> concatenate them in the final node, and then bulk-import into the >> database: typically CSV (or other such format) bulk import is orders >> of magnitude faster than inserting one SQL statement at a time. >> >> -- >> Dmitri Maziuk >> >> >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Warning as error
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 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-
From: Jean-Marc Nuzillard [mailto:jm.nuzill...@univ-reims.fr]
Sent: 21 January 2019 12:33
To: RDKit Discuss
Subject: [Rdkit-discuss] Warning as error
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?
Best,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
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Re: [Rdkit-discuss] Warning as error
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-
From: Jean-Marc Nuzillard [mailto:jm.nuzill...@univ-reims.fr]
Sent: 21 January 2019 12:33
To: RDKit Discuss
Subject: [Rdkit-discuss] Warning as error
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?
Best,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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[Rdkit-discuss] Warning as error
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?
Best,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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Re: [Rdkit-discuss] Dividing inputstream over threads
> 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 without objects ... >With parallel processing your bottleneck is going to be database >inserts. One option is write out CSV file(s) from each thread/job, >concatenate them in the final node, and then bulk-import into the >database: typically CSV (or other such format) bulk import is orders >of magnitude faster than inserting one SQL statement at a time. ... and bulk-inserts of Python data types into the database. Markus On Sun, Jan 20, 2019 at 9:17 PM Dmitri Maziuk via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > On Sun, 20 Jan 2019 12:03:50 +0100 > Shojiro Shibayama wrote: > > > ... I guess SQLalchemy > > in python might be good, but I'm not sure. Hope that you'll find out > > a good library of SQL OR mapper for python. > > 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. > > With parallel processing your bottleneck is going to be database > inserts. One option is write out CSV file(s) from each thread/job, > concatenate them in the final node, and then bulk-import into the > database: typically CSV (or other such format) bulk import is orders > of magnitude faster than inserting one SQL statement at a time. > > -- > Dmitri Maziuk > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
